Manuel Utilisateur GX Infinity en r22061 25 v6.8 302-1288 Rev. A

GeneXpert® Infinity System
GeneXpert Infinity-48s GeneXpert Infinity-80
Operator Manual
Xpertise™ Software Version 6.8
302-1288, Rev. A April 2019

Cepheid GeneXpert Infinity System Xpertise Software License Agreement
Cepheid is the exclusive owner of the Cepheid GeneXpert Infinity system Xpertise Software
program (the "Software"), related documentation and physical media, and of all copyright, trade
secret, patent, trademark and other intellectual and industrial property rights therein. Physical media
and copies of the Software, whether in compact disk, hard disk or other form, shall remain the
property of Cepheid, and such copies are deemed to be on loan to Purchaser during the term of the
License granted hereby. Purchaser expressly acknowledges that no title to or ownership of the
Software, or any copy or portion thereof, is transferred to Purchaser. The ideas and expressions
thereof contained in the Software are confidential, proprietary information and trade secrets of
Cepheid that are provided to Purchaser. Purchaser shall not cause or permit decompilation,
disassembly, or reverse engineering of the Software or disclosure, copying, display, loan,
publication, transfer of possession (whether by sales, exchange, gift, operation of law or otherwise)
or other dissemination of the Software and related documentation, in whole or part, to any third party
without the prior written consent of Cepheid.
License Grant: Cepheid grants Purchaser a non-exclusive, non-transferable license (the "License")
to use only one (1) copy of the Software on the computer provided by Cepheid with the GeneXpert
Instrument(s) and connected to the GeneXpert Instrument(s), and to make only one (1) copy solely
for back-up purposes. Purchaser shall not otherwise copy and shall not modify, duplicate, translate,
disassemble, or decompile the Software without Cepheid's prior written consent. If the Software is
used on a computer other than the one provided by Cepheid for the GeneXpert Instrument, Cepheid
will not guarantee performance and cannot provide technical support for problems arising therefrom.
This License entitles Purchaser to use toll-free telephone support as provided by Cepheid. This
License is effective until terminated. Cepheid may terminate this License if Purchaser fails to comply
with any of the terms or conditions of this License or of the original purchase agreement. If this
License is terminated, Purchaser must destroy all copies of the Software and its related
documentation.
For Government Purchasers, the Software is commercial computer software subject to restricted
rights under FAR 52.227-19 (C) (1, 2).
Trademark and Copyright Statements
Xpertise™, Cepheid®, the Cepheid logo, GeneXpert® and I-CORE® are trademarks of Cepheid.
Adobe® and Acrobat® are registered trademarks of Adobe Systems Incorporated.
Ethernet® is a registered trademark of Xerox Corporation.
Microsoft® and Windows® are registered trademarks of Microsoft Corporation.
All other trademarks are the property of their respective owners.
© Cepheid 2019 - All rights reserved.
Disclaimers
All examples (printouts, graphics, displays, screens, etc.) are for information and illustration
purposes only and shall not be used for clinical or maintenance evaluations. Data shown in sample
printouts and screens do not reflect actual patient names or test results. Labels depicted in the
manual may appear different from actual product labels. Cepheid makes no representations or
warranties about the accuracy and reliability of the information contained in the GeneXpert Infinity
System Operator Manual. The information was developed to be used by persons trained and
knowledgeable in GeneXpert Infinity system operation or under the direct supervision of Cepheid
technical support or service representatives. Updates to this Operator Manual may be issued
periodically and should be maintained with this original manual.
Not all products described in this manual are available in all countries.
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302-1288, Rev. A April 2019
Part 15 Compliance
This equipment has been tested and found to comply with the limits for a Class A digital device,
pursuant to part 15 of the FCC Rules. These limits are designed to provide reasonable protection
against harmful interference when the equipment is operated in a commercial environment. This
equipment generates, uses, and can radiate radio frequency energy and, if not installed and used in
accordance with the instruction manual, may cause harmful interference to radio communications.
Operation of this equipment in a residential area is likely to cause harmful interference in which case
the user will be required to correct the interference at his own expense.
EU Directive Compliance
The GeneXpert Infinity-48s and Infinity-80 systems have been designed and tested to conform to
the laboratory equipment requirements of applicable regulatory agencies. Declaration of conformity
is available by contacting Cepheid Technical Support. See the Technical Assistance section in the
Preface for more information.
Table of Hazardous Substance’s Names and Concentrations
Product Name: GeneXpert® Infinity System

Product Model Number: Infinity-48s, Infinity80
Hazardous Substances Name
Component Name (Pb) (Hg) (Cd) (Cr6+) (PBB) (PBDE)
GeneXpert Disposable Cartridge O O O O O O
Cable Sub-Assemblies O O O O O O
Plastic Parts O O O O O O
Sheet Metal O O O O O O
Hardware (Screw, bolts, etc.) O O O O O O
Power Supply Sub Assembly O O O O O O
Printed Circuit Board Assemblies X O O O O O
Piezo Ultrasonic Transducer X O O O O O
This table is prepared in accordance with the provisions of SJ/T 11364-2014
O: Indicates that the toxic or hazardous substances contained in all of the homogeneous materials for this part is below the limit
requirement in GB/T 26572.
X: Indicates that the toxic or hazardous substances contained in at least one of the homogeneous materials used for this part is
above the limit requirement in GB/T 26572.
California Proposition 65 Warning
Warning
This product can expose you to chemicals, including nickel (metallic), which is known to the
State of California to cause cancer. For more information, go to
https://www.P65Warnings.ca.gov.
4 GeneXpert Infinity System Operator Manual

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Table of Contents
1 Introduction - Use or Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.1 Intended Use. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.2 Manual Audience . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.3 System References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
1.4 Software Version. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
1.5 System Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
1.6 Infinity Systems Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
1.6.1 GeneXpert Infinity-48s . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
1.6.2 GeneXpert Infinity-80 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
1.7 System Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6
1.8 System Capabilities. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-7
1.9 GeneXpert Cartridges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-7
1.10 Xpertise Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-8
2 Setup / Installation Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

2.1 Installing the GeneXpert Infinity System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
2.2 Setting Up the Computer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
2.3 Required Materials for Use with the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
2.4 Turning the System On . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
2.4.1 Windows 7 Login Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4
2.4.2 Windows 10 Login Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6
2.5 Starting the Xpertise Software for the First Time . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7
2.6 Defining Users and Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
2.6.1 User Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
2.6.2 Specifying User Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12
2.6.3 Managing Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-15
2.6.3.1 Adding New Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-16
2.6.3.2 Editing User Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-19
2.6.3.3 Removing Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-20
2.7 Configuring the System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-21
2.7.1 General Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-22
2.7.2 Folders Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-26
2.7.3 Archive Settings Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-28
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Table of Contents
2.7.4 Host Communication Settings Workspace . . . . . . . . . . . . . . . . . . . . . . . . . 2-32

2.7.4.1 Configuring Host Communications for an LIS . . . . . . . . . . . . . . . . . . . 2-32
2.7.4.2 Configuring Host Communications for Cepheid Link . . . . . . . . . . . . . . 2-36
2.7.5 Host Test Code Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-38
2.7.5.1 Configuring a Single-Result Assay for Order Download
and Result Upload . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-39
2.7.5.2 Configuring a Multiple-Result Assay for Order Download
and Result Upload . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-41
2.8 Configuring the System Automation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-43
2.8.1 Automation Configuration Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-44
2.8.2 Cartridge Retention Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-47
2.9 Verifying Proper Installation and Setup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-49
2.10 Managing Assay Definitions and Lot Specific Parameters . . . . . . . . . . . . . . . . . . . . 2-55
2.10.1 Connecting the DVD Drive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-55
2.10.2 Importing Assay Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-57
2.10.3 Assay Priorities – Move to Top . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-62
2.10.4 Deleting Assay Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-64
2.10.5 Importing Lot Specific Parameters Manually . . . . . . . . . . . . . . . . . . . . . . . 2-65
2.10.6 Deleting Lot Specific Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-67
2.10.7 Editing Assay Parameters (Quantitative Assays Only) . . . . . . . . . . . . . . . . 2-69
2.11 Setting the System to Manual or Automation Operation . . . . . . . . . . . . . . . . . . . . . . 2-71
2.12 Restarting the System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-71
2.12.1 Shutting the System Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-71
2.12.1.1 Archive Overdue Reminder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-73
2.12.1.2 Database Management Reminder . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-74
2.12.1.3 Final Shutdown Sequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-76
2.12.2 Restarting the System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-77
2.13 Uninstalling or Reinstalling the Xpertise Software . . . . . . . . . . . . . . . . . . . . . . . . . . 2-77
3 Principles of Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1

3.1 System Operation Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
3.2 GeneXpert Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
3.3 GeneXpert Cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
3.4 I-CORE Module. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
3.5 Heating and Cooling Mechanisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7
3.6 Explanation of Experimental Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7
3.7 Optical System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
3.8 System Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-9
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Table of Contents
4 Performance Characteristics and Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1

4.1 System Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
4.2 Physical Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
4.2.1 GeneXpert Infinity-48s Physical Specifications. . . . . . . . . . . . . . . . . . . . . . . 4-2
4.2.2 GeneXpert Infinity-80 Physical Specifications. . . . . . . . . . . . . . . . . . . . . . . . 4-3
4.3 Electrical Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
4.4 Operational Environmental Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
4.5 Environmental Conditions for Storage and Transport . . . . . . . . . . . . . . . . . . . . . . . . . 4-5
4.6 Sound Pressure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-5
4.7 Product Energy Consumption Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-5
5 Operating Instructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1

5.1 Typical Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
5.2 Overview of Basic System and Software Operation Tasks . . . . . . . . . . . . . . . . . . . . . 5-4
5.2.1 Turning the System On . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-4
5.2.2 Windows 7 Login Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5
5.2.3 Windows 10 Login Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
5.2.4 Starting the Xpertise Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
5.2.5 Logging On . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
5.2.6 Logging Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-16
5.2.7 Changing Your Password . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
5.2.8 Shutting the System Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19
5.2.8.1 Additional Shutdown Screens with LIS Active . . . . . . . . . . . . . . . . . . . 5-20
5.3 System Setup Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-26
5.4 Starting the GeneXpert Infinity System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-26
5.5 Ordering a Test in Automation Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-26
5.5.1 Automation Mode Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-26
5.5.2 Ordering a Test in Automation Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-27
5.5.2.1 Processing STAT Priority Cartridges . . . . . . . . . . . . . . . . . . . . . . . . . . 5-38
5.5.2.2 Automation Mode Tests with Load Errors . . . . . . . . . . . . . . . . . . . . . . 5-41
5.5.2.3 Retaining a Cartridge that is Running . . . . . . . . . . . . . . . . . . . . . . . . . 5-42
5.5.2.4 Operation in Automation Mode with Kiosk Scanner
Not Functioning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-44
5.5.3 Viewing Test Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-53
5.5.3.1 Basic User View Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-55
5.5.3.2 Detail User and Administratve View Results . . . . . . . . . . . . . . . . . . . . 5-60
5.5.4 Searching Test Results by Sample ID . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-69

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Table of Contents
5.5.5 Generating Test Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-72

5.5.5.1 Basic User Test Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-72
5.5.5.2 Administrative and Detail User Test Reports . . . . . . . . . . . . . . . . . . . . 5-75
5.5.6 Monitoring a Test in Progress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-78
5.5.7 Stopping a Test in Progress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-78
5.5.8 Pausing the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-81
5.5.9 EMERGENCY STOP – Stopping and Starting Automation . . . . . . . . . . . . 5-81
5.5.10 Clearing a Test Order in Automation Mode . . . . . . . . . . . . . . . . . . . . . . . . 5-82
5.6 Ordering a Test in Manual Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-83
5.6.1 Manual Mode Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-83
5.6.2 Changing from Automation Mode to Manual Mode . . . . . . . . . . . . . . . . . . 5-84
5.6.3 Ordering a Test in Manual Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-90
5.6.3.1 Manually Entering the Barcode to Order a Test . . . . . . . . . . . . . . . . . 5-101
5.6.3.2 Manual Assay Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-104
5.6.3.3 Manual Mode Load Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-105
5.6.4 Changing from Manual Mode to Automation Mode . . . . . . . . . . . . . . . . . 5-106
5.6.5 Clearing a Test Order in Manual Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . 5-111
5.7 Managing Test Results Data. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-113
5.7.1 Archiving the Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-114
5.7.2 Retrieving Tests from an Archive File . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-119
5.7.3 Backing Up the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-124
5.7.4 Restoring the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-127
5.7.5 Compacting the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-131
5.7.6 Checking the Integrity of the Database. . . . . . . . . . . . . . . . . . . . . . . . . . . 5-134
5.8 Operating with Host Connectivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-137
5.8.1 Ordering a Test with Host Connectivity. . . . . . . . . . . . . . . . . . . . . . . . . . . 5-137
5.8.1.1 Ordering a Test by Selecting from a List of Test Orders
Downloaded Automatically by the Host . . . . . . . . . . . . . . . . . . . . . . . 5-140
5.8.1.2 Ordering a Test by Manually Requesting Test Orders and
Selecting from a List of Test Orders . . . . . . . . . . . . . . . . . . . . . . . . . . 5-143
5.8.1.3 Ordering a Test by Querying the Host with Optional
Patient ID and Sample ID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-144
5.8.2 Aborting a Query. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-152
5.8.3 Canceling a Host Downloaded Test Order . . . . . . . . . . . . . . . . . . . . . . . . 5-153
5.8.4 Uploading Test Results to Host . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-154
5.8.4.1 Automatic Upload of Test Results to the Host . . . . . . . . . . . . . . . . . . 5-156
5.8.4.2 Manual Upload of Test Results to the Host . . . . . . . . . . . . . . . . . . . . 5-156
5.8.4.3 Upload of an External Control Result to the Host. . . . . . . . . . . . . . . . 5-158
5.9 Operating with Cepheid Link Connectivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-159
5.9.1 Scanning a Sample and Cartridge using Cepheid Link . . . . . . . . . . . . . . 5-159
5.9.2 Running Cartridges Scanned from Cepheid Link . . . . . . . . . . . . . . . . . . . 5-168

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6 Calibration Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1

6.1 Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.2 Quality Control. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.3 External Quality Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
6.4 Control Trend Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
6.4.1 Qualitative Assays vs. Quantitative Assays . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
6.4.2 Running Control Trend Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
7 Operational Precautions and Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1

7.1 General Safety Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1
7.2 Moving the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
7.3 Electrical Safety. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
7.4 Chemical Safety Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-3
7.5 Biological Hazard Safety Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-3
7.6 Precautions and Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-3
7.6.1 Security Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
7.6.2 Anti-Virus Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
7.6.2.1 Windows 7 Anti-Virus Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
7.6.2.2 Windows 10 Anti-Virus Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-5
7.6.3 Laboratory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-5
7.6.4 Hardware and Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-5
7.6.5 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-6
7.6.6 Cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-6
7.6.7 Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-6
8 Hazards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1
8.1 Safety Labels on the System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1
8.2 EMERGENCY STOP Button . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-5
9 Service and Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1

9.1 Maintenance Tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-3
9.2 Maintenance Log. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-6
9.3 Guidelines for Cleaning and Disinfecting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-6
9.4 Cleaning the Infinity Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-8
9.4.1 Cleaning the Kiosk Table Top, Monitor, Mouse and Keyboard. . . . . . . . . . . 9-8
9.4.2 Cleaning the Kiosk Scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-9
9.4.3 Cleaning the Instrument Surfaces. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-11
9.4.3.1 Quarterly Maintenance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-11
9.4.3.2 In Case of Spill . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-13

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9.5 Cleaning the Conveyor Belt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-15

9.5.1 Weekly Quick Cleaning of the Conveyor Belt . . . . . . . . . . . . . . . . . . . . . . . 9-15
9.5.2 Quarterly Cleaning of the Conveyor Belt . . . . . . . . . . . . . . . . . . . . . . . . . . 9-17
9.6 Vacuuming the Rear Fan Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-25
9.6.1 Before You Start . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-26
9.6.2 Setting Up the Vacuum Cleaner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-26
9.6.3 Vacuuming the Rear Fan Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-28
9.7 Replacing/Cleaning the Fan Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-29
9.7.1 Determining if Fan Filters can be Replaced/Cleaned . . . . . . . . . . . . . . . . . 9-29
9.7.2 Replacing/Cleaning Fan Filters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-30
9.7.3 Cleaning Fan Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-33
9.8 Cleaning the Cartridge Bays and Plunger Rods . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-35
9.9 Replacing the Waste Container Bag . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-44
9.9.1 Replacing the Waste Container Bag of Cartridges . . . . . . . . . . . . . . . . . . . 9-44
9.9.2 Assembling the Waste Container . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-52
9.10 Checking and Replacing Batteries in the Keyboard and Mouse . . . . . . . . . . . . . . . . 9-56
9.10.1 Checking Battery Levels in the Keyboard and Mouse . . . . . . . . . . . . . . . . 9-56
9.10.1.1 Checking the Keyboard Battery Level . . . . . . . . . . . . . . . . . . . . . . . . . 9-56
9.10.1.2 Checking the Mouse Battery Level. . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-57
9.10.2 Replacing Batteries in the Keyboard and Mouse . . . . . . . . . . . . . . . . . . . . 9-57
9.10.2.1 Replacing the Keyboard Batteries . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-57
9.10.2.2 Replacing the Mouse Battery . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-58
9.11 Annual Instrument Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-60
9.12 Generating Reports for Troubleshooting. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-60
9.12.1 Module Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-60
9.12.2 System Log Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-64
9.13 Performing a Manual Self-Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-69
9.14 Excluding Modules from Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-71
9.15 Repairing the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-73
9.16 Hardware Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-74
9.17 Error Messages. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-75
9.17.1 Run-time Errors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-78
9.17.2 Operation Terminated Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-81
9.17.3 Cartridge Loading Errors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-87
9.17.4 Self-Test Errors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-88
9.17.5 Post-Run Amplification Curve Analysis Errors . . . . . . . . . . . . . . . . . . . . . . 9-91
9.17.6 Automation Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-95

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9.18 Troubleshooting Host Connectivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-102

9.18.1 Host Connectivity Indication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-102
9.18.2 Host Communication Buffer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-102
9.19 Export Log Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-103
9.20 Export Host Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-107
9.21 Clearing Failed Automation Locations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-110
9.21.1 Accessing the Automation Failed Workspace. . . . . . . . . . . . . . . . . . . . . . 9-110
9.21.2 Clear Failed Location – Accumulator, Shuttle and Lobby . . . . . . . . . . . . . 9-113
9.21.3 Clear Failed Location – Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-117
9.22 Failure Handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-121
9.22.1 Failure Locations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-121
9.22.2 Return an Affected Cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-121
9.22.3 Disable New Test Orders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-121
9.22.4 Prompt User for Non-Accessible Module . . . . . . . . . . . . . . . . . . . . . . . . . 9-121
9.22.5 Prompts to Fix a Specific Failure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-121
9.22.6 Prompt User to Switch to Manual Mode or Reboot the Instrument. . . . . . 9-122
9.22.7 Prompt User to Contact Technical Support due to
Repetitive Failures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-122
9.22.8 Prompt for Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-122
9.23 Decontamination for Shipping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-122
10 Features and Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1

10.1 AC Power . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-3
10.2 Uninterruptible Power Source (UPS). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-4
10.3 USB and Ethernet Ports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-5
10.4 Computer Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-6
10.5 Infinity Hardware Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-8
10.5.1 Conveyor. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-8
10.5.2 Kiosk Barcode Scanner. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-9
10.5.3 Lobby . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-10
10.5.4 GeneXpert Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-10
10.5.4.1 Eight-Pack Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-11
10.5.4.2 Module Names . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-11
10.5.5 Accumulator Shelves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-13
10.5.5.1 Infinity-48s Accumulator Shelves/Sites . . . . . . . . . . . . . . . . . . . . . . . 10-14
10.5.5.2 Infinity-80 Accumulator Shelves/Sites . . . . . . . . . . . . . . . . . . . . . . . . 10-15
10.5.6 Shuttle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-15
10.5.7 Waste Disposal Shelf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-17

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10.5.8 Waste Container . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-17

10.5.8.1 Disposal Counter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-18
10.5.8.2 Waste Container Sensor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-19
10.5.8.3 Waste Management Alert Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-19
10.5.8.4 Waste Management Recovery Mode . . . . . . . . . . . . . . . . . . . . . . . . . 10-19
10.5.9 Front Glass Doors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-20
10.5.10 Robotic Gantry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-20
10.5.10.1 Gripper . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-20
10.5.10.2 Gantry Barcode Scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-20
10.5.10.3 Module Door Mechanism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-21
10.5.11 EMERGENCY STOP Button. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-21
10.6 Software Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-22
10.6.1 Cartridge Life Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-22
10.6.2 Assay Shelf Life . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-24
10.6.3 Infinity Scheduler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-24
10.7 User Interface Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-25
10.7.1 Touchscreen User Interface Conventions. . . . . . . . . . . . . . . . . . . . . . . . . 10-25
10.7.2 Access Windows Desktop. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-26
10.8 Overview of the Graphical User Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-26
10.9 Dashboard Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-27
10.9.1 Home Icon. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-28
10.9.2 Manage Host Orders Icon. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-28
10.9.3 Cartridge I/O Icon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-29
10.9.4 View Outstanding Orders Icon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-31
10.9.5 View Another Test Icon. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-34
10.9.6 Glass Doors Icons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-35
10.9.7 Shuttle Open Icon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-35
10.9.8 Database Alert Icon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-35
10.9.9 Module Status Icon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-35
10.9.10 Waste Container Capacity and Contents Icon . . . . . . . . . . . . . . . . . . . . . 10-38
10.9.11 Silence Alarm Icon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-39
10.9.12 Pause Icon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-40
10.9.12.1 Using Pause to Adjust a Cartridge and then Resume . . . . . . . . . . . . 10-40
10.9.12.2 Using Pause to Remove a Cartridge and then Resume . . . . . . . . . . 10-43
10.9.13 Manual Mode Icon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-47
10.9.14 System Error Icon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-48
10.10 Status Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-50
10.11 Message Log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-52

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Table of Contents
10.12 Menu Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-54

10.12.1 ORDERS Menu Button . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-56
10.12.2 RESULTS Menu Button . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-61
10.12.2.1 Specimen Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-63
10.12.2.2 Patient Report (If Use Patient ID is Enabled). . . . . . . . . . . . . . . . . . . 10-69
10.12.2.3 Patient Trend Report (If Use Patient ID is Enabled) . . . . . . . . . . . . . 10-75
10.12.2.4 Test Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-84
10.12.2.5 Control Trend Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-87
10.12.2.6 Assay Statistics Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-87
10.12.3 DATA MANAGEMENT Menu Button . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-92
10.12.4 SETUP Menu Button. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-93
10.12.5 MAINTENANCE Menu Button. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-95
10.13 Workspace Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-99
10.14 Retrieving Cartridges from the Accumulator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-101
10.15 Removing a Cartridge That Has Not Been Ordered . . . . . . . . . . . . . . . . . . . . . . . 10-107
A Glossary. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-1
B Icons and Display Symbology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-1

B.1 Status Bar Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-1
B.2 Dashboard Panel Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-2
B.3 Error Message Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-4
B.4 Menu Panel Command Buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-5
B.5 Access Windows Desktop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-8
B.6 Computer Desktop Icons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-9
C Viewing Export (.csv) Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-1

C.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-1
C.2 Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-2
C.2.1 Apache OpenOffice. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-2
C.2.2 Microsoft Excel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-9
C.3 Opening and Viewing .csv Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-9
C.3.1 Apache OpenOffice. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-9
C.3.2 Microsoft Excel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-13
C.3.3 Setting the Default Program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-13

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Table of Contents

302-1288, Rev. A April 2019
List of Figures
Figure 1-1 GeneXpert Infinity-48s. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
Figure 1-2 GeneXpert Infinity-80 System Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4
Figure 1-3 GeneXpert Cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-7
Figure 1-4 Xpertise Software Features Intended for Diagnostic Use . . . . . . . . . . . . . . . . . . . . . . . . 1-9
Figure 2-1 AC Power Switch. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
Figure 2-2 Windows 7 Account Screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4
Figure 2-3 Windows 7 Password Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
Figure 2-4 Windows 10 Lock Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6
Figure 2-5 Windows 10 Account and Password Screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7
Figure 2-6 Starting the Xpertise Software from the Program Menus - Windows 7 . . . . . . . . . . . . . 2-8
Figure 2-7 Starting the Xpertise Software from the Program Menus - Windows 10 . . . . . . . . . . . . 2-9
Figure 2-8 Xpertise Software Splash Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-10
Figure 2-9 Xpertise Software Database Management Workspace. . . . . . . . . . . . . . . . . . . . . . . . . 2-10
Figure 2-10 Xpertise Software Home Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
Figure 2-12 Setup Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-13
Figure 2-13 User Type Configuration Workspace Before Editing . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-13
Figure 2-14 User Type Configuration Workspace After Editing . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-14
Figure 2-15 Setup Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-16
Figure 2-16 User Administration Workspace – Initial View with No Users . . . . . . . . . . . . . . . . . . . . 2-17
Figure 2-17 Add User Workspace After Entering New User Information . . . . . . . . . . . . . . . . . . . . . 2-17
Figure 2-18 User Administration Workspace Showing Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-18
Figure 2-19 User Administration Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-19
Figure 2-20 Edit User Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-20
Figure 2-21 Setup Menu – Administration User Login . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-21
Figure 2-22 System Configuration Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-22
Figure 2-23 System Configuration Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-23
Figure 2-24 General Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-23
Figure 2-25 General Workspace Activated . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-24
Figure 2-26 Folders Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-27
Figure 2-27 Folders Workspace Activated . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-27
Figure 2-28 Archive Settings Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-28
Figure 2-29 Archive Settings Workspace Activated . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-29
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List of Figures
Figure 2-30 Automatic Archive Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-30

Figure 2-31 Host Communication Settings Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-32
Figure 2-32 Host Communication Settings Workspace Activated. . . . . . . . . . . . . . . . . . . . . . . . . . .2-33
Figure 2-33 Host Communication Settings Workspace After Editing . . . . . . . . . . . . . . . . . . . . . . . .2-34
Figure 2-34 Host Communication Settings Workspace Configured for Cepheid Link. . . . . . . . . . . .2-36
Figure 2-35 Host Test Code Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-39
Figure 2-36 Host Test Code Workspace – Single-Result Assay. . . . . . . . . . . . . . . . . . . . . . . . . . . .2-40
Figure 2-37 Host Test Code Workspace – Single-Result Assay Showing Code Entered. . . . . . . . .2-40
Figure 2-38 Host Test Code Workspace – Multiple-Result Assay . . . . . . . . . . . . . . . . . . . . . . . . . .2-42
Figure 2-39 Host Test Code Workspace – Multiple-Result Assay Showing Codes Entered. . . . . . .2-42
Figure 2-40 Setup Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-43
Figure 2-41 Automation Configuration Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-44
Figure 2-42 Automation Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-45
Figure 2-43 Automation Workspace Activated . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-45
Figure 2-44 Cartridge Retention Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-47
Figure 2-45 Cartridge Retention Workspace Activated . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-48
Figure 2-47 Installation Qualification Report in Adobe Reader . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-51
Figure 2-48 Installation Qualification Report – Page 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-52
Figure 2-51 DVD Drive Supplied with Infinity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-56
Figure 2-52 Plugging in the DVD Drive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-56
Figure 2-53 Inserting the Assay Definition CD into the DVD Drive . . . . . . . . . . . . . . . . . . . . . . . . . .2-57
Figure 2-54 Xpertise Software Home Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-58
Figure 2-56 Xpertise Manage Assays Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-59
Figure 2-57 Import Assay Workspace – Navigate to the DVD Drive. . . . . . . . . . . . . . . . . . . . . . . . .2-59
Figure 2-58 Import Assay Workspace – Select Assay to Import . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-60
Figure 2-59 Example of the CD Directory Structure for Xpertise Assays . . . . . . . . . . . . . . . . . . . . .2-61
Figure 2-60 Changing Assay Priorities in the Manage Assays Workspace . . . . . . . . . . . . . . . . . . .2-63
Figure 2-61 Deleting an Assay from the Manage Assays Workspace . . . . . . . . . . . . . . . . . . . . . . .2-64
Figure 2-62 Manage Assays Workspace Confirmation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-65
Figure 2-63 Manage Assays Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-66
Figure 2-64 Lot Specific Parameters Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-66
LOF-2 GeneXpert Infinity System Operator Manual

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List of Figures
Figure 2-65 Lot Specific Parameters Workspace with Reagent Lot Number Added . . . . . . . . . . . . 2-67
Figure 2-66 Deleting an Assay from the Lot Specific Parameters Workspace . . . . . . . . . . . . . . . . . 2-68
Figure 2-67 Xpertise Reagent Lot Specific Parameters Workspace Confirmation Message . . . . . . 2-68
Figure 2-68 Manage Assays Workspace Showing Quantitative Assay . . . . . . . . . . . . . . . . . . . . . . 2-69
Figure 2-69 Assay Parameters Workspace showing Quantitative Result Unit Drop-down. . . . . . . . 2-70
Figure 2-70 Assay Parameters Workspace Confirmation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-70
Figure 2-72 Software Exit Workspace Confirmation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-72
Figure 2-73 Test Archive Reminder Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-73
Figure 2-74 Archive Test Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-74
Figure 2-75 Database Management Workspace Reminder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-75
Figure 2-76 Database Management Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-75
Figure 2-77 Desktop with Shutdown Infinity Icon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-76
Figure 2-78 Infinity shutdown Confirmation Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-77
Figure 3-1 Example PCR Cycle Diagram for I-CORE Module Heating and Fan Cooling
(Temperature Durations not to Scale). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
Figure 3-2 GeneXpert Cartridge Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Figure 3-3 I-CORE Module (6-Color Module Shown) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
Figure 3-4 Amplification Curve and Cycle Threshold (Ct). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
Figure 5-1 GeneXpert Infinity Systems Typical Workflow in Automation Mode . . . . . . . . . . . . . . . . 5-3
Figure 5-2 AC Power Switch. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-4
Figure 5-3 Windows 7 Account Screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5
Figure 5-4 Windows 7 Password Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Figure 5-5 Windows 10 Lock Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Figure 5-6 Windows 10 Account and Password Screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Figure 5-7 Starting the Xpertise Software from the Program Menus . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Figure 5-8 Starting the Xpertise Software from the Program Menus - Windows 10 . . . . . . . . . . . 5-10
Figure 5-9 Xpertise Software Splash Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Figure 5-10 Xpertise Login Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-12
Figure 5-11 Xpertise Software Data Management Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-13
Figure 5-12 Database Management Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-14
Figure 5-13 Test Archive Reminder Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-15
Figure 5-14 Archive Test Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-16
Figure 5-16 Change Password Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-18
Figure 5-17 Change Password Workspace Confirmation Message . . . . . . . . . . . . . . . . . . . . . . . . . 5-18

302-1288, Rev. A April 2019
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Figure 5-18 Xpertise Software Exit Workspace Confirmation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-19

Figure 5-19 Xpertise is Shutting Down Workspace (Only Appears with LIS Enabled) . . . . . . . . . . .5-20
Figure 5-20 Test Archive Reminder Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-21
Figure 5-21 Archive Test Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-22
Figure 5-22 Database Management Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-23
Figure 5-23 Database Management Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-23
Figure 5-24 Desktop with Shutdown Infinity Icon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-25
Figure 5-25 Infinity shutdown Confirmation Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-25
Figure 5-27 Orders Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-28
Figure 5-28 Order Test – Patient ID Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-29
Figure 5-29 Date of Birth Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-30
Figure 5-30 Order Test – Patient ID Workspace with Optional Demographics Fields Entered . . . . .5-31
Figure 5-31 Order Test – Sample ID Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-32
Figure 5-32 Order Test – Assay Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-32
Figure 5-33 Scanning the Cartridge Barcode using the Kiosk Barcode Scanner . . . . . . . . . . . . . . .5-33
Figure 5-34 Order Test – Assay Selection Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-33
Figure 5-35 Order Test – Test Information Workspace with Priority Set to Normal . . . . . . . . . . . . .5-34
Figure 5-36 Order Test – Load Cartridge Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-34
Figure 5-37 Example Error Message showing Expired Cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . .5-35
Figure 5-38 Placing the Cartridge on the Conveyor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-36
Figure 5-40 Order Test Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-37
Figure 5-41 Order Test – Test Information Workspace with Priority Set to STAT. . . . . . . . . . . . . . .5-38
Figure 5-42 Order Test – Load Cartridge Workspace for Shuttle . . . . . . . . . . . . . . . . . . . . . . . . . . .5-39
Figure 5-43 Load the Cartridge into the Shuttle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-40
Figure 5-46 View Another Test Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-43
Figure 5-47 View Results Workspace – Retain Cartridge After Test Completion . . . . . . . . . . . . . . .5-43
Figure 5-48 Message Log Workspace Showing Kiosk Scanner Error . . . . . . . . . . . . . . . . . . . . . . .5-44
Figure 5-49 Error Icon in Dashboard. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-45
Figure 5-50 Source of Error in Dashboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-45

302-1288, Rev. A April 2019
List of Figures
Figure 5-53 Order Test – Patient ID Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-47

Figure 5-54 Order Test – Sample ID Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-49
Figure 5-55 Order Test – Manual Barcode Entry Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-49
Figure 5-56 Order Test – Assay Selection Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-50
Figure 5-57 Order Test – Test Information Workspace with Priority Set to Normal . . . . . . . . . . . . . 5-51
Figure 5-58 Order Test – Load Cartridge Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-51
Figure 5-59 Placing the Cartridge on the Conveyor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-52
Figure 5-60 Order Test – Patient ID Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-53
Figure 5-62 Results Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-54
Figure 5-63 View Results Workspace Showing Tabs (Detail User View) . . . . . . . . . . . . . . . . . . . . . 5-55
Figure 5-64 View Results Workspace – Test Result Tab (Basic User View) . . . . . . . . . . . . . . . . . . 5-56
Figure 5-65 View Results Workspace – Errors Tab (Basic User View) . . . . . . . . . . . . . . . . . . . . . . 5-58
Figure 5-66 View Results Workspace – Support Tab (Basic User View) . . . . . . . . . . . . . . . . . . . . . 5-59
Figure 5-67 View Results Workspace Showing Tabs (Detail User View) . . . . . . . . . . . . . . . . . . . . . 5-61
Figure 5-68 View Results Workspace – Analyte Result Tab (Detail User View) . . . . . . . . . . . . . . . 5-62
Figure 5-69 View Results Workspace – Detail Tab (Detail User View) . . . . . . . . . . . . . . . . . . . . . . 5-63
Figure 5-70 View Results Workspace – Amplification Curve Tab (Detail User View). . . . . . . . . . . . 5-64
Figure 5-71 View Results Workspace – Export Curve (Detail User View) . . . . . . . . . . . . . . . . . . . . 5-65
Figure 5-72 Export Curve Graph Report Shown in Adobe Reader. . . . . . . . . . . . . . . . . . . . . . . . . . 5-66
Figure 5-73 Export Curve Graph Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-67
Figure 5-74 View Results Workspace – History Tab (Detail User View) . . . . . . . . . . . . . . . . . . . . . 5-68
Figure 5-76 View Another Test Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-70
Figure 5-77 View Another Test Workspace - Results of Search by Sample ID . . . . . . . . . . . . . . . . 5-71
Figure 5-78 View Results Workspace - Search Sample ID . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-71
Figure 5-79 Test Report Workspace (Basic User) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-72
Figure 5-80 Example of a Test Report (Basic User) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-74
Figure 5-81 Test Report Workspace (Administrative and Detail Users) . . . . . . . . . . . . . . . . . . . . . . 5-75
Figure 5-82 Example of a Test Report (Administrative and Details Users) – Page 1 . . . . . . . . . . . . 5-76
Figure 5-83 Example of a Test Report (Administrative and Detail Users) – Page 2. . . . . . . . . . . . . 5-77
Figure 5-84 Orders Menu Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-79
Figure 5-85 Stop Test Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-79
Figure 5-86 Stop Test Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-80
Figure 5-87 Stop Test Workspace Showing Progress Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-81

302-1288, Rev. A April 2019
List of Figures
Figure 5-88 Order Test – Assay Workspace – Scan Cartridge Barcode. . . . . . . . . . . . . . . . . . . . . .5-82
Figure 5-89 Order Test – Assay Workspace Confirmation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-83
Figure 5-92 Change Operation Mode Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-85
Figure 5-93 Change Operation Mode Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-86
Figure 5-94 Change Operation Mode Workspace Confirmation . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-87
Figure 5-95 Leaving Automation Mode – Remove Cartridges Workspace . . . . . . . . . . . . . . . . . . . .5-87
Figure 5-96 Leaving Automation Mode – Remove Cartridges Workspace . . . . . . . . . . . . . . . . . . . .5-88
Figure 5-97 Change Operation Mode Workspace Indicating Manual Mode . . . . . . . . . . . . . . . . . . .5-89
Figure 5-98 Xpertise Home Workspace Showing Manual Mode Icon. . . . . . . . . . . . . . . . . . . . . . . .5-89
Figure 5-102 Order Test – Sample ID Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-92
Figure 5-103 Order Test – Assay Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-93
Figure 5-104 Scanning the Cartridge Barcode Using the Kiosk Barcode Scanner . . . . . . . . . . . . . . .5-94
Figure 5-105 Order Test – Assay Selection Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-94
Figure 5-106 Order Test – Test Information Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-95
Figure 5-107 Order Test – Module Selection Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-95
Figure 5-108 Manual Load – Remove Used Cartridge Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . .5-97
Figure 5-109 Manual Load – Module Preparation and Self-Test Workspace . . . . . . . . . . . . . . . . . . .5-98
Figure 5-110 Manual Load – Load Cartridge Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-98
Figure 5-111 Loading the Cartridge into the GeneXpert Module . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-99
Figure 5-112 Manual Load – Load Cartridge Workspace with Loading Progress Bar . . . . . . . . . . .5-100
Figure 5-113 Test Start Successful – Ready For Next Test Workspace . . . . . . . . . . . . . . . . . . . . . .5-100
Figure 5-114 Order Test – Assay Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-101
Figure 5-115 Order Test – Manual Barcode Entry Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-102
Figure 5-116 GeneXpert Cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-102
Figure 5-117 Order Test – Manual Assay Selection Workspace with Information Entered . . . . . . .5-103
Figure 5-118 Order Test – Assay Selection Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-103
Figure 5-119 Order Test – Test Information Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-104
Figure 5-120 Order Test – Manual Assay Selection Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . .5-105
Figure 5-121 Manual Load – Cartridge Load Error Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-106
Figure 5-122 Xpertise Software Home Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-107

302-1288, Rev. A April 2019
List of Figures
Figure 5-123 Xpertise Software Home Workspace Setup Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-107

Figure 5-124 Change Operation Mode Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-108
Figure 5-125 Change Operation Mode Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-109
Figure 5-126 Change Operation Mode Workspace Confirmation When a Test is in Progress. . . . . 5-109
Figure 5-127 Change Operation Mode Workspace Confirmation When No Test is in Progress . . . 5-110
Figure 5-128 Xpertise Software Exit Confirmation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-111
Figure 5-129 Order Test – Manual Barcode Entry Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-112
Figure 5-130 Order Test – Test Information Confirmation Workspace . . . . . . . . . . . . . . . . . . . . . . . 5-112
Figure 5-131 Xpertise Software Home Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-113
Figure 5-132 Data Management Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-114
Figure 5-133 Archive Test Workspace Showing Test Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-115
Figure 5-134 Archive Test Workspace Confirmation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-117
Figure 5-135 Archive Test Workspace Showing Location for Archiving Tests . . . . . . . . . . . . . . . . . 5-117
Figure 5-136 Archive Test Workspace – Successful Save Confirmation . . . . . . . . . . . . . . . . . . . . . 5-118
Figure 5-137 Archive Test Workspace – Purge Confirmation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-118
Figure 5-138 Archive Test Workspace – Tests Purged Confirmation. . . . . . . . . . . . . . . . . . . . . . . . 5-119
Figure 5-139 Data Management Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-120
Figure 5-140 Retrieve Test Workspace Showing List of Previously Archived Files . . . . . . . . . . . . . 5-120
Figure 5-141 Retrieve Test Workspace Showing Tests to Select. . . . . . . . . . . . . . . . . . . . . . . . . . . 5-121
Figure 5-142 Retrieve Test Workspace Confirmation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-122
Figure 5-143 Retrieve Test Workspace Showing Progress Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-123
Figure 5-144 Retrieve Test Workspace Showing Retrieve Completed. . . . . . . . . . . . . . . . . . . . . . . 5-123
Figure 5-145 Database Management Workspace at Software Exit . . . . . . . . . . . . . . . . . . . . . . . . . 5-124
Figure 5-146 Database Management Workspace at Software Exit . . . . . . . . . . . . . . . . . . . . . . . . . 5-125
Figure 5-147 Database Backup Workspace Showing Database Backup Location . . . . . . . . . . . . . 5-125
Figure 5-148 Database Backup Workspace Showing Progress Bar . . . . . . . . . . . . . . . . . . . . . . . . 5-126
Figure 5-149 Database Backup Workspace – Backup Completed. . . . . . . . . . . . . . . . . . . . . . . . . . 5-126
Figure 5-150 Database Management Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-128
Figure 5-151 Database Restore Workspace Confirmation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-128
Figure 5-152 Database Restore Workspace Confirmation to Back Up Current Database . . . . . . . . 5-129
Figure 5-153 Database Backup Workspace Showing Backup File Location . . . . . . . . . . . . . . . . . . 5-130
Figure 5-154 Database Restore Showing File Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-130
Figure 5-155 Database Restore Workspace Confirmation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-131
Figure 5-156 Database Management Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-132
Figure 5-157 Compact Database Workspace Confirmation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-133

302-1288, Rev. A April 2019
List of Figures
Figure 5-158 Compact Database Workspace – Compact Database Complete . . . . . . . . . . . . . . . .5-133

Figure 5-159 Database Management Workspace Confirmation . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-134
Figure 5-160 Database Management Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-135
Figure 5-161 Database Integrity Check Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-135
Figure 5-162 Database Integrity Check Workspace Completed Confirmation . . . . . . . . . . . . . . . . .5-136
Figure 5-163 Manage Host Orders Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-138
Figure 5-164 Manage Host Orders Workspace Showing Pending Host Orders . . . . . . . . . . . . . . . .5-140
Figure 5-165 Order Test – Scan Cartridge Barcode Workspace – Scan the Cartridge Barcode . . .5-141
Figure 5-166 Scanning the Cartridge Barcode using the Kiosk Barcode Scanner . . . . . . . . . . . . . .5-141
Figure 5-168 Order Test – Load Cartridge Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-142
Figure 5-169 Placing the Cartridge on the Conveyor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-143
Figure 5-171 Orders Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-145
Figure 5-172 Order Test – Patient ID Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-145
Figure 5-173 Order Test – Sample ID Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-146
Figure 5-174 Order Test – Scan Cartridge Barcode Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . .5-147
Figure 5-178 Order Test – Host Order Selection Workspace – Select Host Order. . . . . . . . . . . . . .5-149
Figure 5-179 Order Test – Scan Cartridge Barcode Workspace – Scan Cartridge Barcode . . . . . .5-150
Figure 5-183 Order Test – Host Order Selection Workspace – Waiting for
Host Test Order Query . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-152
Figure 5-184 Manage Host Orders Workspace – Canceling a Test . . . . . . . . . . . . . . . . . . . . . . . . .5-153
Figure 5-185 Manage Host Orders Workspace – Cancel Test Confirmation . . . . . . . . . . . . . . . . . .5-154
Figure 5-186 Upload Result Workspace Showing Test Selection. . . . . . . . . . . . . . . . . . . . . . . . . . .5-155
Figure 5-187 View Results Workspace – Test Result Tab Showing Host Upload Status . . . . . . . . .5-156
Figure 5-188 View Results Workspace Showing Upload Pending . . . . . . . . . . . . . . . . . . . . . . . . . .5-157
Figure 5-189 Upload Result Workspace Showing Completed Tests Ready to be
Uploaded to the Host. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-158
Figure 5-190 Cepheid Link Scanner Login Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-160
Figure 5-191 Cepheid Link Scan Sample Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-161

302-1288, Rev. A April 2019
List of Figures
Figure 5-192 Cepheid Link Scanner Success (Green Check Mark) Screen. . . . . . . . . . . . . . . . . . . 5-161
Figure 5-193 Cepheid Link Scanner Error (Order Not Found (Red X)) Screen . . . . . . . . . . . . . . . . 5-162
Figure 5-194 Sample ID Manual Barcode Entry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-162
Figure 5-195 Cepheid Link Scan Cartridge Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-163
Figure 5-196 Cepheid Link Scanned Cartridge Information Screen . . . . . . . . . . . . . . . . . . . . . . . . . 5-164
Figure 5-197 Cepheid Link Scanned Cartridge Error Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-165
Figure 5-198 Cepheid Link Scan Aliquot Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-165
Figure 5-199 Cepheid Link Confirmation Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-166
Figure 5-200 Cepheid Link Scanner Drop Down Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-167
Figure 5-201 Cepheid Link Scanner Logout Dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-167
Figure 5-203 Orders Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-169
Figure 5-204 Order Test – Assay Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-169
Figure 5-205 Scanning the Cartridge Barcode using the Kiosk Barcode Scanner . . . . . . . . . . . . . . 5-170
Figure 5-206 Order Test – Test Information Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-171
Figure 5-207 Order Test – Load Cartridge Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-171
Figure 5-208 Placing the Cartridge on the Conveyor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-172
Figure 6-1 Xpertise Software Home Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
Figure 6-2 Results Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Figure 6-3 Control Trend Report Workspace Showing Qualitative Assay Selected . . . . . . . . . . . . . 6-5
Figure 6-4 Control Trend Report Workspace for Qualitative Options . . . . . . . . . . . . . . . . . . . . . . . . 6-6
Figure 6-5 Control Trend Report Workspace Showing Quantitative Assay Selected . . . . . . . . . . . . 6-6
Figure 6-6 Control Trend Report Workspace for Quantitative Options . . . . . . . . . . . . . . . . . . . . . . . 6-7
Figure 6-7 Generate Report File Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-8
Figure 6-8 Example Control Trend Report in the Adobe Reader Window . . . . . . . . . . . . . . . . . . . . 6-8
Figure 6-9 Control Trend Report Qualitative Assay Example (Xpert C. difficile G2), Page 1 . . . . . . 6-9
Figure 6-10 Control Trend Report Qualitative Assay Example (Xpert C. difficile G2), Page 2 . . . . . 6-10
Figure 6-11 Control Trend Report Quantitative Assay Example (Xpert HIV-1
Viral Load), Page 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-11
Figure 7-1 Lockout Device Installed on Power Plug . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
Figure 8-1 Location of Class 1 Laser Label on Shuttle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-2
Figure 8-2 Location of Biological Risk Label Inside the Waste Container Housing . . . . . . . . . . . . . 8-2
Figure 8-3 GeneXpert Infinity-48s Rear Panels Showing Hazard Labels . . . . . . . . . . . . . . . . . . . . . 8-3
Figure 8-4 GeneXpert Infinity-80 Rear Panels Showing Hazard Labels. . . . . . . . . . . . . . . . . . . . . . 8-4
Figure 8-5 EMERGENCY STOP Button Location. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-5
Figure 8-6 Emergency Stop Workspace with Cartridge Removal Instructions . . . . . . . . . . . . . . . . . 8-6

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List of Figures
Figure 8-7 Emergency Stop Workspace after Completion of Cartridge Operations . . . . . . . . . . . . .8-7
Figure 8-8 Emergency Stop Workspace to Close Glass Doors . . . . . . . . . . . . . . . . . . . . . . . . . . . .8-7
Figure 8-9 Emergency Stop Workspace with Instructions to Resume Operation . . . . . . . . . . . . . . .8-8
Figure 8-10 Emergency Stop Workspace Completion Message. . . . . . . . . . . . . . . . . . . . . . . . . . . . .8-8
Figure 9-1 Maintenance Menu Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-5
Figure 9-2 GeneXpert Infinity Systems Maintenance Log. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-7
Figure 9-3 Kiosk Table Top . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-9
Figure 9-4 Cleaning the Kiosk Scanner. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-10
Figure 9-5 Cleaning the Instrument Surfaces for Quarterly Maintenance . . . . . . . . . . . . . . . . . . . .9-12
Figure 9-6 Cleaning the Potentially Affected Instrument Surfaces . . . . . . . . . . . . . . . . . . . . . . . . .9-14
Figure 9-7 Quick Cleaning Conveyor Belt from Top of Kiosk . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-16
Figure 9-9 Maintenance Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-18
Figure 9-10 Clean Conveyor Confirmation Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-19
Figure 9-11 Clean Conveyor – Preparing Conveyor Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . .9-19
Figure 9-12 Clean Conveyor – Confirm Empty Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-20
Figure 9-13 Clean Conveyor Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-20
Figure 9-14 Place the Keyboard and Mouse into the Keyboard Drawer . . . . . . . . . . . . . . . . . . . . . .9-21
Figure 9-15 Removing the Kiosk Table Top . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-22
Figure 9-16 Wiping the Conveyor Belt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-23
Figure 9-17 Clean Conveyor Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-24
Figure 9-18 Installing the Kiosk Table Top . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-24
Figure 9-19 vVacuum Cleaner and Attachments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-26
Figure 9-20 Disconnect Hose from Hose Adapter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-27
Figure 9-21 Connect Hose to Hose Attachments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-27
Figure 9-22 Vacuuming the Rear Fan Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-29
Figure 9-23 Determining if Fan Filters can be Replaced. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-30
Figure 9-24 Fan Guard Grips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-31
Figure 9-25 Removing the Fan Filter and Filter Retainer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-32
Figure 9-26 Remove Dirty Filter from Fan Filter Retainer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-33
Figure 9-27 Installing the Fan Filter and Guard. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-34
Figure 9-29 Maintenance Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-36
Figure 9-30 GX Maintenance Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-37
Figure 9-31 Plunger Rod Maintenance Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-37

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List of Figures
Figure 9-32 Plunger Rod Maintenance Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-39

Figure 9-33 Plunger Rod Maintenance Workspace Indicating Plungers Being Lowered . . . . . . . . . 9-39
Figure 9-34 Plunger Rod Maintenance Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-40
Figure 9-35 Plunger Rod Lowered into Cartridge Bay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-40
Figure 9-36 Plunger Rod Maintenance Workspace - Completed . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-42
Figure 9-37 Plunger Rod Maintenance Workspace Indicating Plungers Being Raised . . . . . . . . . . 9-42
Figure 9-38 Plunger Rod Maintenance Workspace Indicating Completion of Maintenance. . . . . . . 9-43
Figure 9-40 Waste Container Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-45
Figure 9-41 Waste Container Workspace – Open Waste Container Door . . . . . . . . . . . . . . . . . . . . 9-46
Figure 9-42 Waste Container Workspace – Empty Waste Container and
Close Waste Container Door . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-46
Figure 9-43 Removing the Waste Container. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-48
Figure 9-44 Placing the Bag into the Waste Container. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-49
Figure 9-45 Installing the Waste Container. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-50
Figure 9-46 Metal Latch on Waste Container Door . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-51
Figure 9-47 Waste Container Workspace Empty Confirmation Screen . . . . . . . . . . . . . . . . . . . . . . 9-51
Figure 9-48 Waste Container Workspace Showing Cartridge Count Reset to Zero. . . . . . . . . . . . . 9-52
Figure 9-49 Waste Container Kit. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-53
Figure 9-50 Assembling the Waste Container (Part 1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-54
Figure 9-51 Assembling the Waste Container (Part 2) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-55
Figure 9-52 Keyboard (Partial) Showing the Function Keys and the Battery Level LED . . . . . . . . . 9-56
Figure 9-53 Mouse, Top and Bottom Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-57
Figure 9-54 Keyboard Battery Compartment, Opened . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-58
Figure 9-55 Mouse Battery Compartment, Opened . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-59
Figure 9-57 Maintenance Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-61
Figure 9-58 GX Maintenance Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-62
Figure 9-59 Module Report Shown in Adobe Reader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-62
Figure 9-60 Module Report Example (Page 1 Shown) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-63
Figure 9-61 System Log Report Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-64
Figure 9-62 System Log Report Shown in Adobe Reader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-66
Figure 9-63 Generate Report File Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-67
Figure 9-64 System Log Report Example (Page 1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-68
Figure 9-65 Perform Self-Test Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-70
Figure 9-66 Perform Self-Test Workspace During Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-70

302-1288, Rev. A April 2019
List of Figures
Figure 9-67 Exclude Modules From Test Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-71

Figure 9-68 Exclude Modules From Test Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-72
Figure 9-69 Exclude Modules From Test Workspace Showing Disabled Modules. . . . . . . . . . . . . .9-73
Figure 9-70 Message Log Workspace Showing Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-76
Figure 9-71 Message Log Report in Adobe Reader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-77
Figure 9-72 View Results Workspace – Errors Tab Showing Error Messages . . . . . . . . . . . . . . . . .9-77
Figure 9-73 Message Log Workspace Showing Host Interface Disconnected . . . . . . . . . . . . . . . .9-102
Figure 9-74 Upload Result Workspace Showing Host Disconnected or Buffer
Almost Full Error . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-103
Figure 9-76 Maintenance Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-104
Figure 9-77 Export Log File Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-105
Figure 9-78 Export Log File Workspace – Progress Bar. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-106
Figure 9-80 Xpertise Software Home Workspace – Administrative Level Login . . . . . . . . . . . . . . .9-107
Figure 9-81 Maintenance Menu – Administrative Level Login . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-108
Figure 9-83 Export Host Settings Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-109
Figure 9-84 Information Workspace Indicating Failed Automation Locations . . . . . . . . . . . . . . . . .9-110
Figure 9-85 Xpertise Software Home Workspace – Administrative Level Login . . . . . . . . . . . . . . .9-111
Figure 9-86 Maintenance Menu – – Administrative Level Login . . . . . . . . . . . . . . . . . . . . . . . . . . .9-111
Figure 9-87 Automation Failed Location Workspace Showing Panels . . . . . . . . . . . . . . . . . . . . . .9-112
Figure 9-88 Automation Failed Location Workspace Showing Accumulator Failed Site 12 . . . . . .9-114
Figure 9-89 Automation Failed Location Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-114
Figure 9-90 Clear Failed Location Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-115
Figure 9-91 Clear Failed Location Workspace with Instructions to Pause . . . . . . . . . . . . . . . . . . .9-115
Figure 9-92 Clear Failed Location Workspace with Continue Instructions . . . . . . . . . . . . . . . . . . .9-116
Figure 9-93 Clear Failed Location Workspace with Prompt to Switch to Manual Mode . . . . . . . . .9-117
Figure 9-94 Automation Failed Location Workspace Showing Module Failed Site D1 . . . . . . . . . .9-118
Figure 9-95 Automation Failed Location Workspace Showing Module Failed Site D1 . . . . . . . . . .9-118
Figure 9-96 Clear Failed Location Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-119
Figure 9-97 Clear Failed Location Workspace – Remove Cartridge in Failed Module . . . . . . . . . .9-120
Figure 9-98 Automation Failed Location Workspace Showing No Failed Module Locations . . . . .9-120
Figure 10-1 AC Power Switch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-3
Figure 10-2 UPS Connection using Cepheid’s Supplied UPS Cables . . . . . . . . . . . . . . . . . . . . . . .10-4
Figure 10-3 USB and Ethernet Ports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-5

302-1288, Rev. A April 2019
List of Figures
Figure 10-4 USB Port Locations on Left Side of Monitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-6

Figure 10-5 Kiosk Computer and Embedded Computer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-7
Figure 10-6 Monitor, Mouse and Keyboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-8
Figure 10-7 Conveyor and Other Components. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-9
Figure 10-8 Lobby Position and Other Components. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-10
Figure 10-9 Eight-Pack Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-11
Figure 10-10 Infinity-48s Module Locations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-12
Figure 10-11 Infinity-80 Module Locations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-13
Figure 10-12 Infinity-48s Accumulator Shelf/Site Locations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-14
Figure 10-13 Infinity-80 Accumulator Shelf/Site Locations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-15
Figure 10-14 Shuttle Loading Drawer in Open Position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-16
Figure 10-15 Shuttle Sites in the Loading Drawer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-16
Figure 10-16 Waste Disposal Shelf . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-17
Figure 10-17 Waste Container Location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-18
Figure 10-18 Waste Container Sensor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-19
Figure 10-19 Gantry shown on Infinity-48s System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-21
Figure 10-20 Gantry Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-22
Figure 10-21 Xpertise Software Graphical User Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-26
Figure 10-22 Manage Host Orders Icon Menu Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-28
Figure 10-23 Manage Host Orders Workspace Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-29
Figure 10-24 Cartridge I/O Workspace – Shuttle Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-30
Figure 10-25 Cartridge I/O Workspace – Accumulator Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-30
Figure 10-26 View Outstanding Orders Icon Menu Map. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-31
Figure 10-27 View Outstanding Orders Workspace Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-32
Figure 10-28 View Outstanding Orders Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-33
Figure 10-29 View Order Workspace Example. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-33
Figure 10-30 View Another Test Workspace Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-34
Figure 10-31 Module Status Icon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-36
Figure 10-32 Module Status Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-37
Figure 10-33 Waste Container Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-39
Figure 10-35 Pause - Confirmation Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-41
Figure 10-36 Pause - Cartridge Adjustment Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-42
Figure 10-37 Pause - Resume Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-42

302-1288, Rev. A April 2019
List of Figures
Figure 10-39 Pause - Confirmation Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-44

Figure 10-40 Pause - Cartridge Adjustment Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-44
Figure 10-41 Pause - Scan Cartridge Barcode Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-45
Figure 10-42 Pause - Removed Cartridge Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-46
Figure 10-43 Pause - Scan Cartridge Barcode Workspace – Cannot Find Cartridge Scanned . . . .10-46
Figure 10-44 Pause - Resume Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-47
Figure 10-45 Message Log Workspace Showing Kiosk Scanner Error . . . . . . . . . . . . . . . . . . . . . .10-48
Figure 10-46 Error Icon in Dashboard. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-49
Figure 10-47 Source of Error in Dashboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-49
Figure 10-48 Status Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-50
Figure 10-49 Message Log Workspace showing System Errors and Messages . . . . . . . . . . . . . . .10-52
Figure 10-50 Message Log Workspace in Adobe Reader showing System
Errors and Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-53
Figure 10-51 Xpertise Software Home Page Showing Main Menu Buttons . . . . . . . . . . . . . . . . . . .10-54
Figure 10-52 Menu Panel Menu Map . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-55
Figure 10-53 Xpertise Software Home Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-56
Figure 10-54 Xpertise Software Home Page – Orders Menu Shown . . . . . . . . . . . . . . . . . . . . . . . .10-56
Figure 10-56 Find Order Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-58
Figure 10-57 View Order Workspace Showing Found Order . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-60
Figure 10-58 Find Order Workspace Example Showing the Status of Orders . . . . . . . . . . . . . . . . .10-60
Figure 10-59 View Results Workspace Example Showing Completed Found Order . . . . . . . . . . . .10-61
Figure 10-61 Xpertise Software Home Page showing Results Menu . . . . . . . . . . . . . . . . . . . . . . . .10-63
Figure 10-63 Specimen Report Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-64
Figure 10-64 Specimen Report Workspace – Confirmation Screen . . . . . . . . . . . . . . . . . . . . . . . . .10-66
Figure 10-65 Generate Report File Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-66
Figure 10-66 Specimen Report Example Shown in Adobe Reader . . . . . . . . . . . . . . . . . . . . . . . . .10-67
Figure 10-67 Specimen Report Example Page. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-68
Figure 10-69 Patient Report Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-70
Figure 10-70 Patient Report Workspace – Confirmation Screen . . . . . . . . . . . . . . . . . . . . . . . . . . .10-71
Figure 10-71 Generate Report File Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-71
Figure 10-72 Patient Report Example Shown in Adobe Reader . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-73
Figure 10-73 Patient Report Example Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-74

302-1288, Rev. A April 2019
List of Figures
Figure 10-74 Xpertise Software Home Page showing Results Menu . . . . . . . . . . . . . . . . . . . . . . . . 10-76
Figure 10-75 Patient Trend Report Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-76
Figure 10-76 Generate Report File Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-77
Figure 10-77 Patient Trend Report Example Shown in Adobe Reader . . . . . . . . . . . . . . . . . . . . . . 10-78
Figure 10-78 Patient Trend Graph Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-79
Figure 10-79 Patient Trend Report Example – Page 1. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-80
Figure 10-80 Patient Trend Report Example – Page 2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-81
Figure 10-81 Find Patient ID Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-82
Figure 10-82 Find Patient ID Workspace showing Matching Search Criteria . . . . . . . . . . . . . . . . . . 10-83
Figure 10-84 Test Summary Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-85
Figure 10-85 Export Test Summary Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-86
Figure 10-86 Test Summary Report Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-86
Figure 10-88 Assay Statistics Report Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-88
Figure 10-89 Generate Report File Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-90
Figure 10-90 Assay Statistics Report in Adobe Reader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-90
Figure 10-91 Assay Statistics Report Example Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-91
Figure 10-92 Xpertise Software Home Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-92
Figure 10-93 Xpertise Software Home Page showing Data Management Menu . . . . . . . . . . . . . . . 10-92
Figure 10-95 Xpertise Software Home Page – Setup Menu Shown (Administration User) . . . . . . . 10-94
Figure 10-97 Xpertise Software Home Page – Maintenance Menu Shown with
Detail User Login . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-96
Figure 10-98 Xpertise Software Home Page – Maintenance Menu Shown with
Administrator User Login. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-96
Figure 10-99 About Xpertise Software Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-98
Figure 10-100 Xpertise Software License Agreement Shown in Adobe Reader . . . . . . . . . . . . . . . . 10-99
Figure 10-101 Xpertise Software Graphical User Interface Workspace Sections . . . . . . . . . . . . . . 10-100
Figure 10-102 View Outstanding Orders Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-102
Figure 10-103 View Outstanding Orders Workspace Confirmation Screen . . . . . . . . . . . . . . . . . . . 10-102
Figure 10-104 View Outstanding Orders Workspace After Canceling Order . . . . . . . . . . . . . . . . . . 10-103
Figure 10-105 Cartridge I/O Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-103
Figure 10-106 Cartridge I/O Workspace showing Shuttle Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-104
Figure 10-107 Cartridge I/O Workspace showing Shuttle Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-105

302-1288, Rev. A April 2019
List of Figures
Figure 10-108 Cartridge I/O Workspace showing Remove Cartridges . . . . . . . . . . . . . . . . . . . . . . .10-105

Figure 10-109 Open the Shuttle Door and Remove the Cartridges . . . . . . . . . . . . . . . . . . . . . . . . .10-106
Figure 10-110 Cartridge I/O Workspace showing Accumulator Tab . . . . . . . . . . . . . . . . . . . . . . . . .10-107
Figure 10-111 Xpertise Software Screen showing Red View Outstanding Orders Icon . . . . . . . . . .10-108
Figure 10-112 View Outstanding Orders Workspace showing Cartridge Detected . . . . . . . . . . . . .10-108
Figure 10-113 View Outstanding Orders Workspace Confirmation to Cancel Order . . . . . . . . . . . .10-109
Figure 10-114 View Outstanding Orders Workspace showing Cartridge Rejected. . . . . . . . . . . . . .10-110
Figure 10-115 Cartridge I/O Workspace Shuttle Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-110
Figure 10-116 Cartridge I/O Workspace Accumulator Tab Showing Rejected Cartridge . . . . . . . . .10-111
Figure B-1 Access to Windows Desktop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-8
Figure C-1 Opening a .csv File to Configure Apache OpenOffice . . . . . . . . . . . . . . . . . . . . . . . . . . C-2
Figure C-2 Registration Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-3
Figure C-3 User Name Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-3
Figure C-4 Text Import Screen showing Default Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-4
Figure C-5 Text Import Screen with New Settings Selected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-5
Figure C-6 All Cells Selected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-6
Figure C-7 Drop-Down Menu to Select Column Width . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-6
Figure C-8 Column Width Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-7
Figure C-9 Final View of File with Columns Adjusted . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-8
Figure C-10 Format Saving Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-8
Figure C-11 Opening a .csv File with Apache OpenOffice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-10
Figure C-12 Text Import Screen with Correct Settings Selected . . . . . . . . . . . . . . . . . . . . . . . . . . . C-10
Figure C-13 All Cells Selected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-11
Figure C-14 Drop-Down Menu to Select Column Width . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-11
Figure C-15 Final View of File with Columns Adjusted . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-12
Figure C-16 Choosing the Default Program to Open .csv Files. . . . . . . . . . . . . . . . . . . . . . . . . . . . C-14
Figure C-17 Text Import Screen with Correct Settings Selected . . . . . . . . . . . . . . . . . . . . . . . . . . . C-14

302-1288, Rev. A April 2019
List of Tables
Table 1-1 GeneXpert Infinity System Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5
Table 2-1 Example User Permission Policies for in vitro Diagnostic Use . . . . . . . . . . . . . . . . . 2-11
Table 2-2 User Task Descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-14
Table 2-3 Explanation of Different Setup Options for General and
Host Communication Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-35
Table 3-1 GeneXpert System Excitation and Emission Ranges (6-Color) . . . . . . . . . . . . . . . . . 3-9
Table 4-1 Dimensions of the GeneXpert Infinity-48s System . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
Table 4-2 Weight of the GeneXpert Infinity-48s System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
Table 4-3 Clearance Requirements for the GeneXpert Infinity-48s System . . . . . . . . . . . . . . . . 4-2
Table 4-4 Dimensions of the GeneXpert Infinity-80 System . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3
Table 4-5 Weight of the GeneXpert Infinity-80 System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3
Table 4-6 Clearance Requirements for the GeneXpert Infinity-80 System . . . . . . . . . . . . . . . . . 4-3
Table 4-7 Electrical Requirements for GeneXpert Infinity-48s and
GeneXpert Infinity-80 Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
Table 5-1 Typical Workflow for Processing a Specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Table 5-2 Manage Host Orders Workspace Buttons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-139
Table 9-1 Maintenance Tasks and Frequency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-3
Table 9-2 Contents of Waste Container Kit. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-53
Table 9-3 Hardware Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-74
Table 9-4 Run-time Error Codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-78
Table 9-5 Operation Terminated Error Codes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-81
Table 9-6 Cartridge Loading Error Codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-87
Table 9-7 Self-Test Error Codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-88
Table 9-8 Data Reduction Error Codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-91
Table 9-9 Automation Subsystem Error Codes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-95
Table 10-1 Possible Cartridge Automation States . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-22
Table 10-2 User Interface Conventions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-25
Table 10-3 Automation Subsystem Reminder Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-53
Table 10-4 Automation Subsystem Informational Messages . . . . . . . . . . . . . . . . . . . . . . . . . . 10-54
Table B-1 Status Bar Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .B-1
Table B-2 Dashboard Panel Icons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .B-2
Table B-3 Error Message Icons and Buttons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .B-4
Table B-4 Menu Panel Command Buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .B-5
Table B-5 Computer Desktop Icons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .B-9
GeneXpert Infinity System Operator Manual LOT-1

302-1288, Rev. A April 2019
List of Tables
LOT-2 GeneXpert Infinity System Operator Manual

302-1288, Rev. A April 2019
Preface
About This Manual

The GeneXpert Infinity System Operator Manual provides instructions on how to operate
the GeneXpert Infinity system. The software-related instructions in this operator manual
assume you have basic computer skills. You should be familiar with the Microsoft®
Windows® graphical user interface. If you do not have these skills, refer to the
documentation for Windows.
Safety Information
Chapter 8, Hazards in this manual provides important safety information that you should
use when operating the GeneXpert Infinity system. Read and understand the safety
information thoroughly before you begin operating the system. Using the system without
reading the safety chapter or without proper training can result in serious injury, damage
to the system, invalid results, or loss of data.
Make sure you follow the precautionary statements presented in this manual:
Warning
A warning indicates a possibility of adverse reactions, injury or death to the user or other
persons if the precautions or instructions are not observed.
Caution
A caution indicates that damage to the system, loss of data or invalid results could occur if
the user fails to comply with the advice given.
An important note highlights information that is critical for the completion of a task or the
Important
optimal performance of the system.
A note identifies information that is useful for completion of a task or identifies information that
Note
applies only in specific cases.
The warnings and cautions always use the same keyword but the icon may change to
more clearly indicate the type of hazard.

302-1288, Rev. A April 2019
Symbols Used in the Manual and on the Infinity
Instrument Labels
The following symbols are used in this manual and on the Infinity instrument labels:
Symbol Meaning
In vitro diagnostic medical device
CE marking – European Conformity
Do not reuse
Consult instructions for use
Manufacturer
Authorized representative in the European Community
Separate collection for electrical and electronic equipment waste per Directive
2002/96/EC in the European Union.
This type of warning label is on the shuttle. The shuttle area contains a visible
Class 1 laser. Class 1 lasers are safe under reasonably foreseeable conditions
of operation, including the use of optical instruments for intra beam viewing.
Do not stare into the laser beam.
This type of warning label indicates a potential biological hazard risk. Biological
samples such as tissues, body fluids, and blood of humans and/or animals
have the potential to transmit infectious diseases. Follow your local, state/
provincial, and national safety regulations for handling and disposing the
samples.
This type of warning label indicates that hazardous high voltage sections are
present in the electrical system in the GeneXpert Infinity system. Do not open
covers or panels with this warning. Doing so can expose you to electrical
hazards resulting in injuries or death.
This type of label warning indicates the need to be careful of pinching fingers
while removing the kiosk top plate.
A heavy object warning indicates an object is heavy and that it is possible for
personnel to be injured if they lift improperly. Follow instructions and observe
proper lifting techniques or use lifting aids when lifting heavy objects.
This type of symbol indicates a caution that data loss could occur if the
recommendations listed are not followed. This includes procedures that
overwrite the database or other data manipulation procedures.

302-1288, Rev. A April 2019
Symbol Meaning
This type of symbol indicates a warning or caution for which there is no other
identified symbol. Follow the instructions following the symbol to avoid injury or
equipment damage.
Cepheid Headquarters Locations
Corporate Headquarters European Headquarters

Cepheid Cepheid Europe SAS
904 Caribbean Drive Vira Solelh
Sunnyvale, CA 94089-1189 81470 Maurens-Scopont
USA France
Telephone: +1 408.541.4191 Telephone: +33 563 825 300
Fax: +1 408.541.4192 Fax: +33 563 825 301
www.cepheid.com www.cepheidinternational.com
Technical Assistance
Before contacting Cepheid Technical Support, collect the following information:
• Product name
• Lot number
• Serial number of the instrument
• Error messages (if any)
• Software version and, if applicable, Computer Service Tag number
Region Telephone Email

US – Technical Support +1 888.838.3222 [email protected]
US – Technical Service +1 888.838.3222 [email protected]
+ 1800 130 821
Australia and New Zealand [email protected]
+ 0800 001 028
Brazil and Latin America + 55 11 3524 8373 [email protected]
China + 86 021 5406 5387 [email protected]
France + 33 563 825 319 [email protected]
Germany + 49 69 710 480 480 [email protected]
India, Bangladesh, Bhutan,
+ 91 11 48353010 [email protected]
Nepal and Sri Lanka
Italy +39 800 902 567 [email protected]
South Africa +27 861 22 76 35 [email protected]
United Kingdom +44 3303 332 533 [email protected]

302-1288, Rev. A April 2019
Region Telephone Email
Belgium, Netherlands, and
+ 33 563 825 319 [email protected]
Luxembourg
Other European, Middle East +33 563 825 319
[email protected]
and African countries +971 4 253 3218
Other countries not listed above +1 408.400.8495 [email protected]
Contact information for other Cepheid offices is available on our website at

www.cepheid.com or www.cepheidinternational.com under the SUPPORT tab. Select the
Contact Us option.
Cepheid Europe SAS

EC REP Vira Solelh
81470 Maurens-Scopont
France
Telephone: +33 563 825 300
Fax: +33 563 825 301
www.cepheidinternational.com
Cepheid
904 Caribbean Drive
Sunnyvale, CA 94089
USA
Telephone: +1 408-541-4191
Fax: +1 408-541-4192

302-1288, Rev. A April 2019
1 Introduction - Use or Function
This chapter provides an overview of the GeneXpert® Infinity-48s and the GeneXpert
Infinity-80 systems. The topics are as follows:
• Section 1.1, Intended Use
• Section 1.2, Manual Audience
• Section 1.3, System References
• Section 1.4, Software Version
• Section 1.5, System Description
• Section 1.6, Infinity Systems Overview
• Section 1.7, System Configurations
• Section 1.8, System Capabilities
• Section 1.9, GeneXpert Cartridges
• Section 1.10, Xpertise Software
1.1 Intended Use

The GeneXpert Infinity system automates and integrates sample preparation, nucleic acid
amplification, and detection of the target sequence in simple or complex samples using
real-time Polymerase Chain Reaction (PCR). The system is suited for in vitro diagnostic
applications that require hands-off processing of patient samples (specimens) and
provides both summarized and detailed test results data in tabular and graphic formats.
The GeneXpert Infinity system is designed exclusively for the use of Cepheid Xpert®
assay applications. It allows a laboratory healthcare professional to run tests on the
Infinity platform using predefined assays.
1.2 Manual Audience

The GeneXpert Infinity System Operator Manual is for use by GeneXpert Infinity system
operators who operate the system on a regular basis. It is also for use by lab managers to
perform system setup, administration and routine system maintenance.
GeneXpert Infinity System Operator Manual 1-1

302-1288, Rev. A April 2019
Introduction - Use or Function
1.3 System References

The GeneXpert Infinity System Operator Manual describes operation of the GeneXpert
Infinity-48s and the GeneXpert Infinity-80 systems. Most operating procedures are
applicable to both systems so the system reference will be GeneXpert Infinity system or
Infinity system. When a procedure or instruction is specific to the system model, the
complete model reference will be listed in the text.
1.4 Software Version

This manual describes operation of the GeneXpert Infinity systems with Xpertise
software version 6.8.
1.5 System Description

The GeneXpert Infinity systems are an extension of the GeneXpert product family which
consists of the GeneXpert I, GeneXpert II, GeneXpert IV, and GeneXpert XVI systems.
The GeneXpert Infinity systems contain two product models: GeneXpert Infinity-48s
and GeneXpert Infinity-80. The GeneXpert Infinity systems are fully-automated,
high-throughput, on-demand, random-access, enclosed systems that fully integrate the
processes required for real-time PCR-based molecular diagnostic testing with minimal
hands-on time. They are complete all-in-one molecular diagnostics systems with
unparalleled user interfaces.
The systems combine sample preparation with the amplification and detection process.
The systems have the following smart technology built-in:
• modules that include a six-channel optics system capable of exciting and detecting
multiple fluorescent dyes in the same reaction tube
• a flexible master scheduler prioritizes test runs that meet dynamic workflow needs
• smart alerts that keep the user informed
• bi-directional connectivity with your LIS and HIS networks providing seamless
communication flow of all incoming and outgoing test orders and results
• Cepheid Link connectivity to enable cartridge traceability
• RemoteXpert web based SSL application for fast and easy remote access for support
from Cepheid Technical Support representatives
1-2 GeneXpert Infinity System Operator Manual

302-1288, Rev. A April 2019
1.6 Infinity Systems Overview

1.6.1 GeneXpert Infinity-48s
Figure 1-1. GeneXpert Infinity-48s
1 9
16
17
18 15 18
2 11
6 5 8 10
7
4 12 14
3
13
19
20
Figure 1-1. GeneXpert Infinity-48s System Features
Infinity-48s system components called out in Figure 1-1 are summarized in Table 1-1,
and are described in more detail in Chapter 10, Features and Functions.

302-1288, April 2019
1.6.2 GeneXpert Infinity-80

Figure 1-2. GeneXpert Infinity-80 System Features
1
9
17 16
18 15
2 18
6 5 11
8 10
7
12 14
3 4
13
19
20
Figure 1-2. GeneXpert Infinity-80 System Features
Infinity-80 system components called out in Figure 1-2 are summarized in Table 1-1,
and are described in more detail in Chapter 10, Features and Functions.

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Table 1-1. GeneXpert Infinity System Features
Reference Component Description

1 Monitor with Touchscreen The touchscreen is used to make selections in the software.
Allows you to the scan the Patient ID (optional) and the
specimen’s Sample ID barcode, and the cartridge barcode,
2 Kiosk Barcode Scanner
which enters the cartridge type (e.g., Xpert MRSA) and settings
into the system.
3 Keyboard Tray and Keyboard The keyboard is used for data entry.
4 Mouse The mouse can be used to make selections in the software.
This computer runs the Xpertise software. The keyboard and
5 Kiosk Computer (hidden) barcode reader are attached to this computer. It communicates
with the embedded computer and GeneXpert modules.
This computer communicates with the kiosk computer system. It
6 Embedded Computer (hidden) controls the automation robotic control system, gripper, glass
door latch, and shuttle.
The conveyor moves the cartridge with the sample from the kiosk
7 Conveyor
into the GeneXpert Infinity system.
This is the transition location between the conveyor and the
8 Lobby gantry, where a cartridge is held before being picked up by the
gantry and moved into a GeneXpert module.
There are 6 shelves on the Infinity-48s and 10 shelves on the
Infinity-80. Each shelf contains 8 module positions.
This is a waiting area in which:
• A cartridge waits to be loaded into a module when no
module is available to run the cartridge.
9 Accumulator Shelves • A cartridge to be retained is placed after the test is
completed.
• A cartridge is temporarily held because it cannot be
processed due to an unreadable barcode or unrecognized
cartridge serial number when there is no room in the shuttle.
The accumulator shelves can hold up to 48 cartridges on the
Infinity-48s and 80 cartridges on the Infinity-80.
There are 6 panels on the Infinity-48s and 10 panels on the
Infinity-80. Each panel contains 8 modules. A sample-prepped
10 GeneXpert Modules Area cartridge is inserted into a module where the sample is
processed for detection of a specific genetic sequence or
organism.
This is the area where the system can place a used or rejected
cartridge, to be accessed by the operator. A sensor is present in
this shuttle to detect and indicate if any cartridges are present.
11 Shuttle The shuttle can also be used to submit test and STAT orders.
The system places the used or rejected cartridges in shuttle only
when requested by the user through Cartridge I/O workspace.
The shuttle can hold up to 4 cartridges.
A cartridge is moved into this area after the test is completed.
12 Waste Disposal Shelf When this shelf is full, the next used cartridge pushes the oldest
used cartridge into the waste container.
A cartridge is dropped into this area when the waste disposal
13 Waste Container (inside bottom of kiosk) shelf is full. The waste container holds up to 400 cartridges. A
sensor detects the presence or absence of the waste container.

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Table 1-1. GeneXpert Infinity System Features (Continued)
Reference Component Description

Allows cartridge auto-load and auto-unload handling.
The robotic gantry picks up sample-prepared cartridges from the
lobby, accumulator and shuttle, and places the cartridges into the
appropriate modules for processing.
14 Robotic Gantry System (Gantry) After test completion, the robotic arm moves tested cartridges
from the GeneXpert module to be off-loaded to the shuttle, the
waste disposal shelf or the accumulator. If instructed, the
cartridge(s) in the accumulator can be moved to the shuttle for
retrieval.
Grips, holds and/or releases the cartridge. It is located on the
15 Gripper
gantry.
Scans the cartridge barcode when the cartridge is inside the
16 Gantry Barcode Scanner
GeneXpert Infinity system.
When this hardware emergency stop button is pressed, the
transport system (gantry) is stopped immediately. The stopping
17 EMERGENCY STOP button
of operation and the restarting of operation is described in
Section 8.2.
Use to manually open or close glass doors. Two sets of
18 Left and Right Door Handles interlocks are provided to pause all movement of the whole
gantry and conveyor if any of the glass doors are opened.
The AC power switch is used to switch the AC power to the
19 AC Power Switch system ON or OFF.
Note: Always use the proper shut-down utility from kiosk PC first.
Provides brownout protection, transient suppression and also
Uninterruptible Power Source (UPS)
20 keeps the system powered in case of AC power loss for a
(not shown)
minimum of 5 minutes to allow switchover to generator power.
1.7 System Configurations

The GeneXpert Infinity-48s system consists of:
• Forty-eight module framework
• Up to six panels, each containing eight modules
• Available in variable throughput configurations: 16, 24, 32, 40, 48
The GeneXpert Infinity-80 system consists of:
• Eighty-module framework
• Up to ten panels, each containing eight modules
• Available in variable throughput configurations: 16, 24, 32, 40, 48, 56, 64, 72, 80

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1.8 System Capabilities

• Automated cartridge load – loading, staging, and dispensing of cartridges
• 24/7 robotic cartridge handling capability
• Intuitive, easy-to-use computer interface
• Touchscreen and keyboard options
• Standalone system
• Master scheduler software built-in
• True on-demand, random access
• Ability to perform 6-color assays
• LIS interface connectivity
• Cepheid Link connectivity
• Unlimited online test menu capability
1.9 GeneXpert Cartridges

The samples are prepared and processed in the single-use, assay-specific GeneXpert
cartridges. See Figure 1-3. You add the sample and applicable reagents into a cartridge,
scan in the ID information for the sample and cartridge, and then load the cartridge onto
the conveyor of the Infinity system.
The cartridges are not supplied with the system and must be purchased separately. For
ordering information, contact Cepheid. See the Technical Assistance section in the
Preface for the contact information.
Figure 1-3. GeneXpert Cartridge

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1.10 Xpertise Software

The Xpertise software is installed on the built-in computer of the GeneXpert Infinity
system. This section describes the software features that are for diagnostic use.
The Xpertise software (see Figure 1-4) allows you to perform the following tasks:
Administrative Tasks – Configure the system to define system users and set up
permissions (access privileges), import and delete diagnostic assay definition files, and
manage the test data in the database.
Test and Monitor Tasks – Start a test, stop a test in progress, monitor a test in
progress, view the test results, edit test information, and generate the following:
• test reports
• external control trend reports
• specimen reports
• patient reports
• patient trend reports
• assay statistics reports
Automated Robotic – Auto-loads and auto-unloads sample cartridge handling.
Master Scheduler – Prioritizes test runs by STAT priority of samples, shelf-life of
prepared sample and assay type.
Lab Manager Smart Alerts – Monitors sample test ordering to keep you informed
of system capacity, sample stability, and cartridge scanning and loading errors
Maintenance Tasks – Performs a GeneXpert module self-test manually for
troubleshooting, checking the calibration test counts, clearing failed locations using
Automation Failed Location, generating system logs, exporting log files, and cleaning
the conveyor.
For a summary of the software icons for diagnostic use, see Figure 1-4.

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Figure 1-4. Xpertise Software Features Intended for Diagnostic Use
View Outstanding Orders View Another Test Modules Available Status
Load or Retrieve Cartridges Waste Capacity / Contents
Manage Host Orders Database Alert
Exit Program
Change Password
Logout
Dashboard
Home Login
Current User Name
Pause
Program Icons
Test Icons
Administration Icons
Maintenance Icon
Message Log
Figure 1-4. Xpertise Software Features Intended for Diagnostic Use

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2 Setup / Installation Procedures
Except when noted, the procedures in this chapter are for the GeneXpert Infinity systems
administrator or equivalent personnel. The topics are as follows:
• Section 2.1, Installing the GeneXpert Infinity System
• Section 2.2, Setting Up the Computer
• Section 2.3, Required Materials for Use with the System
• Section 2.4, Turning the System On
• Section 2.5, Starting the Xpertise Software for the First Time
• Section 2.6, Defining Users and Permissions
• Section 2.6.1, User Types
• Section 2.6.2, Specifying User Permissions
• Section 2.6.3, Managing Users
• Section 2.7, Configuring the System
• Section 2.7.1, General Workspace
• Section 2.7.2, Folders Workspace
• Section 2.7.3, Archive Settings Workspace
• Section 2.7.4, Host Communication Settings Workspace (including setup for
Cepheid Link)
• Section 2.7.5, Host Test Code Workspace
• Section 2.8, Configuring the System Automation
• Section 2.8.1, Automation Configuration Workspace
• Section 2.8.2, Cartridge Retention Workspace
• Section 2.9, Verifying Proper Installation and Setup
• Section 2.10, Managing Assay Definitions and Lot Specific Parameters
• Section 2.10.1, Connecting the DVD Drive
• Section 2.10.2, Importing Assay Definitions
• Section 2.10.3, Assay Priorities – Move to Top
• Section 2.10.4, Deleting Assay Definitions
• Section 2.10.5, Importing Lot Specific Parameters Manually
• Section 2.10.6, Deleting Lot Specific Parameters

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Setup / Installation Procedures
• Section 2.10.7, Editing Assay Parameters (Quantitative Assays Only)

• Section 2.11, Setting the System to Manual or Automation Operation
• Section 2.12, Restarting the System
• Section 2.12.1, Shutting the System Down
• Section 2.12.2, Restarting the System
• Section 2.13, Uninstalling or Reinstalling the Xpertise Software
2.1 Installing the GeneXpert Infinity System

Caution
Only Cepheid-trained personnel should perform installation.
The installation manual for the GeneXpert Infinity system provides information on how
to safely:
• remove the system from the crate
• install the system at a prepared site
Use the GeneXpert Infinity-48s System Installation Manual for the Infinity-48s system. Use the
Note
GeneXpert Infinity-80 System Installation Manual for the Infinity-80 system.
2.2 Setting Up the Computer

Caution
Only Cepheid-trained personnel should perform computer setup.
Only Cepheid-trained personnel should set up the computer or alter any of the computer
settings. If the computer settings need to be adjusted, contact Cepheid. See the Technical
Assistance section in the Preface for the contact information.

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2.3 Required Materials for Use with the System

The following items are required for use with the GeneXpert Infinity system but are not
included in the package:
• Assay-specific GeneXpert cartridges
• Assay-specific requirements (refer to the assay package insert and your local and
national regulatory guidelines)
• Printer (optional)
To order the GeneXpert cartridges or a printer, contact Cepheid. See the Technical
Assistance section in the Preface for the contact information.
2.4 Turning the System On

After the system has been installed, use the following procedure to turn the system on
and log onto the system.
After the system has been powered off, wait two minutes before turning the system back on.
Important
The system may not boot up correctly if it is turned back on in less than two minutes.
1. To turn on the GeneXpert Infinity system, turn the power switch clockwise to the ON
position ( | ) as shown in Figure 2-1.
Figure 2-1. AC Power Switch

The power switch is located on the front, lower right side of the GeneXpert Infinity
system. See Figure 1-1 for the Infinity-48s or Figure 1-2 for the Infinity-80.
2. Wait approximately 1 minute for the system to boot.
The computer may have either Windows 7 or Windows 10 installed.

Note For the Windows 7 login procedure, see Section 2.4.1.
For the Windows 10 login procedure, see Section 2.4.2.

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2.4.1 Windows 7 Login Procedure

1. On Windows 7, after power-up the Windows Account screen will be displayed. See
Figure 2-2.
The GeneXpert Infinity system computer is configured with two Windows accounts.
The Cepheid-Admin account is used for all customer tasks such as running tests,
system configuration and software updates. The Cepheid-Techsupport account is for
use only by Cepheid Technical Support, as shown in Figure 2-2.
Figure 2-2. Windows 7 Account Screen

2. On the Windows Account screen, select the Cepheid-Admin user account (see
Figure 2-2. The Windows Password screen appears. See Figure 2-3.
The initial login (default) password is provided below. You will be required to change the password
Note
upon first login. Do not change the user name or profile settings.

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3. On the Windows Password screen (see Figure 2-3), enter the password. The default
password is cphd and must be changed upon initial login (as instructed by the
software). After the password has been changed by the system administrator, enter
the assigned password for future logins. The Windows 7 desktop screen is displayed.
Remember to record and store the new password information in a safe location.
After the first login to the system, there will be no additional prompts to change the
password.
Figure 2-3. Windows 7 Password Screen

4. Start the Xpertise software. See Section 2.5.

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1. On Windows 10, after power-up, the Windows Lock screen appears. See Figure 2-4.
Click anywhere on the screen to display the Windows Account and Password screen.
See Figure 2-5.
use only by Cepheid Technical Support. See Figure 2-5.
Figure 2-4. Windows 10 Lock Screen

2. On the Windows Account and Password screen, select the Cepheid-Admin user
account (see Figure 2-5).
The initial login (default) password is provided below. You will be required to change the password
Note
upon first login. Do not change the user name or profile settings.
3. On the Windows Account and Password screen (see Figure 2-5), enter the password.
The default password is cphd and must be changed upon initial login (as instructed
by the software). After the password has been changed by the system administrator,
enter the assigned password for future logins. The Windows 10 desktop is displayed.
Remember to record and store the new password information in a safe location.

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After the first login to the system, there will be no additional prompts to change the
password
Figure 2-5. Windows 10 Account and Password Screen

4. Start the Xpertise software. See Section 2.5.
2.5 Starting the Xpertise Software for the First Time

The first time the software is started, a user name and password do not have to be
provided. After defining the administrator profile (see Section 2.6, Defining Users and
Permissions), the software will ask for a user name and password each time the software
is started. See Section 5.2.5, Logging On.
Windows 7 - Starting the Software

After the system is installed and the computer is setup, you can start the software in one
of two ways:
• On the Windows desktop, double-click the Xpertise Software icon.
or
• On the Windows taskbar, select the icon, and select All Programs ->Cepheid ->
Xpertise Software. See Figure 2-6.

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Figure 2-6. Starting the Xpertise Software from the Program Menus - Windows 7
Windows 10 - Starting the Software
After the system is installed and the computer is setup, you can start the software in one
of two ways:
or
• On the Windows taskbar, select the icon, and select Cepheid -> Xpertise Software.
See Figure 2-7.

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Windows 7 and 10
The GeneXpert Infinity system splash screen momentarily appears (see Figure 2-8),
followed by the Xpertise Database Management workspace. See Figure 2-9. Select NO in
the Database Management workspace. The Xpertise Software Home workspace is
displayed. See Figure 2-10.

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Figure 2-8. Xpertise Software Splash Screen

Figure 2-9. Xpertise Software Database Management Workspace
Figure 2-9. Xpertise Software Database Management Workspace

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Figure 2-10. Xpertise Software Home Workspace
2.6 Defining Users and Permissions

Before running any tests on the GeneXpert Infinity system, define the GeneXpert
Infinity system administrator and other system users. All the administrator functions are
accessible from the Setup menu in the Xpertise Software Home workspace. See
Figure 2-11.
2.6.1 User Types

The GeneXpert Infinity system allows an administrator to set up task permissions for
different user types: Basic and Detail. As the system administrator, you can use this
feature to limit access to the software functions based on your organization’s policies.
For example, you might want to set up the policies presented in Table 2-1.
Table 2-1. Example User Permission Policies for in vitro Diagnostic Use
Perform Admin.
Perform and System
User Type Run Test View Results Maintenance Functions
Basic Yes Summary only No No
Detail Yes All details Limited No
Administrator* Yes All details All Yes
* The Administrator user type has permissions to perform all the tasks and the permissions cannot be
changed.

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2.6.2 Specifying User Permissions

Use the following procedure to specify user permissions for each user type:
1. In the Xpertise Software Home workspace, select the SETUP button. See
Figure 2-11. The Setup menu is displayed. See Figure 2-12.
2. Select the USER TYPE CONFIGURATION button (see Figure 2-12). The User Type
Configuration workspace appears and displays a permissions table. See Figure 2-13.
3. Select the EDIT button to activate the workspace (see Figure 2-13) to allow you to
make changes. The workspace will change to its active or data entry mode (content
not grayed out). See Figure 2-14.
A. To allow a user type to perform certain tasks, select the task check boxes in the
user type column. See Table 2-2 for a complete list and description of the tasks.
B. To remove a permission, clear the task check box in the user type column.
C. To return all user types to the default permission selections, select the RESET TO
DEFAULT button. This button is available in editing mode only.
4. When you are finished specifying the permissions, select the SAVE button (see
Figure 2-14) to save the changes and select the CLOSE button to close the
workspace. See Figure 2-13.

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Figure 2-12. Setup Menu

Figure 2-13. User Type Configuration Workspace Before Editing
Figure 2-13. User Type Configuration Workspace Before Editing

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Figure 2-14. User Type Configuration Workspace After Editing
Figure 2-14. User Type Configuration Workspace After Editing
Table 2-2. User Task Descriptions
Default User Settings

Task Description Basic Detail Admin.
Order Test and View Outstanding Allows you to order a test (Section 5.5.2) and view
X X X
Order outstanding orders (Section 10.9.4).
Cartridge I/O Allows you to retrieve cartridges (Section 10.14). X X X
Stop One Test or All Tests Allows you to stop one test or all tests (Section 5.5.7). X X X
Edit Test Details Allows you to edit the in vitro diagnostic test information
X X X
(Section 5.5.3.1).
Access Manage Assays Allows you to access the Manage Assays workspace
X X X
(Section 2.10).
Delete Assay and Lot Specific Allows you to delete an assay definition (Section 2.10.4) or
X X
Parameters lot specific parameters (Section 2.10.6).
Manage Assay Definition Allows you to import assay definition (.gxa) and lot specific
X X X
parameter (.gxr) files (Section 2.10).
Archive Test(s) Allows you to archive test data (Section 5.7.1). X X X
Purge Test(s) Allows you to purge a test from the database (Section 5.7.1). X X
Retrieve Test(s) Allows you to retrieve test data from the test archives
X X
(Section 5.7.2).
Backup Database Allows you to back up the database (Section 5.7.3). X X X
Restore Database Allows you to restore the database (Section 5.7.4). X
Compact DB and Run Database Allows you to compact the database (Section 5.7.5) and run
X
Integrity Check database integrity checks (Section 5.7.6).

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Table 2-2. User Task Descriptions (Continued)
Default User Settings

Task Description Basic Detail Admin.
View Specimen, Patient and Allows you to generate a Specimen Report
Patient Trend Reports (Section 10.12.2.1), Patient Report (Section 10.12.2.2) or X X X
Patient Trend Report (Section 10.12.2.3).
View Control Trend and Assay Allows you to generate Control Trend Reports (Section 6.4)
X X
Statistics Reports and Assay Statistics Reports (Section 10.12.2.6).
View System Log Allows you to create and display a report about recent self-
X X
tests and instrument errors (Section 9.12.2).
Edit System Configuration Allows you to modify the system configuration information
X
(Section 2.7).
View IQ Report Allows you to view the installation qualification report
X X X
(Section 2.9).
Change Operation Mode Allows you to change to automation (Section 5.6.4) or
X X
manual operation (Section 5.6.2) mode.
Resume from Emergency Stop Allows you to resume from emergency stop (Section 5.5.9). X X
Perform Maintenance Allows you to clean the conveyor belt (Section 9.5) and to
lower the plungers in the GeneXpert modules for cleaning X X X
(Section 9.8).
Run Self-Test Allows you to perform an instrument module self-test
X X X
(Section 9.13).
Exclude Modules From Test Allows you to exclude modules that may not be functional
X X X
from being used for tests (Section 9.14).
View About Box Allows you to display the About window, view the software
version number, copyright information and software license X X X
agreement. (Section 10.12.5)
2.6.3 Managing Users

As the GeneXpert Infinity system administrator, you can:
• add users to the system and control their access to the Xpertise software by
organizing the users according to privilege level (user types)
• edit the user profiles
• remove users from the system

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2.6.3.1 Adding New Users

The first user you add must be the administrator. Having the administrator profile allows you
to add other users and configure the system.
Important
Until you define the administrator profile, anyone using the software has full access to all of
the tasks.
Most of the system configuration and setup described in this chapter must be completed using an
Note administrator login and screens shown will be as an administrator login. For most of the remainder
of the manual, the screens shown will be at a detail user login or basic user login, where required.
To add a user:
1. In the Xpertise Software Home workspace (see Figure 2-11), select the SETUP
button, then select the USER ADMINISTRATION button. See Figure 2-15. The User
Administration workspace is displayed. See Figure 2-16.

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Figure 2-16. User Administration Workspace – Initial View with No Users
Figure 2-16. User Administration Workspace – Initial View with No Users

Figure 2-17. Add User Workspace After Entering New User Information
Figure 2-17. Add User Workspace After Entering New User Information
2. Select the ADD button (see Figure 2-16). The Add User workspace is displayed. See
Figure 2-17.

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3. In the User Name field, type a unique user name containing 6 to 10 characters that
can include spaces. The first user you should add is the administrator; therefore;
type, for example, MyAdmin (or an equivalent user name).
4. (Optional) In the Full Name field, type the full or actual name of the user. In this
example, the full name of the administrator will be Administration User. The full
name can contain a maximum of 32 characters. Do not use special characters, such
as quotation marks (" "). If you do not provide a name, the software will
automatically insert the user name into this field. This name appears in the test
reports.
5. In the Password and Confirm Password fields, type the password for the user. The
password must contain 6 to 10 characters.
6. In the User Type list, select the type for this user (see Section 2.6.1). For the
administrator, select Admin from the list.
7. When you are finished, select the OK button to save the changes and close the
workspace. The User Administration workspace is displayed with the user
information. See Figure 2-18.
Figure 2-18. User Administration Workspace Showing Users
Figure 2-18. User Administration Workspace Showing Users

8. To add additional users, select the ADD button (see Figure 2-18) and repeat Step 3
through Step 7.
9. When all users have been added, select the CLOSE button. See Figure 2-18.
As additional users need to be added to the system, repeat this entire procedure. Before
continuing with additional users profiles or other system configuration functions, the
administrator should log into the system using an administrator user profile.

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2.6.3.2 Editing User Profiles

Only users with administrative privileges can edit, add or remove user profiles. To
change a user or password or to make other changes to a user profile:
2. In the User Administration workspace (see Figure 2-19), in the User Name column,
select the user you want to edit. The EDIT button will become active (not grayed out).
3. Select the EDIT button. The Edit User workspace is displayed. See Figure 2-20.
4. Revise the information as desired, and then select the OK button to save the changes
and close the workspace. The User Administration workspace is displayed with the
user information. See Figure 2-19.
5. After editing user profiles is complete, select the CLOSE button. See Figure 2-19.
Figure 2-19. User Administration Workspace
Figure 2-19. User Administration Workspace

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Figure 2-20. Edit User Workspace
Figure 2-20. Edit User Workspace
2.6.3.3 Removing Users

To remove a user profile:
2. In the User Administration workspace (see Figure 2-19), in the User Name column,
select the user you want to remove. The REMOVE button will become active (not
grayed out).
3. Select the REMOVE button. The user will be removed from the system.
4. After removing a user profile, select the CLOSE button. See Figure 2-19.
When you remove a user from the system, any tests previously created by that user will remain in
Note
the database.

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2.7 Configuring the System

Only users with administrative privileges can configure the GeneXpert Infinity system.
button, then select the SYSTEM CONFIGURATION button (see Figure 2-21). The
System Configuration menu is displayed. See Figure 2-22.
Figure 2-21. Setup Menu – Administration User Login
Figure 2-21. Setup Menu – Administration User Login

2. Using the system configuration menu buttons, set up the following:
• a name for the system, date and time formats, and options for ordering a test
(Section 2.7.1, General Workspace)
• default hard disk path names for various operations (Section 2.7.2, Folders
Workspace)
• control how the archive reminder is performed (Section 2.7.3, Archive Settings
Workspace)
• LIS interface (Section 2.7.4, Host Communication Settings Workspace)
• specify host test codes (Section 2.7.5, Host Test Code Workspace)
3. Set the automation settings. See Section 2.8, Configuring the System Automation.
Using the automation configuration menu buttons, set up the following:
• set up the automation features (Section 2.8.1, Automation Configuration
Workspace)
• set up the cartridge retention conditions (Section 2.8.2, Cartridge Retention
Workspace)

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Figure 2-22. System Configuration Menu
2.7.1 General Workspace

Use the General workspace to assign your Infinity system a unique name, select the date
and time format, and set options for ordering a test.
button, then select the SYSTEM CONFIGURATION button. See Figure 2-21.
2. Select the GENERAL button. See Figure 2-23. The General workspace is displayed.
See Figure 2-24.
3. To activate the General workspace, select the EDIT button. See Figure 2-24. The
General workspace is now activated and may be edited as shown in Figure 2-25.
4. Provide the requested information for the General workspace as follows:
• System Name field – Type a unique name for your system. The system name
will be displayed in all of the reports.
• Date Format drop-down – Select the format for the month, day, and year.
• Time Format drop-down – Select the 24-hour or the 12-hour format.

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Figure 2-24. General Workspace
Figure 2-24. General Workspace

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Figure 2-25. General Workspace Activated
Figure 2-25. General Workspace Activated

5. Select or clear the following check boxes:
• Use Patient ID – If Patient ID is enabled, you can select and use a Patient ID
barcode. Selecting Use Patient ID will enable the check boxes below it to
become active:
• Patient ID – If Use Patient ID is enabled, Patient ID will also be enabled and
cannot be unchecked. This field is optional and does not need to have an
entry if there is no patient ID. The Patient ID field can contain up to 32
alphanumeric characters excluding illegal filename characters.
• Patient ID 2 – If Use Patient ID is enabled, Patient ID 2 may be enabled to
allow entry of additional patient identification. This field is optional and
does not need to have an entry if there is no additional patient ID. Select the
check box to enable Patient ID 2. The Patient ID 2 field can contain up to 32
alphanumeric characters excluding illegal filename characters.
• Patient Name – If Use Patient ID is enabled, Patient Name may be enabled to
allow entry of the patient’s name. This field is optional and does not need
to have an entry if you do not want to enter a patient name.
The patient name Last Name field can contain up to 194 alphanumeric
characters excluding illegal filename characters. The patient name First
Name field can contain up to 30 alphanumeric characters excluding illegal
filename characters.

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• Patient Demographics – Select to enable the visibility of the Patient

Demographics fields. Demographics data is associated with the
corresponding patient’s test result.
Upon test creation, patient demographic information (Patient Name, Date
of Birth, Ethnicity, Gender and Postal Code) will be encrypted and saved in
the GeneXpert database and will not be shown in the software.
The checkbox for Patient Demographics will be unchecked by default in the General workspace.
Note The system administrator can check or uncheck the Patient Demographics option. Demographics
data can only be used with future connectivity solutions.
For screenshots shown later in this manual, the Patient ID field will be shown as enabled and the
Note
Patient ID 2, Patient Name and Patient Demographics fields will also be enabled.
• Require Start Test Login – This option allows the system administrator to
configure if Start Test Login is required for traceability of the person who
started a test and the period for the Start Test Login.
The options provided to the administrator are:
• Never – Start Test Login is never displayed when the SUBMIT button is
selected in the Order Test workspace.
• Always – This option is the default. Start Test Login is always displayed
when the SUBMIT button is selected in the Order Test workspace.
• Start Test Login Timeout (In Minutes) – If this option is selected, the system
monitors the time lag since the most recent user login or Start Test Login.
After this amount of time elapses, then the Start Test Login appears when
the SUBMIT button has been selected.
The timeout counter will be reset when any user logs in. The system
administrator can select from 1 to 60 minutes using the drop-down list or
enter a value in the same range. The default is 30 minutes.
• Print Test Report At End of Test – Option to allow a test report to be
automatically printed to the Windows system default printer in the default
format.
• Include Amplification Curve - If Print Test Report At End of Test is enabled,
the amplification curve will be included in the test reports if this option is
checked.
The printed report will be displayed under the user definitions as the user who is logged in when the
Note
report is printed. If no user is logged in, the report will be printed as a basic user defined.
• Assay Statistics Deletion Reminder – The GeneXpert Infinity system stores data
for all assays run on the system to create the Assay Statistics report. This data
will be kept for one year and a reminder will be displayed to delete data older
than one year if this reminder is enabled. If this reminder is not enabled, data
older than one year will be automatically deleted after one year. The default is
checked (enabled).

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• Database Management Reminders - Option to allow the system to provide

database management reminders. The default is enabled.
If Database Management Reminders are enabled, the user is prompted when the
Xpertise software starts up and when the software exits to perform database
management tasks. The prompt appears only if the user has privileges to
perform these tasks. If the user does not have these privileges or if Database
Management Reminders are disabled, no reminders will be displayed.
Caution It is important to periodically back up the complete database according to your institution’s
guidelines. Failure to periodically back up the database could result in loss of data in the event of
equipment failure. If Database Management Reminders is disabled, it is the responsibility of the
institution to set a schedule for database backup.
6. After completing all items on the General workspace, select the SAVE button to save
changes (see Figure 2-25) or select the CANCEL button to cancel changes.
2.7.2 Folders Workspace

Use the Folders workspace to change the location or path of the Export, Report, Backup
and Database log folders. To change the path of the folder(s):
2. Select the FOLDERS button to display the Folders workspace. See Figure 2-23.
3. In the Folders workspace, select the EDIT button (see Figure 2-26). The Folders
workspace is now activated and may be edited as shown in Figure 2-27.
4. Provide the requested information for the Folders workspace as follows:
• Export Folder field – Type the path to the folder in which all of the exported test
data will reside. Alternatively, you can use the default path supplied.
• Report Folder field – Type the path to the folder in which all of the reports will
reside. Alternatively, you can use the default path supplied.
• Backup Folder field – Type the path to the folder in which the backup database
will reside. Alternatively, you can use the default path supplied.
• DB Log Folder field – Type the path to the folder in which the database log files
will reside. Alternatively, you can use the default path supplied.
Caution The default folders are located on the computer hard drive. To guard against loss of data, the files in
the these folders should be periodically copied to a different computer or server. If the GeneXpert
Infinity system is connected to a network, it is possible to archive files directly to a network server by
changing the Folders workspace locations to folder locations located on the network server.
5. After completing all items on the Folders workspace, select the SAVE button to save
the changes (see Figure 2-27) or select the CANCEL button to cancel changes.

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Figure 2-26. Folders Workspace
Figure 2-26. Folders Workspace

Figure 2-27. Folders Workspace Activated
Figure 2-27. Folders Workspace Activated

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2.7.3 Archive Settings Workspace

Use the Archive Settings workspace to control the behavior of test result archive
reminders and the automatic archiving of test results.
You may decide to do the archiving on your own, to be reminded to archive manually or
to have the archiving done automatically. You may always archive manually no matter
what choice you make.
You can select how often you would like to be reminded to archive your files: Never,
Weekly, or Monthly.
To set the archiving behavior, perform the following steps:
2. Select the ARCHIVE SETTINGS button to display the Archive Settings workspace.
See Figure 2-23.
3. In the Archive Settings workspace, select the EDIT button (see Figure 2-28). The
Archive Settings workspace is now active and can be edited as shown in
Figure 2-29.
Figure 2-28. Archive Settings Workspace
Figure 2-28. Archive Settings Workspace

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Figure 2-29. Archive Settings Workspace Activated
Figure 2-29. Archive Settings Workspace Activated

4. Select the desired options:
• Manually – If this option is selected, archiving will be performed manually by
the user, at the user’s convenience, and will follow the manual archive process
as described in Section 5.7.1, Archiving the Tests.
• Manually, With Reminder – The reminder will be applied to users who have the
Archive Test privilege. This default option is similar to the previous option, but
with the addition of a periodic reminder for the user to perform an archive.
The user can choose to receive reminders weekly or monthly. The default will
be weekly.
The system will attempt to remind the user to perform an overdue archive if the
last archive was performed in the last week or the last month (depending on the
reminder period selected). In such an event, the reminder will be displayed to
the user when:
• The Xpertise software application starts.
• The Xpertise software application normally terminates.
• The user logs in (excluding start test login).
If the user selects YES in the archive-reminder prompt, the Archive Test
workspace will be shown as described in Section 5.7.1, Archiving the Tests.
If the user selects NO in the reminder prompt, the software will proceed
normally, and the user will be reminded next time the reminder criteria are met.

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Figure 2-30. Automatic Archive Settings
Figure 2-30. Automatic Archive Settings

• Automatically – If this option is selected, test results are automatically archived
once a day. The time the automatic archive starts is set by the user. See
Figure 2-30. Once selected, automatic archives are done at the set time no
matter which user is logged on.
Once automatic archiving is selected, you must respond to the following
questions:
• What time each day should automatic archive start?
• Where should the archive files be saved?
• Should old tests be purged from the database after they have been
automatically archived?
• If old tests are to be purged, how long should they be kept in the database
before they are deleted?
The At Time of Day drop-down list is used to choose the hour of the day when
automatic archive starts.
Note When you select the Automatically radio button, the At Time of Day drop-down list appears.
The Automatic Archive Folder is used to choose where archive files are saved.
These files are not deleted by the Xpertise software. Error messages will be
displayed if the disk where the archive files are saved is full.
You should periodically transfer the archive files to an external storage unit and delete them
Important
from the hard disk to prevent the disk from getting full.

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The Purge Previously Auto-Archived Tests checkbox is used to cause old

automatically archived tests to be deleted from the database.
The Purge Tests After drop-down list is used to set the length of time tests will
remain in the database after they have been automatically archived. Previously
archived tests will be purged from the database when the selected time has
elapsed.
It is important to understand that when tests have been purged, they have not been
permanently deleted from the computer. They have been removed from the main system
Important database and saved to an archive file even when the Purge Previously Auto-Archived Tests
option has been selected. Tests may be retrieved from the archive file if needed for later use.
See Section 5.7.2, Retrieving Tests from an Archive File.
Automatic archiving:
• takes over the user interface while the archive happens
• waits for the user to finish any critical user interface activities before it
starts
• only archives tests that have not been automatically archived already
• does not stop tests or automation
• suspends LIS interactions while the archive happens
• LIS connection will be temporarily disabled if automatic delete is also
enabled in the auto-archive configuration.
• is only done while the Xpertise software is running
If automatic archiving is selected and the Xpertise software is not running at the
time automatic archiving is set to start, the next time the application is started, a
reminder message will be displayed.
If the user accepts the automatic archive reminder, the automatic archive will be
done. If the user dismisses the automatic archive reminder, the Xpertise
software will proceed normally.
5. After completing all items on the Archive Settings workspace, select the SAVE
button to save the changes (see Figure 2-29) or select the CANCEL button to cancel
changes.

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2.7.4 Host Communication Settings Workspace

Use the Host Communication Settings workspace to enable and configure the
communication between the Xpertise software and a Laboratory Information System
(LIS) or Cepheid Link.
To configure the host communication settings for an LIS, see Section 2.7.4.1, Configuring Host
Note Communications for an LIS. To configure the host communication settings for Cepheid Link, see
Section 2.7.4.2, Configuring Host Communications for Cepheid Link.
2.7.4.1 Configuring Host Communications for an LIS

To enable and configure host communications for the GeneXpert Infinity systems to an
LIS:
2. Select the HOST COMMUNICATIONS SETTINGS button (see Figure 2-23) to display
the Host Communications Settings workspace. See Figure 2-31.
3. In the Host Communications Settings workspace, select the EDIT button (see
Figure 2-31) to allow editing of the host communication settings. The Host
Communications Settings workspace is now active and can be edited as shown in
Figure 2-32.
Select the CANCEL button if you do not wish to edit the host communication
settings.
Figure 2-31. Host Communication Settings Workspace
Figure 2-31. Host Communication Settings Workspace

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4. To enable host communication, select the Enable Host Communication check box in
the upper left corner of the workspace (see Figure 2-32). This allows other options to
be selected in the Host Communication Settings workspace.
Within the hospital or laboratory network, each GeneXpert system should have a unique
Important system name which is used in the communication. The host administrator should control the
process for defining system names.
Figure 2-32. Host Communication Settings Workspace Activated
Figure 2-32. Host Communication Settings Workspace Activated
All of the information to be entered into this workspace must be provided by the LIS network
Important
administrator. It is not provided by Cepheid.
Do not check the Use Cepheid Link checkbox when configuring the host communication
Important
settings for a hospital LIS system.
5. In the General section of the Host Communication Settings workspace, enter the
appropriate information and select the appropriate items to interface with the LIS
network.
• Host ID field – Type in a unique host name to identify a host or Data
Management System (DMS) that is connected to this GeneXpert Infinity
system. The maximum number of characters is 20.
• Automatic Host Query After Sample ID Scan check box – Select to enable the
Infinity system to query for test orders associated with the scanned or entered
Sample ID and Patient ID (optional). This option cannot be selected if Auto
Submit Order is selected in the Automation workspace.

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• Automatic Test Order Download check box – Select to enable the Infinity system
to periodically query all test orders from the host.
• Automatic Result Upload check box – Select to enable the Infinity system to
automatically upload results to the host as soon as the test is completed.
• Use Instrument Specimen ID check box – Select to enable the Infinity system to
generate a unique specimen ID which is returned to the host. The Instrument
Specimen ID is a unique ID for this sample. It should be stored in the host and
used for future communication for this sample. This option is applicable if the
facility does not provide unique sample identification.
If the facility provides unique sample identification, this setting should be
disabled.
6. In the Protocol section of the Host Communication Settings workspace, select either
HL7-compatible or ASTM-compatible protocol.
7. In the Communication Settings section of the Host Communication Settings
workspace, select either Server or Client to provide a socket connection between the
two systems.
• Server IP Address field – If the Server option is selected, an IP address with
4-part value (N.N.N.N) should be entered. The value should match the IP address
of the host server. N is between 0-255. If the Client option is selected, the IP
address field remains blank.
• Port # field – The port number should be between 1024 to 65535.
Figure 2-33. Host Communication Settings Workspace After Editing
Figure 2-33. Host Communication Settings Workspace After Editing

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Table 2-3 describes the settings for the three different host setup options:
• Automatic Order Download and Result Upload
• Host Query
• Manual Query
A check mark in the table indicates the appropriate selections.
Table 2-3. Explanation of Different Setup Options for General and Host Communication Settings
Automatic Order
Download and
Settings Result Upload Manual Query Host Query
Host Communication Settings Workspace (see Figure 2-32)
• General
• Automatic Host Query After Sample ID Scan


• Automatic Test Order Download

• Automatic Result Upload
 
• Use Instrument Specimen ID Optional Optional Optional
• Protocol HL7 or ASTM HL7 or ASTM HL7 or ASTM
• Communication Settings Server or Client Server or Client Server or Client
8. After you have set up the host communications, as required, select the SAVE button.
See Figure 2-33.
Select the CANCEL button if you do not want to save the host communication
settings.
Cepheid recommends to always confirm that LIS or HIS uploaded results match GeneXpert results
after any changes to the GeneXpert or host system, including, but not limited to, changes to the
following:
• GeneXpert software version
Note
• GeneXpert assay definition files and version
• GeneXpert host communication settings
• Host middleware software or configuration changes
• LIS software or configuration changes

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2.7.4.2 Configuring Host Communications for Cepheid Link

Once the system has been configured for Cepheid Link, it cannot be used for non-LIS
originated test orders or for running external controls without disabling Cepheid Link.
Important
Cepheid Link may be enabled again after running non-LIS originated test orders or external
controls.
To enable and configure host communications for the GeneXpert Infinity systems to
Cepheid Link:
2. Select the HOST COMMUNICATIONS SETTINGS button (see Figure 2-23) to display
the Host Communications Settings workspace. See Figure 2-31.
3. In the Host Communications Settings workspace, select the EDIT button (see
Figure 2-31) to allow editing of the host communication settings. The Host
Communications Settings workspace is now active and can be edited as shown in
Figure 2-32.
Select the CANCEL button if you do not wish to edit the host communication
settings.
4. To enable host communication, select the Enable Host Communication check box in
the upper left corner of the workspace (see Figure 2-34). This allows other options to
be selected in the Host Communication Settings workspace.
Figure 2-34. Host Communication Settings Workspace Configured for Cepheid Link
Figure 2-34. Host Communication Settings Workspace Configured for Cepheid Link

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Within the hospital or laboratory network, each GeneXpert system should have a unique
Important system name which is used in the communication. The host administrator should control the
process for defining system names.
All of the information to be entered into this workspace must be provided by the LIS network
Important
administrator. It is not provided by Cepheid.
5. Select the Use Cepheid Link checkbox to set up the host communication for Cepheid
Link. After selecting the Use Cepheid Link checkbox, most of the configuration will
be automatically set up. See Figure 2-34.
6. In the General section of the Host Communication Settings workspace, enter the
appropriate information and select the appropriate items to interface with the LIS
network.
• Host ID field – Type in a unique host name to identify a host or Data
Management System (DMS) that is connected to this GeneXpert Infinity
system. The maximum number of characters is 20.
• Automatic Host Query After Sample ID Scan check box – This check box is
disabled when connecting to Cepheid Link,
• Automatic Test Order Download check box – This check box is disabled when
connecting to Cepheid Link,
• Automatic Result Upload check box – This check box is enabled when
connecting to Cepheid Link,
• Use Instrument Specimen ID check box – Select to enable the Infinity system to
generate a unique specimen ID which is returned to the host. The Instrument
Specimen ID is a unique ID for this sample. It should be stored in the host and
used for future communication for this sample. This option is applicable if the
facility does not provide unique sample identification.
If the facility provides unique sample identification, this setting should be
disabled.
7. In the Protocol section of the Host Communication Settings workspace, select either
HL7-compatible or ASTM-compatible protocol.
8. In the Communication Settings section of the Host Communication Settings
workspace, the host must be set to Server to communicate with Cepheid Link.
• Server IP Address field – An IP address with 4-part value (N.N.N.N) should be
entered. The value should match the IP address of the Cepheid Link server. N is
between 0-255.
• Port # field – The port number must be 3000 to communicate with the Cepheid
Link server.

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9. After you have set up the host communications for the Cepheid Link server, select
the SAVE button. See Figure 2-34.
Select the CANCEL button if you do not want to save the host communication
settings.
Cepheid recommends to always confirm that LIS uploaded results match GeneXpert results after
any changes to the GeneXpert or host system, including, but not limited to, changes to the following:
Caution
2.7.5 Host Test Code Workspace

During initial system installation or on a system with no assays installed, there are no
host test codes to enter. During system installation, do not configure this workspace.
Anytime assays have been installed on the GeneXpert Infinity system, navigate back to
the Host Test Code workspace to configure the host test codes.
To download orders and upload results, assays must have host test codes assigned.
In order to perform the required assay, the same test code must be entered in the host, the
Important
GeneXpert Infinity system and the Cepheid Link system, if applicable.
Host test codes to be entered into this workspace must be provided by the LIS network
Important
administrator. They are not provided by Cepheid.
Use the Host Test Code workspace to enter the test code which the host uses for
downloads of test orders and uploads of test results.
To navigate to the Host Test Code workspace:
2. Select the HOST TEST CODE button (see Figure 2-23). The Host Test Code
workspace is displayed. See Figure 2-35.
3. In the Host Test Code workspace, select the EDIT button (see Figure 2-35). The Host
Test Code workspace is now active and can be edited.
There are two types of host test codes entries:
• Single-Result Assays: See Section 2.7.5.1, Configuring a Single-Result Assay
for Order Download and Result Upload
• Multiple-Result Assays: See Section 2.7.5.2, Configuring a Multiple-Result
Assay for Order Download and Result Upload.

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Figure 2-35. Host Test Code Workspace
Figure 2-35. Host Test Code Workspace
2.7.5.1 Configuring a Single-Result Assay for Order Download and Result

Upload
The single-result assay provides results for a single organism and target. To configure a
single-result assay for order download and result upload:
1. In the Define Host Test Codes table section of the Host Test Code workspace,
highlight the assay you want to configure (see Figure 2-35), and then select the EDIT
button.
2. Select the Enable check box (see Figure 2-36) to allow the host to download test
orders and the Infinity system to upload results to the host using the defined assay
test code.
3. In the Assay Host Test Code field of the Host Test Code workspace (see
Figure 2-37), type in the code that was entered into the host. You can type in 1 to 15
characters.
Note All result test codes must be unique.
Important
Important

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Figure 2-36. Host Test Code Workspace – Single-Result Assay
Figure 2-36. Host Test Code Workspace – Single-Result Assay

Figure 2-37. Host Test Code Workspace – Single-Result Assay Showing Code Entered
Figure 2-37. Host Test Code Workspace – Single-Result Assay Showing Code Entered
4. Select the SAVE button to save the setting for this assay. See Figure 2-37. The
software will check for uniqueness of the test code before saving.
Select the CANCEL button if you do not want to save the setting for this assay.

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Cepheid recommends that you use the same test code for a new version of the same assay.
Note However, if you want to change the test code of the current assay, make the change before
importing the next version.
Caution
2.7.5.2 Configuring a Multiple-Result Assay for Order Download and Result

Upload
The multiple-result assay provides results for multiple organisms and targets. To
configure a multiple-result assay for order download and result upload:
1. In the Define Host Test Codes table section of the Host Test Code workspace,
highlight the assay you want to configure (see Figure 2-35), and then select the EDIT
button.
2. Select the Enable check box (see Figure 2-38) to allow the host to download test
orders and the Infinity system to upload results to the host using the defined assay
test code.
3. In the Assay Host Test Code field of the Host Test Code workspace (see
Figure 2-39), type in the code that was entered into the host. You can type in 1 to 15
characters.
Important
Important
4. Type the result test codes into the Result Test Code fields. See Figure 2-39. For a
multiple result assay, there will be two or more result test codes to enter.
Note All result test codes must be unique.
5. Select the SAVE button to save the setting for this assay. See Figure 2-39. The
software will check for uniqueness of the test codes before saving.
Select the CANCEL button if you do not want to save the setting for this assay.
Cepheid recommends that you use the same test codes for a new version of the same assay.
Note However, if you want to change the test codes of the current assay, make the change before
importing the next version.

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Figure 2-38. Host Test Code Workspace – Multiple-Result Assay
Figure 2-38. Host Test Code Workspace – Multiple-Result Assay

Figure 2-39. Host Test Code Workspace – Multiple-Result Assay Showing Codes Entered
Figure 2-39. Host Test Code Workspace – Multiple-Result Assay Showing Codes Entered

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Caution
2.8 Configuring the System Automation

Only users with administrative privileges can configure the GeneXpert Infinity system
automation.
button, then select the AUTOMATION CONFIGURATION button (see Figure 2-40). The
Automation Configuration menu is displayed. See Figure 2-41.

2. Using the automation configuration menu buttons, you can specify the following:
• the automation specifications such as reserving STAT modules, waste container
specifications, utilization levels and configuring the kiosk scanner
(Section 2.8.1, Automation Configuration Workspace)
• defining cartridge retention conditions for each assay (Section 2.8.2, Cartridge
Retention Workspace)

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2.8.1 Automation Configuration Workspace

This workspace allows you to change the Infinity automation settings for the system.
To navigate to the Automation Configuration workspace:
button, then select the AUTOMATION CONFIGURATION button. See Figure 2-21.
2. In the Automation Configuration menu, select the AUTOMATION button (see
Figure 2-41). The Automation workspace is displayed. See Figure 2-42.
Figure 2-41. Automation Configuration Menu
Figure 2-41. Automation Configuration Menu

3. If you need to update the kiosk scanner to read a particular barcode symbology,
select the CONFIGURE KIOSK SCANNER button (see Figure 2-42). This will turn on
the kiosk scanner and allow you to read a configuration barcode to update the kiosk
scanner setting and update the scanner for the new barcode symbology.
Note Updating the kiosk scanner symbology is not applicable to most customers.
For customers planning to use the I 2 of 5 symbology. due to the construction of the I 2 of 5
Caution symbology, it is possible for a scan line covering only a portion of the code to be interpreted
as a complete scan, yielding less data than is encoded in the bar code. To prevent this, select
specific lengths (I 2 of 5 - One Discrete Length) for I 2 of 5 applications. For assistance, call
Cepheid Technical Support. See the Technical Assistance section in the Preface for the
contact information.
4. To edit automation settings, select the EDIT button to activate the Automation
workspace for editing (see Figure 2-42). The Automation workspace is now
activated and may be edited as shown in Figure 2-43.

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Figure 2-42. Automation Workspace
Figure 2-42. Automation Workspace

Figure 2-43. Automation Workspace Activated
Figure 2-43. Automation Workspace Activated

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5. Select the desired options:

• Auto Submit Order – When this option is checked and the Sample ID has been
entered and the cartridge barcode has been scanned, then the system
automatically triggers the Submit command. Default is unchecked.
• Enable Assay Priority – This option affects how the system schedules the next
cartridge to be run:
• Unchecked – When this option is selected, tests will be handled in the order
of submission. Default is unchecked.
• Checked – If this option is checked, the order of the assays in Manage
Assays workspace will be used to determine the priority for the assays with
the assay at the top of the list being the highest priority.
• Enable Audible Alarm – The audible alarm option allows you to turn on or off the
audible alarm feature when an error code that is factory-defined as an audible
error occurs. Default is checked.
• STAT Modules Reserved – You can enter from 0 to the maximum number of
modules installed in the system to reserve for STAT cartridges. These reserved
modules will also be used to process cartridges that would otherwise expire if
scheduled for a non-STAT module. The default value is 0.
• Waste Container Almost Full Cartridge Count – This option sets the almost full
value for the waste container. You can enter a value between 1 and 400
cartridges. The default value is 350.
• System Utilization Level – The software displays the system utilization based on
the number of modules currently running and the number of modules
recognized by the system excluding the disabled modules.
You can select boundary limits in percentages to report the system utilization
level. The user interface provides two selections:
• Upper Limit for Low Usage – This option allows you to enter the upper limit
in % for low usage. The default is 50%.
• Upper Limit for Medium Usage – This option allows you to enter the upper
limit in % for medium usage. The default is 75%.
6. After completing all items in the Automation workspace, select the SAVE button to
save the changes (see Figure 2-43) or select the CANCEL button to cancel changes. If
you choose the cancel the changes, a confirmation workspace will be displayed
asking you whether to save the changes or ignore the changes.
7. Select the CLOSE button to exit the Automation workspace. See Figure 2-42.

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2.8.2 Cartridge Retention Workspace

The Cartridge Retention workspace settings determine the destination of a used cartridge
after it is unloaded from a GeneXpert module. Retained cartridges are transported to the
accumulator after they have completed the test, and can be delivered to the shuttle for
return to the user upon request.
During initial system installation or on a system with no assays installed, there are no
cartridge retention options to set. During system installation, do not configure this
workspace.
Anytime assays have been installed on the GeneXpert Infinity system, navigate back to
the Cartridge Retention workspace to configure the used cartridge destinations, if
desired. To navigate to the Cartridge Retention workspace:
button, then select the AUTOMATION CONFIGURATION button. See Figure 2-21.
2. In the Automation Configuration menu, select the CARTRIDGE RETENTION button
(see Figure 2-41). The Cartridge Retention workspace is displayed. See Figure 2-45.
3. In the Cartridge Retention workspace, select the EDIT button (see Figure 2-44). The
Cartridge Retention workspace is now activated and may be edited as shown in
Figure 2-45.
Figure 2-44. Cartridge Retention Workspace
Figure 2-44. Cartridge Retention Workspace

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Figure 2-45. Cartridge Retention Workspace Activated
Figure 2-45. Cartridge Retention Workspace Activated
The possible results for all assays are listed in the package insert for that assay. Not all colors will
Note
apply to all assays.
Select the check box next to Enable Cartridge Retention to enable/disable retention
settings.
• Unchecked – All cartridges will be disposed in the waste container. The default
is Unchecked.
• Checked – If this box is checked, the user can select which of the used cartridges
will be retained according to an assay and the result color.
If this option is checked, choose which assays to retain in the table. You can
select one color or multiple colors.
• At least one color must be selected.
• The default color is red.
At the end of the test, the cartridge will be retained if:
• The assay is selected as an assay to be retained, and
• at least one of the result colors of the test result is in the retained result color
selection for this assay.
4. After completing all items in the Cartridge Retention workspace, select the SAVE
button to save the changes (see Figure 2-45) or select the CANCEL button to cancel
changes. If you choose to cancel the changes, a confirmation workspace will be
displayed asking you whether to save the changes or ignore the changes.
5. Select the CLOSE button to exit the Cartridge Retention workspace. See Figure 2-42.

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2.9 Verifying Proper Installation and Setup

This section describes tasks that all users with the appropriate permissions can perform.
See Section 2.6, Defining Users and Permissions.
After the Infinity system has been installed, the computer set up, users and permissions
defined and the system configured, you should verify that the system is properly
installed and set up.
button, then select the INSTALLATION QUALIFICATION button. See Figure 2-46.
The Setup menu shown in Figure 2-46 will contain additional buttons if logged in as an
Note
administrator.
The Adobe® Reader®window appears and displays the GeneXpert Infinity System
Installation Qualification Report. See Figure 2-47.
2. Print the report. If the computer is not connected to a printer, save the file to a
location where you can print the report.
3. Review the following sections in the report:
• System Information – Check that the Status column displays Pass in each row.
• Instrument Information – The report shows the instrument serial number, and the
version and status of the instrument software.
• Gateway Information – Provides gateway name, serial number and firmware
version.
• Module Information – Provides module name, serial number, firmware version,
internal temperature °C and status. Check that the Status column displays Pass
for each module.
If a Not Available message is shown, call Cepheid Technical Support. See the
Technical Assistance section in the Preface for the contact information.
• Available Assays – Check the assays in the list (see Figure 2-49). If the No
Assays message is shown, see the instructions provided with your in vitro
diagnostics assay kit and Section 2.10.2 for instructions on how to import assay
definition files.
If this report is run after system installation but before assays have been
installed on the system, the No Assays message will be displayed. If the No
Assays message is shown after you import the assay definition files, call
Cepheid Technical Support. See the Technical Assistance section in the Preface
for the contact information.

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4. Verify that the system complies with the setup requirements described in this chapter
and sign and date the Verified by section of the Installation Qualification Report. See
Figure 2-50.
5. Sign and date the Performed by and Reviewed and approved by sections of
Installation Qualification Report. File a copy of the report for your records. See
Figure 2-50.

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Figure 2-47. Installation Qualification Report in Adobe Reader
Figure 2-47. Installation Qualification Report in Adobe Reader

302-1288, April 2019
Figure 2-48. Installation Qualification Report – Page 1
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2.10 Managing Assay Definitions and Lot Specific

Parameters
This section describes tasks that all users with the appropriate permissions can perform. User
Note permissions are described in Section 2.6. For this section, the screenshots will show a Detail user
level.
An assay definition contains a series of programmed steps that the GeneXpert Infinity
system uses to perform sample preparation, amplification, and detection procedures. You
can obtain assay definition files (.gxa) from Cepheid and import them into the software
(Section 2.10.2). You can also delete assay definitions that are no longer in use
(Section 2.10.4).
Some assay definitions require lot specific parameters to determine the test results. The
cartridge barcodes contain the lot specific parameter information that is automatically
imported when you scan the barcode. If, for some reason, the barcode scanner is not
working or is not available, you can supply the lot specific parameter information
manually by importing the .gxr file (Section 2.10.5). You can also delete lot specific
parameter information that is no longer in use (Section 2.10.6).
2.10.1 Connecting the DVD Drive

The usual way to import assay definitions is by using the DVD drive provided with the
system to import the assay definitions from the CDROM. The DVD drive must be
plugged into the USB connectors on the side of the monitor.
To plug in the DVD drive and load the assay definition file CDROM:
1. Locate the DVD drive. The drive is supplied with the system but customers decide
where to store the DVD drive. It may be located on the shelf above the waste
container. Contact your lab manager if you cannot locate the DVD drive. The DVD
drive supplied is shown in Figure 2-51.
2. Place the DVD drive on the kiosk top.
3. On the side of the monitor, locate the two USB ports and plug both DVD drive
connectors into the two USB ports on the side of the monitor. See Figure 2-52.

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Figure 2-51. DVD Drive Supplied with Infinity
Figure 2-51. DVD Drive Supplied with Infinity

Figure 2-52. Plugging in the DVD Drive
Figure 2-52. Plugging in the DVD Drive

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Figure 2-53. Inserting the Assay Definition CD into the DVD Drive
Figure 2-53. Inserting the Assay Definition CD into the DVD Drive
4. Press the Eject button on the front of the DVD drive to open the door.
5. Insert the assay definitions CD into the DVD drive and close the DVD drive door.
See Figure 2-53. The green light on the front of the DVD drive will flash while the
drive reads the CD.
This completes the installation of the DVD drive and the assay definitions CD. Import
the assay definitions following the procedure in Section 2.10.2.
2.10.2 Importing Assay Definitions

Although you can import assay definitions, the Xpertise software does not allow you to modify the
Note
assay definitions.
To import new assay definitions:

1. In the Xpertise Software Home workspace, select the SETUP button. See
Figure 2-54. The Setup menu is displayed. See Figure 2-55.
2. Select the MANAGE ASSAYS button (see Figure 2-55). The Manage Assays
workspace appears and displays a list of all assays previously imported. See
Figure 2-56.
If this is the initial system installation, the Manage Assays workspace shown in Figure 2-56 will not
Note
display any assays.
3. Select the IMPORT button (see Figure 2-56). The Import Assay workspace is

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302-1288, Rev. A April 2019
Figure 2-56. Xpertise Manage Assays Workspace
New Assay Appears

Here After Import
Figure 2-56. Xpertise Manage Assays Workspace

Figure 2-57. Import Assay Workspace – Navigate to the DVD Drive
DVD Drive on Infinity System
Figure 2-57. Import Assay Workspace – Navigate to the DVD Drive

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Figure 2-58. Import Assay Workspace – Select Assay to Import
Figure 2-58. Import Assay Workspace – Select Assay to Import

4. Under the Look in: drop-down, navigate to the DVD drive. See Figure 2-57.
5. Under the DVD directory, select the Infinity Systems folder to view the list of assay
definition files applicable to the Xpertise software. See Figure 2-59 to view the
directory structure of the CD.
6. Select the assay definition (.gxa) file then select the OPEN button on the Import
Assay workspace. See Figure 2-58.
The new assay name and version number will appear in the assay list in the Manage
Assays workspace. See Figure 2-56. Check the assay name and version number to
verify that you have imported the correct assay definitions.
7. If you need to import additional assay definition files from the same CD, repeat
Step 1 through Step 6.
For combination assays that have multiple .gxa files, import only the assay definition files for assays
Note
that will be performed in your lab.
8. Remove the CD from the DVD drive and store the CD in a safe location in the event
it is needed in the future.
9. Disconnect the DVD drive from the USB ports and store the DVD drive for future
use.

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Figure 2-59. Example of the CD Directory Structure for Xpertise Assays
Figure 2-59. Example of the CD Directory Structure for Xpertise Assays

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10. (Optional) After an assay has been imported, if you would like to configure the
automation to retain cartridges for this assay for specific conditions, see
Section 2.8.2, Cartridge Retention Workspace.
11. (Optional) After an assay has been imported, if your system is connected to an LIS
network, you must update your host test code in order to download tests to the
Infinity system and/or upload test results from the Infinity system to the LIS
network. For instructions on updating host test codes, see Section 2.7.4.2,
Configuring Host Communications for Cepheid Link.
Cepheid recommends to always confirm that LIS or HIS uploaded results match GeneXpert result
after any changes to the GeneXpert or host system, including, but not limited to, changes to the
following:
Note
2.10.3 Assay Priorities – Move to Top

If Enable Assay Priority is enabled in Automation workspace of the System
Configuration (see Section 2.8), the order that assays are listed in the Manage Assays list
will be the prioritized order. Sometimes, it is necessary to change the assay priorities to
optimize lab efficiency.
To change the priority of an assay, highlight an assay and select the MOVE TO TOP button
to move the assay to the highest priority at the top of the list. In Figure 2-60, the Xpert
Flu A assay has been moved from sixth priority to first priority. This process may be
repeated, as needed, until all assays are in the desired priority.

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Figure 2-60. Changing Assay Priorities in the Manage Assays Workspace
Select Assay to Prioritize
New Assay Priorities
Figure 2-60. Changing Assay Priorities in the Manage Assays Workspace

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2.10.4 Deleting Assay Definitions

Caution
Deleting assay definitions from the system is a permanent operation. Ensure that the assay
definitions are no longer needed. If they are needed, they will need to be imported again from
the assay definitions CDROM.
To delete an assay definition file:

1. In the Manage Assays workspace (see Figure 2-61), select the name of the assay to
be deleted in the assay list and then select the DELETE button. A confirmation
message appears. See Figure 2-62.
2. Select the YES button to delete the assay definition. See Figure 2-62. The assay
definition file will be deleted and removed from the list of assays.
Figure 2-61. Deleting an Assay from the Manage Assays Workspace
Select Assay to Delete
Figure 2-61. Deleting an Assay from the Manage Assays Workspace

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Figure 2-62. Manage Assays Workspace Confirmation
Figure 2-62. Manage Assays Workspace Confirmation
2.10.5 Importing Lot Specific Parameters Manually

Some assay definitions require lot specific parameters to determine the test results. The
cartridge barcodes contain the lot specific parameter information that is automatically
imported when you scan the barcode. If, for some reason, the barcode scanner is not
working or is not available, you can supply the lot specific parameter information
manually by importing the .gxr file.
Contact Cepheid Technical Support to obtain .gxr files. After obtaining .gxr files, store them on the
Note
computer and note where the files are located.
To check if a specific assay requires Lot Specific Parameters, see if the box is checked
for the assay under the Need Lot Specific Parameters column of the Manage Assays
workspace.
To import lot specific parameters manually:
1. In the Manage Assays menu (see Figure 2-63), select the assay name in the Assay
list that requires lot specific parameters.
2. Select the LOT SPECIFIC PARAMETERS button. See Figure 2-63. The Lot Specific
Parameters workspace is displayed (see Figure 2-64). The Lot Specific Parameters
workspace will display a list of lot specific parameters files currently loaded for that
assay or will not show any lot specific parameters if it is a new assay.
3. In the Lot Specific Parameters workspace, select the IMPORT button (see
Figure 2-64).

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Figure 2-63. Manage Assays Workspace
Select Assay to Import Lot

Specific Parameters
Figure 2-63. Manage Assays Workspace

Figure 2-64. Lot Specific Parameters Workspace
Figure 2-64. Lot Specific Parameters Workspace

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Figure 2-65. Lot Specific Parameters Workspace with Reagent Lot Number Added
Figure 2-65. Lot Specific Parameters Workspace with Reagent Lot Number Added
4. Under the Look in: drop-down, navigate to the location of the .gxr file to be
imported.
5. Select the lot specific parameters (.gxr) file then select the OPEN button on the Lot
Specific Parameters dialog box.
6. The new lot number appears in the Reagent Lot Specific Parameters list. See
Figure 2-65.
7. Select the CLOSE button in the Reagent Lot Specific Parameters workspace to return
to the Manage Assays menu. See Figure 2-65.
2.10.6 Deleting Lot Specific Parameters

Caution
Deleting lot specific parameters from the system is a permanent operation. Ensure that the
lot specific parameters are no longer needed. If they are needed, they will need to be
imported again by scanning a cartridge or by manually importing a new .gxr file.
To delete lot specific parameters:

1. In the Manage Assays menu (see Figure 2-63), select the assay name in the Assay
list that the lot specific parameters will be deleted.
2. Select the LOT SPECIFIC PARAMETERS button. The Reagent Lot Specific Parameters
workspace box is displayed. See Figure 2-65.
3. Select the lot number you want to delete then select the DELETE button. See
Figure 2-66.

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Figure 2-66. Deleting an Assay from the Lot Specific Parameters Workspace
Figure 2-66. Deleting an Assay from the Lot Specific Parameters Workspace
Figure 2-67. Xpertise Reagent Lot Specific Parameters Workspace Confirmation Message
Figure 2-67. Xpertise Reagent Lot Specific Parameters Workspace Confirmation Message
4. A confirmation message appears. See Figure 2-67.
5. Select the OK button to delete the lot specific parameters.
6. Select the CLOSE button to return to the Manage Assays menu. See Figure 2-66.

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2.10.7 Editing Assay Parameters (Quantitative Assays Only)

In the Manage Assays workspace, the EDIT button is only enabled for quantitative assays
and is disabled for all other assays. The Assay Parameters workspace shows the
Quantitative Result Unit for quantitative assays.
To edit the Quantitative Result Unit for a quantitative assay definition file:
1. In the Manage Assays workspace (see Figure 2-68), select the name of the
quantitative assay to be edited in the assay list and then select the EDIT button. The
Assay Parameters workspace is displayed. See Figure 2-69.
2. Use the Quantitative Result Unit drop-down to select the desired units to show on
reports and graphs. See Figure 2-69. Select the desired unit IU/mL (International
Units per milliliter) or copies/mL (DNA copies per milliliter) shown in this example.
The units and default may vary from assay to assay.
3. Select the SAVE button (see Figure 2-69). The new quantitative result unit is saved
and the Assay Parameters workspace will display a confirmation message indicating
that the unit has been changed. See Figure 2-69.
Figure 2-68. Manage Assays Workspace Showing Quantitative Assay
Select Quantitative Assay to Edit
Figure 2-68. Manage Assays Workspace Showing Quantitative Assay

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Figure 2-69. Assay Parameters Workspace showing Quantitative Result Unit Drop-down
Figure 2-69. Assay Parameters Workspace showing Quantitative Result Unit Drop-down
Figure 2-70. Assay Parameters Workspace Confirmation
Figure 2-70. Assay Parameters Workspace Confirmation

4. In the Assay Parameters workspace (see Figure 2-70), select the OK button. The
Assay Parameters workspace closes. The Manage Assays workspace is displayed.
See Figure 2-68.

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2.11 Setting the System to Manual or Automation

Operation
See Section 5.6.2, Changing from Automation Mode to Manual Mode or Section 5.6.4,
Changing from Manual Mode to Automation Mode in this manual.
2.12 Restarting the System

Note This section describes tasks that all user types can perform.
Under some troubleshooting scenarios (see Chapter 9), you might need to restart the
system. To do this, perform the steps in Section 2.12.1 and Section 2.12.2.
2.12.1 Shutting the System Down

1. Make sure the system is not currently processing any samples. You should wait for
the system to finish all processes before shutting down or restarting the system.
2. Quit the Xpertise software by selecting the Exit icon located in the upper right-hand
side of the workspace (see Figure 2-71). The software Exit confirmation is
If a test is in-progress, the test will be stopped.
If there are outstanding cartridges waiting for processing, they will be on-hold. Before the
Important system restarts, please make sure the outstanding cartridges are not expired. You can find
out when an order will expire by selecting the View Outstanding Orders icon, which lists
when the outstanding tests will expire.
3. Select the OK button (see Figure 2-72).

Select the CANCEL button (see Section 2-72) to not exit the Xpertise software and
return to the Xpertise Software Home workspace.

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Figure 2-72. Software Exit Workspace Confirmation
Figure 2-72. Software Exit Workspace Confirmation
If LIS is enabled, two additional workspaces may be displayed after clicking the Exit icon and OK
Note
button (see Section 5.2.8.1).

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2.12.1.1 Archive Overdue Reminder

• If an archive is not overdue or if the archive setting in Figure 2-29 is not set to
Manually, with Reminder, the Test Archive Reminder workspace (see Figure 2-73)
will not be displayed. Go directly to Section 2.12.1.2.
• If an archive is overdue, the Test Archive Reminder workspace is displayed. See
Figure 2-73.
• If you do not want to archive, select NO in the Test Archive Reminder
workspace. Continue the shutdown sequence without archiving in
Section 2.12.1.2.
or
• If you want to archive, select YES in the Test Archive Reminder workspace to
continue the shutdown sequence with archiving. The Archive Test workspace is
displayed (see Figure 2-74).
Perform Step 2 through Step 7 in the procedure in Section 5.7.1, Archiving the Tests
Figure 2-73. Test Archive Reminder Workspace

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Figure 2-74. Archive Test Workspace
2.12.1.2 Database Management Reminder

• If the Database Management Reminders box in the General workspace (see
Figure 2-25) is not checked, the Database Management workspace reminder (see
Figure 2-75) will not be displayed and no further action will be required. The
Xpertise software program will close and the Windows desktop will be displayed.
See Figure 2-77. Go to Section 2.12.1.3 to complete the system shutdown sequence.
• If the Database Management Reminders box in the General workspace (see
Figure 2-25) is checked, the Database Management workspace reminder (see
Figure 2-75) will be displayed asking if you would like to perform database
management tasks.
A. If you do not want to perform database management tasks, select the NO
button. The Xpertise software program will close and the Windows desktop will
be displayed. See Figure 2-77. Go to Section 2.12.1.3 to complete the system
shutdown sequence.
or
B. If you do want to perform database management tasks, select the YES
button. The Database Management menu workspace appears (see Figure 2-76).
The database management tasks shown in Figure 2-76 will depend upon the privileges set by the
Note
system administrator and the login level of the user.
Follow the instructions in the workspace. See Section 5.6.5, Clearing a Test
Order in Manual Mode for detailed instructions on how to perform the database
management tasks you desire.

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After performing database management tasks, select the CLOSE button (see
Figure 2-76). The Xpertise software program will close and the Windows
desktop will be displayed. See Figure 2-77. Go to Section 2.12.1.3 to complete
the system shutdown sequence.
Figure 2-75. Database Management Workspace Reminder
Figure 2-75. Database Management Workspace Reminder

Figure 2-76. Database Management Workspace

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2.12.1.3 Final Shutdown Sequence

1. Double-click on the Shutdown Infinity icon on the kiosk computer desktop. See
Figure 2-77. The Infinity shutdown confirmation dialog box appears. See
Figure 2-78.
Caution
Always shut down the instrument from the kiosk computer, using the Shutdown Infinity icon
on the desktop. Do not use the shutdown function of the Windows Start menu or the main
system power switch.
2. Select the OK button. See Figure 2-78.

3. Wait for 2 minutes for the Infinity system to shut down.
Caution
If you do not wait 2 minutes, the embedded PC will power down before it has finished
shutting down. This may corrupt the software on the embedded PC.
4. Turn the AC power switch counter-clockwise to the OFF position (O). The power
switch is located on the lower right side of the Infinity system (viewing from the
front of the system). See Figure 1-1 for the Infinity-48s or Figure 1-2 for the
Infinity-80 system.
Important
The system may not boot up correctly if it is turned back on in less than two minutes
Figure 2-77. Desktop with Shutdown Infinity Icon

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Figure 2-78. Infinity shutdown Confirmation Dialog Box
2.12.2 Restarting the System

To restart the system, follow the procedures in Section 2.4, Turning the System On and
Section 2.5, Starting the Xpertise Software for the First Time.
Important
The system may not boot up correctly if it is turned back on in less than two minutes
2.13 Uninstalling or Reinstalling the Xpertise Software

The Xpertise software is already installed on the built-in computers of the GeneXpert
Infinity system. Do not attempt to uninstall or reinstall the software. If the software
becomes corrupted, or if you experience a system failure, do not attempt to reinstall the
software. Call Cepheid Technical Support for assistance to minimize the chance of
permanent data loss. See the Technical Assistance section in the Preface for the contact
information.

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3 Principles of Operation
This chapter explains how the GeneXpert Infinity systems work. The topics are as
follows:
• Section 3.1, System Operation Overview
• Section 3.2, GeneXpert Module
• Section 3.3, GeneXpert Cartridge
• Section 3.4, I-CORE Module
• Section 3.5, Heating and Cooling Mechanisms
• Section 3.6, Explanation of Experimental Methods
• Section 3.7, Optical System
• Section 3.8, System Calibration
3.1 System Operation Overview

GeneXpert Infinity systems automate and integrate sample purification, nucleic acid
amplification, and detection of the target sequence using real-time reverse transcriptase
PCR (RT-PCR) and real-time PCR assays.
Each GeneXpert module processes one sample. To run an assay, prepare the GeneXpert
cartridge, order a test and place the cartridge on the conveyor or shuttle. During the test,
the system performs the following steps:
1. Moves the cartridge into a GeneXpert module for processing.
2. Moves the sample and reagents into different chambers in the cartridge for sample
preparation.
3. Moves the sample and reagent mixture into the reaction tube.
4. Processes sample in cartridge, amplifies and detects.
5. Reports a result.
6. Unloads the cartridge from the GeneXpert module.

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Principles of Operation
The GeneXpert Infinity system contains the following components to automate loading
and unloading of cartridges in GeneXpert modules:
• Conveyor – transports cartridge from the kiosk to the lobby.
• Lobby – end of the conveyor where the gantry (robotic arm) picks up a cartridge.
• Gantry – robotic arm to transport cartridges from the lobby to the GeneXpert
modules and to unload cartridges from GeneXpert modules.
• Accumulator – stages cartridges pending module availability. If instructed, the
cartridge(s) in the accumulator can be moved to the shuttle for retrieval. The
accumulator also holds cartridges that have been retained after the test is finished.
• Shuttle – holds used or rejected cartridges, to be accessed by the operator. Transports
STAT priority cartridges into the instrument.
• GeneXpert Module – contains the following components that enable automated
sample processing in the cartridge and filling of the tube with the sample-reagent
mixture for PCR.
3.2 GeneXpert Module

Each GeneXpert module processes one sample. The sample and applicable reagents are
inserted into a GeneXpert cartridge and a test is created on the GeneXpert Infinity
system to run the test. The cartridge is then loaded into an available instrument module
and then is started.
Each instrument module contains the following components that enable automated
sample processing in the cartridge and filling of the tube with the sample-reagent
mixture for PCR:
• Valve Drive – Rotates the cartridge valve body to address the different cartridge
chambers.
• Plunger Rod – Dispenses fluids into the different cartridge chambers.
• Ultrasonic Horn – Lyses the sample (if applicable).
• I-CORE® Module – The I-CORE (Intelligent Cooling/heating Optical REaction)
module performs PCR amplification and detection.
A cartridge loading and unloading mechanism assures the proper movement of the
cartridge in the GeneXpert module. In addition, the system is designed to perform a self-
test before each test starts to verify that the system is functioning properly.

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During the test, the system performs the following steps:

1. Moves the sample and reagents into different chambers in the cartridge for sample
preparation.
2. Hydrates the reagent beads.
3. Performs probe checks to ensure that the sample preparation is successful (only if
the assay definition requires this step).
4. Moves the sample and the reagent mixture which contains reverse transcription (if
applicable) and real-time PCR specific components into the reaction tube.
5. Starts the RT-PCR (if applicable) and PCR cycles and real-time detection (see
Figure 3-1).
The GeneXpert Infinity system uses the I-CORE module heating and fan cooling system
to perform the real-time polymerase chain reaction used to exponentially amplify and
detect the organism’s DNA or cDNA sequence of interest.
Polymerase chain reaction is an amplification method that increases quantities of specific
copies of DNA or cDNA sequences. Real-time polymerase chain reaction uses
fluorescence to detect the specific sequences and includes a mechanism to determine the
cycle at which the DNA or cDNA of interest first appears at appreciable copies (called
the cycle threshold).
Figure 3-1. Example PCR Cycle Diagram for I-CORE Module Heating and Fan Cooling (Temperature Durations not to Scale)
Initial Denaturation Denaturation

95 °C 95 °C
Extension
72 °C
Annealing
120 Sec. 5 Sec. 60 °C
10 Sec.
30 Sec.
Figure 3-1. Example PCR Cycle Diagram for I-CORE Module Heating and Fan Cooling
(Temperature Durations not to Scale)

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Polymerase chain reaction consists of a series of cycles during which the DNA or cDNA
is heated and cooled at specific temperatures for a certain duration.
After Initial Denaturation (when the polymerase used to amplify the DNA or cDNA is
activated) a cycle occurs, which is usually a three-step process, consisting of:
1. The Denaturation step which divides the DNA strands.
2. An Annealing step in which a primer is needed by the polymerase to amplify the
DNA. The primer will bind to the DNA or cDNA sequence if complementary.
3. The Extension step, where the DNA strands will be extended.
The PCR cycle diagrammed in Figure 3-1 indicates 40 cycles performed by the I-CORE
module. The denaturation temperature is 95 °C; the annealing temperature is 60 °C; and,
the extension temperature is 72 °C. Each of these temperatures must be held by the
module for a specific duration, as indicated in Figure 3-1. The initial denaturation takes
place for 120 seconds for one cycle. The denaturation (5 seconds), annealing (30
seconds) and extension (10 seconds) steps cycle consecutively forty times before the
polymerase chain reaction is finally completed.
3.3 GeneXpert Cartridge

The disposable, single-use GeneXpert cartridge holds the samples and reagents to
perform the assay on the GeneXpert Infinity system. Each cartridge consists of the
following components (see Figure 3-2):
• Processing Chambers – Holds samples, reagents, processed sample, and waste
solutions. One chamber is designated as an air chamber to equilibrate pressures
within the cartridge.
• Valve Body – Rotates and allows fluid to move to different cartridge chambers and to
the reaction tube. Within the valve body, the specimen is isolated, PCR inhibitors are
removed and specimens are ultrasonically lysed (if applicable). After the sample is
processed, it is mixed with PCR reagents and moved into the integrated reaction
tube.
• Reaction Tube – Enables rapid thermal cycling and optical excitation and detection
of the tube contents. The reaction tube is automatically inserted into the I-CORE
module when the cartridge is loaded into the GeneXpert module.
The cartridge is designed to keep the reagent contained within the cartridge. It is a
closed-system vessel.
The GeneXpert cartridges are not supplied with the Infinity system. To order the
assay-specific cartridges, contact Cepheid. See the Technical Assistance section in the
Preface for the contact information.

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Figure 3-2. GeneXpert Cartridge Components
Processing Chambers
Reaction Tube
Valve Body
Figure 3-2. GeneXpert Cartridge Components

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3.4 I-CORE Module

The I-CORE module is the hardware component within each instrument module that
performs PCR amplification and fluorescence detection. As part of the cartridge load
process, the reaction tube is inserted into the I-CORE module. See Figure 3-3. The
sample and reagent mixture are pushed from the cartridge into the reaction tube. During
the amplification process, the I-CORE heater heats and the fan cools the reaction tube
contents. The optical blocks excite the dye molecules and detect the fluorescence
emitted.
Figure 3-3. I-CORE Module (6-Color Module Shown)
I-CORE Module (Side View)

Fan
Cartridge
Inserts into the I-CORE
Heater Reaction Tube
Optical Blocks Reaction Tube

(Inside the I-CORE)
Figure 3-3. I-CORE Module (6-Color Module Shown)

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3.5 Heating and Cooling Mechanisms

Within the I-CORE, the heater consists of two ceramic plates that have high thermal
conductivity to assure temperature uniformity and rapid heat transfer. See Figure 3-3.
Resistive heater elements are deposited on the ceramic plates using thick film
technologies and a thermistor attached directly to each plate monitors its temperature. A
high-efficiency fan cools the reaction tube contents by moving ambient air across the
heater plates. During thermocycling, the instrument firmware controls the temperature
inside the instrument module. The firmware incorporates a control loop to ensure rapid
heating of the plates while minimizing the temperature overshoot around the desired
target temperature.
3.6 Explanation of Experimental Methods

The GeneXpert system uses real-time polymerase chain reaction (real-time PCR) to
detect the organism’s DNA of interest.
Real-time polymerase chain reaction is a variant of polymerase chain reaction and uses
the same method of PCR with denaturation, annealing and extension at specified time
durations to amplify DNA. Real-time PCR uses fluorescence in the form of either
intercalating dyes or probes to detect amplified copies of the DNA of interest and to
visualize and monitor the amplified product in real time.
In real-time PCR, primers specifically designed to be complementary to the organism’s
DNA bind to the DNA and extend it. For example in 5’-nuclease technology, a probe
which has a reporter dye and quencher attached to it is also complementary to the
organism’s DNA and binds to the DNA downstream to the primer. The primer and probe
together add a higher level of specificity to identify a sequence specific to the organism.
As the DNA strand gets extended, the probe is destroyed and the reporter and quencher
are dissociated and become free in solution. The fluorescent signal increases with each
amplification.
The cycle at which the fluorescence becomes detected after appreciable copies of the
DNA are made is the cycle threshold (Ct). The most basic definition of a cycle threshold
is the first cycle in which there is significant increase in fluorescence above the
background fluorescence (see Figure 3-4).
The real-time PCR generates an amplification curve with number of cycles on the x-axis
and fluorescence on the y-axis. The increase in fluorescence is proportional to the
amount of amplicon generated and can be used to define cycle threshold. As the
amplification curve plateaus, it will reach a fluorescent end-point at which other factors
are rate-limiting. If the organism’s DNA is not detected by the real-time PCR reaction,
the amplification curve will be flat.

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Figure 3-4. Amplification Curve and Cycle Threshold (Ct)
PLATEAU
ENDPOINT
FLUORESCENCE
CYCLE THRESHOLD
Fluorescence
THRESHOLD LINE
(Fluorescence Units) LOG LINEAR
BASELINE
Cycles
Figure 3-4. Amplification Curve and Cycle Threshold (Ct)
3.7 Optical System

Within the I-CORE, the optical system consists of two blocks (see Figure 3-3):
• Six-color Exciter Module – Contains high intensity light-emitting diodes (LEDs) to
excite the reporter dye molecules.
• Six-color Detector Module – Contains silicon photodetectors and filters to detect the
six spectral bands.
The optical blocks are positioned within the I-CORE such that their apertures mate with
the optical windows of the reaction tube, allowing excitation and emission detection of
the reaction mixture. By using probes labeled with different fluorescent reporter dyes, up
to six targets can be detected simultaneously in a single reaction tube. The emission
spectra of fluorescent dyes can overlap, and a particular dye could produce signal in
more than one channel. To compensate for the spectral overlap, the system uses
appropriate calibration and data analysis algorithms to determine the concentrations of
each reporter dye. Table 3-1 shows the excitation and detection spectral bands for the six
channels.

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Table 3-1. GeneXpert System Excitation and Emission Ranges (6-Color)
Optical Channel Excitation (nm) Emission (nm)

1 375-405 420-480
2 450-495 510-535
3 500-550 565-590
4 555-590 606-650
5 630-650 665-685
6 630-650 >700
3.8 System Calibration

The thermal reaction chamber thermistors are calibrated to ±1.0 °C using National
Institute of Standards and Technology (NIST) traceable standards. During the
manufacturing process, the temperature of the heating system is measured at two
temperatures: 60 °C and 95 °C. Calibration coefficients that correct for small errors in
the raw thermistor readings of the heaters are stored in the memory of each I-CORE
module.
The optical system is calibrated using standard concentrations of individual unquenched
fluorescent dye-oligos. For each optical channel, the signal produced by a tube alone (the
blank signal) is subtracted from the raw signal produced by the dye-oligo standard to
determine the spectral characteristics. Using the individual spectral characteristics of the
pure dye-oligos, signals from an unknown mixture of dye-oligos can be resolved into
corrected signals for the individual dye-oligos in the mixture.

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4 Performance Characteristics and Specifications
This chapter lists the performance characteristics and specifications for the GeneXpert
Infinity-48s and GeneXpert Infinity-80 systems. The topics are as follows:
• Section 4.1, System Classification
• Section 4.2, Physical Specifications
• Section 4.3, Electrical Requirements
• Section 4.4, Operational Environmental Parameters
• Section 4.5, Environmental Conditions for Storage and Transport
• Section 4.6, Sound Pressure
• Section 4.7, Product Energy Consumption Information
4.1 System Classification

The GeneXpert Infinity systems are:
• Designed for stationary automated operation
• Intended for use worldwide
• Intended for evaluating preprocessed biological material
• Intended for indoor use only

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Performance Characteristics and Specifications
4.2 Physical Specifications

4.2.1 GeneXpert Infinity-48s Physical Specifications
Table 4-1 through Table 4-3 list the physical specifications of the GeneXpert Infinity-48s
system and UPS.
Table 4-1. Dimensions of the GeneXpert Infinity-48s System
Component Dimensions
GeneXpert Infinity-48s System 217 cm (85 in) wide, 200 cm (78.5 in) high, 89 cm (35 in) deep
UPS
There are two UPS models that are provided with the GeneXpert Infinity systems. The UPS specifications for both models
are:
• Synergy SII Series, 208 Vac. Non-isolated, 8.7 cm (3.4 in) high, 44 cm (17.2 in) wide, 66.8 cm (26.3 in) deep
50/60 Hz, Single Phase
• International Units: Model S3K0XHU-0X3XX
• North American Units: Model S3K0XHU
OR
• Synergy SIII Series, 208 Vac. Non-isolated, 8.7 cm (3.4 in) high, 44 cm (17.2 in) wide, 68.5 cm (27 in) deep
• International Units: Model ACDEF3000-22
• North American Units: Model ACDEF3000-22
Table 4-2. Weight of the GeneXpert Infinity-48s System
Component Weight
GeneXpert Infinity-48s System (fully-loaded) Approximately 725 kg (1600 lbs)
Synergy II UPS Shipping Weight: 39 kg (86 lbs)
Synergy III UPS Shipping Weight: 37 kg (83 lbs)
Table 4-3. Clearance Requirements for the GeneXpert Infinity-48s System
GeneXpert Infinity-48s System • Recommended clearance: 81 cm (32 in) in the back of the system to facility wall
• Right side: 30 cm (12 inches)
• Front side: 96 cm (38 inches)
• Left side: 81 cm (32 inches)
• Position the system so that there is enough clearance to connect/disconnect
cables, and to remove/replace modules and equipment.

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4.2.2 GeneXpert Infinity-80 Physical Specifications

Table 4-4 through Table 4-6 list the physical specifications of the GeneXpert Infinity-80
system and UPS.
Table 4-4. Dimensions of the GeneXpert Infinity-80 System
GeneXpert Infinity-80 System 274 cm (108 in) wide, 200 cm (78.5 in) high, 89 cm (35 in) deep
UPS
There are two UPS models that are provided with the GeneXpert Infinity systems. The UPS specifications for both models
are:
• Synergy SII Series, 208 Vac. Non-isolated, 8.7 cm (3.4 in) high, 44 cm (17.2 in) wide, 66.8 cm (26.3 in) deep
• International Units: Model S3K0XHU-0X3XX
• North American Units: Model S3K0XHU
OR
• Synergy SIII Series, 208 Vac. Non-isolated, 8.7 cm (3.4 in) high, 44 cm (17.2 in) wide, 68.5 cm (27 in) deep
• International Units: Model ACDEF3000-22
• North American Units: Model ACDEF3000-22
Table 4-5. Weight of the GeneXpert Infinity-80 System
Component Weight
GeneXpert Infinity-80 System (fully-loaded) Approximately 953 kg (2100 lbs)
Synergy II UPS Shipping Weight: 39 kg (86 lbs)
Synergy III UPS Shipping Weight: 37 kg (83 lbs)
Table 4-6. Clearance Requirements for the GeneXpert Infinity-80 System
GeneXpert Infinity-80 System • Recommended clearance: 81 cm (32 in) in the back of the system to facility wall
• Right side: 30 cm (12 inches)
• Front side: 96 cm (38 inches)
• Left side: 81 cm (32 inches)
• Position the system so that there is enough clearance to connect/disconnect
cables, and to remove/replace modules and equipment.

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4.3 Electrical Requirements

The electrical requirements for both the Infinity-48s and Infinity-80 systems are shown
in Table 4-7.
Table 4-7. Electrical Requirements for GeneXpert Infinity-48s and GeneXpert Infinity-80 Systems
Item Specifications
Line Voltage: 200-240Vac
Frequency: 50 – 60 Hz ±0.5%
Power Consumption – Maximum 16A max @ 200V~
Current:
Line Circuit Breaker: 20A
Mains supply fluctuation Up to ± 10% of the nominal voltage
Transient over-voltages Up to 2500V peak (impulse withstand category II)
UPS Nominal input voltage:
Synergy SII Series, 208 Vac. Non- XHU models (high voltage): 208 Vac (factory default)
isolated, 50/60 Hz, Single Phase 200, 208, 220, 230, 240 Vac (selectable)
• International Units: Model Available output voltage:
S3K0XHU-0X3XX
• North American Units: Model XHU models (high voltage): 208 Vac (factory default)
S3K0XHU 200, 208, 220, 230, 240 Vac (selectable)
4.4 Operational Environmental Parameters

Your laboratory must meet the following requirements:
• General environment: Indoor only
• Pollution degree: 2
• Operating temperature: 15–30 °C (60–85 °F)
• Ambient humidity: 20%–80%, non-condensing
The maximum thermal output of the system is 8278 BTU/Hour (2426W), although
typical operating output may be lower. Consult your facilities department regarding
ventilation requirements for this level of heat output in your laboratory.

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4.5 Environmental Conditions for Storage and

Transport
The required storage conditions are as follows:
• Temperature: -30 °C to +45 °C
• Humidity: 0%–95% ambient humidity, non-condensing
4.6 Sound Pressure

The sound pressure specifications are as follows:
• Audible sound pressure range: < 69 dB (reference level 20 µPa)
• Ultrasonic sound pressure between 20kHz to 100kHz: < 110 dB SPL (reference level
20 µPa) with a maximum in the 40 kHz one-third octave bands
4.7 Product Energy Consumption Information

Energy Annual Energy
Supplier Model Efficiency On Mode Power Consumption Standby Power
Supplier Name Identifier Class Consumption (W) (KWh) Consumption (W)
Cepheid GeneXpert Infinity-48s G 2426 5840 1248
Cepheid GeneXpert Infinity-80 G 2426 5840 1248

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5 Operating Instructions
This chapter explains how to use the GeneXpert Infinity system to run diagnostic tests
and manage the results. The following information is provided in this chapter:
• Section 5.1, Typical Workflow
• Section 5.2, Overview of Basic System and Software Operation Tasks
• Section 5.2.1, Turning the System On
• Section 5.2.2, Windows 7 Login Procedure
• Section 5.2.3, Windows 10 Login Procedure
• Section 5.2.4, Starting the Xpertise Software
• Section 5.2.5, Logging On
• Section 5.2.6, Logging Off
• Section 5.2.7, Changing Your Password
• Section 5.3, System Setup Procedure
• Section 5.4, Starting the GeneXpert Infinity System
• Section 5.5, Ordering a Test in Automation Mode
• Section 5.5.1, Automation Mode Overview
• Section 5.5.2, Ordering a Test in Automation Mode
• Section 5.5.3, Viewing Test Results
• Section 5.5.4, Searching Test Results by Sample ID
• Section 5.5.5, Generating Test Reports
• Section 5.5.6, Monitoring a Test in Progress
• Section 5.5.7, Stopping a Test in Progress
• Section 5.5.8, Pausing the System
• Section 5.5.9, EMERGENCY STOP – Stopping and Starting Automation
• Section 5.5.10, Clearing a Test Order in Automation Mode
• Section 5.6, Ordering a Test in Manual Mode
• Section 5.6.1, Manual Mode Overview
• Section 5.6.2, Changing from Automation Mode to Manual Mode
• Section 5.6.3, Ordering a Test in Manual Mode

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Operating Instructions
• Section 5.6.4, Changing from Manual Mode to Automation Mode

• Section 5.6.5, Clearing a Test Order in Manual Mode
• Section 5.7, Managing Test Results Data
• Section 5.7.1, Archiving the Tests
• Section 5.7.2, Retrieving Tests from an Archive File
• Section 5.7.3, Backing Up the Database
• Section 5.7.4, Restoring the Database
• Section 5.7.5, Compacting the Database
• Section 5.7.6, Checking the Integrity of the Database
• Section 5.8, Operating with Host Connectivity
• Section 5.8.1, Ordering a Test with Host Connectivity
• Section 5.8.2, Aborting a Query
• Section 5.8.3, Canceling a Host Downloaded Test Order
• Section 5.8.4, Uploading Test Results to Host
• Section 5.9, Operating with Cepheid Link Connectivity
• Section 5.9.1, Scanning a Sample and Cartridge using Cepheid Link
• Section 5.9.2, Running Cartridges Scanned from Cepheid Link
5.1 Typical Workflow

Table 5-1 lists the typical workflow for processing a specimen using the GeneXpert
Infinity systems.
Table 5-1. Typical Workflow for Processing a Specimen
Step Task Section

1 Start the GeneXpert Infinity system. Section 5.4
2 Check the list of assays available. Import the assay definition files, Package Insert shipped with the cartridges.
if necessary.
Section 2.10
3 Order a test. Section 5.5.2
4 Load prepared cartridges onto the conveyor for automatic Figure 5-38 in Section 5.5.2
processing by the Infinity system.
5 Monitor the test progress. Section 5.5.6
6 View the test results. Section 5.5.3
7 Generate test result reports. Section 5.5.5
8 Manage the test results data. Section 5.6
Figure 5-1 shows the typical workflow for processing a specimen sample using the
Infinity systems in Automation mode.
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Figure 5-1. GeneXpert Infinity Systems Typical Workflow in Automation Mode
START
NO
Cartridge prepared? Prepare cartridge.
YES
The Infinity system knows which modules are available and
Scan cartridge schedules the cartridge to go to a module according to its priority.
and submit order. The order is processed. The cartridge information is checked. If the
cartridge is expired or has already been used, the order cannot be
completed and the cartridge will not be processed.
Place cartridge The screen prompts loading and the conveyor starts up when the
onto conveyor. cartridge is placed on the conveyor. The cartridge is moved to the lobby position.
Cartridge is automatically
The gantry moves to the lobby to scan the cartridge.
scanned by the gantry.
Kiosk scanner NO You will be alerted. You can retrieve If you choose to, you can
& gantry scanner Place cartridge in accumulator.
the cartridge when desired. re-order the cartridge/test.
match?
YES
Hold in accumulator.
YES
Destination Wait until a test is completed and

NO Accumulator site NO
module there is a module available before
available? available? ordering a new test.
YES
The system gantry loads

cartridge into an available
module.
After test completion,

the gantry removes
the cartridge.
Cartridge to NO Cartridge is placed onto the waste shelf

be retained? and then pushed into the waste container.
YES
The gantry moves the cartridge

to the accumulator.
Figure 5-1. GeneXpert Infinity Systems Typical Workflow in Automation Mode

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5.2 Overview of Basic System and Software Operation

Tasks
This section describes the basic system tasks and provides a brief overview of the
GeneXpert Infinity system Xpertise software.
• Section 5.2.1, Turning the System On
• Section 5.2.4, Starting the Xpertise Software
• Section 5.2.5, Logging On
• Section 5.2.6, Logging Off
5.2.1 Turning the System On

Use the following procedure to turn the system on and log onto the system:
1. To turn on the GeneXpert Infinity system, turn the power switch clockwise to the on
position ( | ) as shown in Figure 5-2.

The power switch is located on the front, lower right side of the GeneXpert Infinity
system. See Figure 1-1 for the Infinity-48s or Figure 1-2 for the Infinity-80.
2. Wait approximately1 minute for the system to boot.
The computer may have either Windows 7 or Windows 10 installed.

Note For the Windows 7 login procedure, see Section 5.2.2.
For the Windows 10 login procedure, see Section 5.2.3.
Important In order to maintain system security, users should change their password every 90 days.

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1. On Windows 7, after power-up the Windows Account screen will be displayed. See
Figure 5-3.
use only by Cepheid Technical Support, as shown in Figure 5-3.

2. On the Windows 7 Account screen, select the Cepheid-Admin user account (see
Figure 5-3. The Windows Password screen appears. See Figure 5-4.
3. On the Windows 7 Password screen (see Figure 5-4), enter the password assigned by
the system administrator. The Windows 7 desktop screen is displayed.

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4. Start the Xpertise software. See Section 5.2.4.

1. On Windows 10, after power-up, the Windows Lock screen appears. See Figure 5-5.
Click anywhere on the screen to display the Windows Account and Password screen.
See Figure 5-6.
use only by Cepheid Technical Support. See Figure 5-6.

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2. On the Windows Account and Password screen, select the Cepheid-Admin user
account (see Figure 5-6).

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3. On the Windows 10 Account and Password screen (see Figure 5-6), enter the
password assigned by the system administrator.
4. Start the Xpertise software. See Section 5.2.4

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5.2.4 Starting the Xpertise Software

Do not change the Cepheid user profile. Changing the profile can cause loss of data during a
Caution test.
Windows 7
Start the software in one of two ways:
• On the Windows desktop, double-select the Xpertise Software icon.
or
• On the Windows taskbar, select the Windows Start icon, and select All Programs –>
Cepheid –> Xpertise Software. See Figure 5-7.
Figure 5-7. Starting the Xpertise Software from the Program Menus

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Windows 10
Start the software in one of two ways:
or
• On the Windows taskbar, select the icon, and select Cepheid -> Xpertise Software.
See Figure 5-8.
Windows 7 and 10: The GeneXpert Infinity system splash screen momentarily
appears (see Figure 5-9), followed by the Xpertise Login workspace. See Figure 5-10.

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5.2.5 Logging On
Each time the Xpertise software is started, the Login workspace is displayed and asks for
a user name and password. See Figure 5-10. In the User Name box, enter your GeneXpert
Infinity system user name. In the Password box, enter your password. Select the OK
button to log on and start the software. Upon successful completion of your login, the
Database Management workspace will be displayed. See Figure 5-11.
If the Login workspace does not appear during software startup after an administrator has
Important
been defined for the system, contact your GeneXpert Infinity system administrator.
If another user is logged onto the system, it is not necessary to log the other user out before logging
in. Select the Login icon located in the upper right-hand corner of the workspace and the Login
Note
workspace will be displayed. Enter your login information, you will be logged onto the system and
the other user will be automatically logged out.

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Figure 5-10. Xpertise Login Workspace
Figure 5-10. Xpertise Login Workspace
Note If you forget your password, contact your GeneXpert Infinity system administrator.
Most of the screenshots shown in this manual will be at a detail user login. Basic user login will be
Note shown when needed to show workspaces relating to that specific user and administrator user login
will be shown, where required.
If you are the GeneXpert Infinity system administrator and you forget your password,
contact Cepheid Technical Support. See the Technical Assistance section in the Preface
for the contact information. Cepheid Technical Support will supply a temporary
password to allow you to log in and change the password. The temporary password
expires after 1 day.

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Figure 5-11. Xpertise Software Data Management Workspace
Figure 5-11. Xpertise Software Data Management Workspace

A database management reminder will be displayed depending upon the Database
Management setting in the System Configuration General workspace:
1. If the Database Management Reminders box in the System Configuration General
workspace (see Figure 2-25) is not checked, the Database Management workspace
(see Figure 5-11) will not be displayed and no action concerning the database will be
required. The software will continue to load and you can go to Section 5.2.5.2 to
continue the startup sequence.
or
2. If the Database Management Reminders box on the System Configuration General
workspace (see Figure 2-25) is checked, the Database Management workspace (see
Figure 5-11) will be displayed asking if you want to perform Database Management
tasks.
A. If you select NO in the Database Management workspace (see Figure 5-11), the
Xpertise software continues to load and you can go to Section 5.2.5.2 to
continue the startup sequence.
or
B. If you select YES in the Database Management workspace (see Figure 5-11),
you will be asked to select the task to be performed (see Figure 5-12).

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Depending on the user’s privileges, there may be additional options in the Database Management
Note
3. Follow the instructions in the workspace (see Figure 5-12) and select the DATABASE
BACKUP button. See Section 5.7, Managing Test Results Data for detailed
instructions on how to perform the database management tasks you desire.
4. When the database management task is complete, a confirmation workspace is
displayed. Select the OK button to close the confirmation workspace.
5. Select the CLOSE button (see Figure 5-12). Continue with Section 5.2.5.2.

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If an archive is not overdue or if the archive setting in Figure 2-29 is set to Manually,
Figure 5-13 will not appear, and the Xpertise Software Home workspace will be
displayed (see Figure 5-15). Continue with Section 5.3, System Setup Procedure.
If an archive is overdue, the Test Archive Reminder workspace will be displayed (see
Figure 5-13).
• If you do not want to archive, select NO in the Test Archive Reminder workspace
(see Figure 5-13). The startup sequence will continue without archiving and the
Software Home workspace is displayed (see Figure 5-15). Continue with
Section 5.3, System Setup Procedure.
or
• If you would like to archive, select YES in the Test Archive Reminder workspace
(see Figure 5-13) to continue the startup sequence with archiving. The Archive Test
To archive tests, perform Step 2 through Step 7 of the procedure in Section 5.7.1,
Archiving the Tests. When archiving is complete, the system will continue the startup
sequence and the Xpertise Software Home workspace is displayed (see Figure 5-15).
Continue with Section 5.3, System Setup Procedure.

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5.2.6 Logging Off

To log off the Xpertise software workspace, select the Logout icon located in the upper
right corner of the Xpertise Software Home workspace. See Figure 5-15.
You should log off if you are going to be away from the system for an extended period
of time. Logging off prevents the software from recording other users’ activities under
your user name.
Note If you log out while a test is in progress, the system will finish the test and save the results.

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Exit Icon
Change Password Icon
Logout Icon
Login Icon
5.2.7 Changing Your Password

Important In order to maintain system security, users should change their password every 90 days.
Cepheid recommends that users change their passwords every 90 days to protect their
identity on the Infinity system. Your institution may have additional requirements for
changing passwords. Follow your institution’s policies regarding passwords. To change
your Infinity system password:
1. In the Xpertise Software Home workspace, select the Change Password icon located
in the upper right corner of the Xpertise software workspace (see Figure 5-15). The
Change Password workspace is displayed. See Figure 5-16.
2. In the Current Password box, type your current password.
3. In the New Password and Confirm New Password boxes, type your new password
(must be 6 to 10 characters).
4. Select the OK button to save the change (see Figure 5-16). If the information entered
is acceptable, a confirmation message will be displayed indicating that the password
was successfully changed. See Figure 5-17.
Select the CANCEL button if you do not want to change your password.

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Figure 5-16. Change Password Workspace
Figure 5-16. Change Password Workspace

Figure 5-17. Change Password Workspace Confirmation Message
Figure 5-17. Change Password Workspace Confirmation Message

5. Select the OK button to close the Change Password workspace.

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5.2.8 Shutting the System Down

Use the following procedure to end the software session and shut the system down:
1. Make sure the system is not currently processing any samples. Wait for the system to
finish all processes before shutting down or restarting the system.
2. Quit the Xpertise software by selecting the Exit icon located in the upper right-hand
side of the workspace. The Exit icon is shown in Figure 5-15. The software Exit
3. Press the OK button.
If a test is in-progress, dialog warnings will notify the user that tests are in-progress. The
user can choose not to exit the software and allow the tests to complete or the user can
choose to exit the software which will stop the tests.
Important If there are outstanding cartridges waiting for processing, they will be on-hold. Before the
system restarts, please make sure the outstanding cartridges are not expired. You can find
out when an order will expire by selecting the View Outstanding Orders icon, which lists
when the outstanding tests will expire.
Figure 5-18. Xpertise Software Exit Workspace Confirmation
Figure 5-18. Xpertise Software Exit Workspace Confirmation

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5.2.8.1 Additional Shutdown Screens with LIS Active

If LIS is enabled, an additional screen will be briefly displayed after selecting the Exit
icon and OK button (in the previous section).
1. If the automatic test result upload feature is on, all tests with Upload-Pending,
Uploading and Re-Uploading status will be uploaded to LIS.
A message indicating that Xpertise is shutting down, please wait will be displayed
(see Figure 5-19). The system will wait for a response from the LIS if Xpertise has
made a recent request for new test orders.
Figure 5-19. Xpertise is Shutting Down Workspace (Only Appears with LIS Enabled)
Figure 5-19. Xpertise is Shutting Down Workspace (Only Appears with LIS Enabled)
2. Starting with the workplace shown in Figure 5-19, a 30-second timeout period
begins. During this timeout period, the outstanding test results will be uploaded to
the LIS.
3. After this timeout period, (or if the LIS shutdown sequence completes successfully
in 30 seconds or less), the system will no longer try to exchange data with LIS. The
system shutdown will proceed to the next section of showing the archive reminder in
Section 5.2.8.2 (if applicable).
Depending on the upload status of the test results and whether or not automatic upload is enabled,
Xpertise will try to send the result the next time in connects.
Note
Test results may always be manually re-uploaded at any time that LIS is connected.

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If an archive is not overdue or if the archive setting in Figure 2-29 is set to Manually,
Figure 5-20 will not appear. Continue with Section 5.2.8.3, Database Management
Reminder.
If an archive is overdue, the Test Archive Reminder workspace will be displayed (see
Figure 5-13).
• If you do not want to archive, select NO in the Test Archive Reminder workspace
(see Figure 5-20). The software exit sequence will continue without archiving.
Continue with Section 5.2.8.3, Database Management Reminder.
or
• If you would like to archive, select YES in the Test Archive Reminder workspace
(see Figure 5-20) to continue the software exit sequence with archiving. The Archive
Test workspace is displayed. See Figure 5-21.
To archive tests, perform Step 2 through Step 7 of the procedure in Section 5.7.1,
Archiving the Tests. When archiving is complete, the system will continue the
software exit sequence. Continue with Section 5.2.8.3, Database Management
Reminder.

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A database management reminder will be displayed depending upon the Database
Management setting in the System Configuration General workspace:
1. If the Database Management Reminders box in the System Configuration General
workspace (see Figure 2-25) is not checked, the Database Management workspace
(see Figure 5-22) will not be displayed and no action concerning the database will be
required. The Xpertise software will exit and the Windows desktop will be
displayed.
or
2. If the Database Management Reminders box on the System Configuration General
workspace (see Figure 2-25) is checked, the Database Management workspace (see
Figure 5-22) will be displayed asking if you want to perform Database Management
tasks.
A. If you select NO in the Database Management workspace (see Figure 5-22), the
Xpertise software will exit and the Windows desktop will be displayed.
or
B. If you select YES in the Database Management workspace (see
Figure 5-22),you will be asked to select the task to be performed (see
Figure 5-23).

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Depending on the user’s privileges, there may be additional options in the Database Management
Note

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3. Follow the instructions in the workspace (see Figure 5-23) and select the DATABASE
BACKUP button. See Section 5.7, Managing Test Results Data for detailed
instructions on how to perform the database management tasks you desire.
4. When the database management task is complete, a confirmation workspace is
displayed. Select the OK button to close the confirmation workspace.
5. Select the CLOSE button (see Figure 5-23) to exit the Xpertise software. The
Windows desktop will be displayed. See Figure 5-24.
6. Double-click on the Shutdown Infinity icon on the kiosk computer desktop. See
Figure 5-24. The Infinity shutdown confirmation dialog box appears. See
Figure 5-25.
Caution
Always shut down the instrument from the kiosk computer, using the System Shutdown icon
on the desktop. Do not use the shutdown function of the Windows Start menu or the main
system power switch.

Select Cancel to not shut down the system.
8. Wait for 2 minutes for the Infinity system to shut down.
Caution
If you do not wait 2 minutes, the embedded PC will power down before it has finished
shutting down. This may corrupt the software on the embedded PC.
9. Turn the AC power switch counter-clockwise to the off position ( O ). The power
switch is located on the lower right side of the Infinity system (viewing from the
front of the system). See Figure 1-1 for the Infinity-48s or Figure 1-2 for the Infinity-
80 system.
Important Cepheid recommends powering down the Infinity system a minimum of one time per week.

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5.3 System Setup Procedure

Before processing tests on the GeneXpert Infinity system, complete the following items:
• Check the waste container. Empty the waste container if it is almost full. See
Section 10.9.10, Waste Container Capacity and Contents Icon.
• If there are cartridges remaining in the system from previous operations, remove
rejected cartridges. See Section 10.14, Retrieving Cartridges from the Accumulator.
5.4 Starting the GeneXpert Infinity System

To start the GeneXpert Infinity system:
1. Turn on the GeneXpert Infinity system if you have not already done so. See
Section 5.2.1, Turning the System On.
2. Start the Xpertise software. See Section 5.2.4, Starting the Xpertise Software.
3. Log onto the system using your assigned user name and password. See
Section 5.2.5, Logging On.
As the software is starting, the system checks the status of the automation system,
performs self-test on the GeneXpert modules, and then displays an active Xpertise
Software Home workspace. See Figure 5-26.
5.5 Ordering a Test in Automation Mode

This section describes procedures for operating the GeneXpert Infinity system in
Automation mode.
Note Automation mode is the default operation mode.
5.5.1 Automation Mode Overview

To start a test in Automation mode:
1. Use the kiosk barcode scanner or use the keyboard to manually enter the test
information:
2. Enter other optional information, such as sample type and notes.
If you do not need to enter other information, enable Auto Submit in the System Configuration
Note workspace. After Sample ID and cartridge barcode information are available, the system will
automatically submit your order.
3. Submit the test information.

4. Place the cartridge onto the conveyor.
5. The cartridge is moved to the lobby area.

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6. The gantry scans the cartridge barcode.

7. The gantry transfers the cartridge from the lobby into the assigned module.
8. The test starts.
9. After a cartridge has completed the test, the gantry removes the cartridge from the
module and either moves it to the waste container or places it on an accumulator
shelf.
5.5.2 Ordering a Test in Automation Mode

The Infinity system is operating in Automation mode if the Manual mode icon is not
present in the dashboard.
1. In the Xpertise Software Home workspace, select the ORDERS button. See
Figure 5-26. The Orders Menu workspace will be displayed. See Figure 5-27.

2. Select the ORDER TEST button. See Figure 5-27.
The ordering process will be demonstrated using a series of workspace screenshots
that direct you to either scan or type in test information.
For screenshots shown in this manual, the Patient ID field will be shown as enabled and the Patient
ID 2, Patient Name and Patient Demographics fields will also be enabled. The Patient ID, Patient
Note ID 2, Patient Name and Patient Demographics fields are optional and may be left blank if they are
not required. If these options are not enabled in the System Configuration General workspace, they
will not be displayed.

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The following sequence of workspace screenshots will show how to order a test:
• Scan or type the Patient ID (optional) – see Figure 5-28
• Type in optional patient information (Patient ID 2, Last Name, First Name,
Patient Demographics fields) – see Figure 5-28
• Select priority – normal (unchecked) or STAT (checked) – see Figure 5-31
• Scan or type the Sample ID – see Figure 5-31
• Scan cartridge barcode – see Figure 5-32 and Figure 5-33
Figure 5-27. Orders Menu

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Figure 5-28. Order Test – Patient ID Workspace

The Order Test – Patient ID workspace is displayed if Patient ID is enabled. See
Figure 5-28. The Order Test – Sample ID workspace is displayed if Patient ID is not
enabled. See Figure 5-31.
A. In the Order Test - Patient Information workspace, scan or type in the Patient ID
(if the Patient Information workspace is enabled in the System Configuration
workspace). See Figure 5-28.
B. If Patient ID 2 is enabled, type in the Patient ID 2 information. See Figure 5-28.
C. If the patient name fields are enabled, type in the patient’s first name and last
name into their respective fields. See Figure 5-28.
D. If the patient demographics fields are enabled, enter the Date of Birth
• The date of birth may be entered directly into the Date of Birth field
following the format shown in the field.
or
• The date of birth may be entered from the Date of Birth workspace.
a. To enter the date of birth using the Date of Birth workspace, select the
DOB CALENDAR button on the Order Test - Patient Information
workspace (see Figure 5-28). The Date of Birth workspace will be

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Figure 5-29. Date of Birth Workspace
Figure 5-29. Date of Birth Workspace

b. In the Date of Birth workspace, select the year of birth using the drop-
down menu.
c. Select the month by using the << Previous and Next >> buttons to
display the month of birth.
d. Select the day of the month to specify the date.
e. Touch the OK button. The Date of Birth workspace will close and the
date will be placed in the Date of Birth field in the Order Test - Patient
ID workspace. See Figure 5-30.
E. Enter the postal code. The Xpertise software does not validate the postal code.
In the United States, the postal code is referred to as the zip code.
F. Select the gender using the drop-down menu.
G. Select the ethnicity using the drop-down menu.

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Figure 5-30. Order Test – Patient ID Workspace with Optional Demographics Fields Entered
Figure 5-30. Order Test – Patient ID Workspace with Optional Demographics Fields Entered
After performing these steps, a workspace will display all the information entered in
the top area of the workspace. From the bottom part of the workspace, information
can be added or changed, such as test type, sample type and notes.
If any of the information has been entered incorrectly, the information can be
corrected manually or by selecting buttons to open the various workspaces again.
3. Select the CONTINUE button (see Figure 5-30). The Order Test – Sample ID
Select the CLEAR ORDER button if you do not want to order a test.
4. Select the STAT Priority check box if the sample needs to be processed quickly. Scan
or enter the Sample ID (see Figure 5-31). After the Sample ID is scanned, the Order
Test – Assay workspace is displayed. If the sample ID is entered manually, select the
CONTINUE button to display Order Test – Assay workspace. See Figure 5-32.

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Figure 5-31. Order Test – Sample ID Workspace

Figure 5-32. Order Test – Assay Workspace

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Figure 5-33. Scanning the Cartridge Barcode using the Kiosk Barcode Scanner
5. As shown in Figure 5-33, scan the cartridge barcode (Item #1) using the kiosk
barcode scanner (Item #2). For multiple-test assays, the Order Test – Assay
Selection workspace is displayed (see Figure 5-34). For single-test assays, the Order
Test – Test Information workspace is displayed. See Figure 5-35.
6. For multiple-test assays only (see Figure 5-34), select the assay to be used for the test
and select the CONTINUE button. The Order Test – Test Information workspace is
Figure 5-34. Order Test – Assay Selection Workspace

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Figure 5-35. Order Test – Test Information Workspace with Priority Set to Normal
* = Scanned Item
Figure 5-36. Order Test – Load Cartridge Workspace

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7. Review the information in the Order Test – Test Information workspace (see
Figure 5-35). Entries with an asterisk (*) next to the item have been scanned instead
of entered manually. Enter optional information into the notes field or change the
Test Type if running an External Quality Control, then select the SUBMIT button or
select the CLEAR ORDER button if you do not want to order a test. The Order Test –
Load Cartridge workspace is displayed. See Figure 5-36.
If Auto Submit is enabled, the Order Test – Test Information workspace will not be displayed. Load
Note the cartridge onto the conveyor. Go to Step 11 to enter the next order. If notes must be entered, they
can be entered on the View Results workspace for the test.5
After the order is submitted, the Xpertise software will confirm that the cartridge has not been
Note previously used and is within the expiration dating. If the cartridge has expired or has been
previously used, an error message will be displayed. See Figure 5-37.
8. If required, log in to start the test.

9. After selected the SUBMIT button, the cartridge will be processed according the
priority of the cartridge.
A. If the cartridge priority is set to Normal, continue with Step 10.
or
B. If the cartridge priority is set to STAT, the cartridge will be processed through
the shuttle. See Section 5.5.2.1, Processing STAT Priority Cartridges.
Figure 5-37. Example Error Message showing Expired Cartridge
Figure 5-37. Example Error Message showing Expired Cartridge

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10. As instructed in the Order Test – Load Cartridge workspace (see Figure 5-36) and
shown in Figure 5-38, load (or place) the cartridge (item #1) in the loading zone on
the conveyor (item #3), outside the yellow and black lines (item #4). Make sure you
place the cartridge on the conveyor with the label (item #2) facing you.
The conveyor belt moves the cartridge into the system. The gantry scans the
cartridge and places the cartridge into an available GeneXpert module or onto an
accumulator shelf if no modules are currently available.
Figure 5-38. Placing the Cartridge on the Conveyor

11. As soon as the cartridge has been scanned, the Order Test – Patient ID workspace
will be displayed to allow the operator to enter the next test. See Figure 5-39.
• To enter the next test, enter the information requested in Step 2 and continue the
procedure through Step 10 until all tests have been ordered.
or
• If no other tests will be ordered, select the END ORDER TEST button (see
Figure 5-39). If no information has been entered into any of the fields in the
Order Test – Patient ID workspace, the Order Test menu will close.
If information has been entered into any of the fields in the Order Test – Patient
ID workspace, a confirmation workspace will be displayed to verify that you
want to exit the Order Test menu. See Figure 5-40.
In the Order Test workspace confirmation, select YES to exit the Order Test
menu.
Select NO to remain in the Order Test menu and enter additional tests.

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Figure 5-40. Order Test Workspace
Figure 5-40. Order Test Workspace

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5.5.2.1 Processing STAT Priority Cartridges

This procedure describes how to process a STAT cartridge and continues from Step 9 in
Section 5.5.2, Ordering a Test in Automation Mode.
If the test needs to run immediately, the STAT Priority box on the Order Test – Sample ID
workspace must be checked (see Figure 5-31) before the cartridge is scanned. When the
priority is set to STAT, the cartridge will be run from the shuttle immediately instead of
being queued up on the conveyor. The priority shown on the Order Test – Test
Information workspace will indicate STAT. See Figure 5-41.
Figure 5-41. Order Test – Test Information Workspace with Priority Set to STAT
Figure 5-41. Order Test – Test Information Workspace with Priority Set to STAT
1. Review the information in the Order Test – Test Information workspace (see
Figure 5-41). Enter optional information or notes, then select the SUBMIT button or
select the CLEAR ORDER button if you do not want to order a test. A message
indicating that there is a request to open the shuttle will be displayed briefly
followed by the Order Test –Load Cartridge workspace with instructions to load the
cartridge into the shuttle. See Figure 5-42. The shuttle will partially open.
After the order is submitted, the Xpertise software will confirm that the cartridge has not been
Note previously used and is within the expiration dating. If the cartridge has expired or has been
previously used, an error message will be displayed. See Figure 5-37.

3. The shuttle door will unlatch. See Figure 5-43.
4. Pull the shuttle open. See Figure 5-43.

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Figure 5-42. Order Test – Load Cartridge Workspace for Shuttle
Figure 5-42. Order Test – Load Cartridge Workspace for Shuttle

shown in Figure 5-43, load (or place) the cartridge into the shuttle. Make sure you
place the cartridge into the shuttle with the label facing you.
6. Manually close the shuttle. See Figure 5-43.
The gantry scans the cartridge on the shuttle and places the cartridge into an
available GeneXpert module or onto an accumulator shelf if no modules are
currently available.
To order additional tests, see Section 5.5.2, Ordering a Test in Automation Mode.

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Figure 5-43. Load the Cartridge into the Shuttle
Shuttle Unlatches Open Shuttle
Load Cartridge into Shuttle Close Shuttle
Figure 5-43. Load the Cartridge into the Shuttle

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5.5.2.2 Automation Mode Tests with Load Errors

The GeneXpert Infinity systems perform preload and post-load self-tests. If a module
fails the cartridge preload or post-load self-tests, the cartridge is transferred to another
available module and the process is repeated for a second time.
If a cartridge fails during the second loading, the cartridge is transferred to an
accumulator site and the user is informed via the monitor. The user can then move the
cartridge from the accumulator to the shuttle when a shuttle site becomes available. To
retrieve cartridges from the accumulator, see Section 10.14, Retrieving Cartridges from
the Accumulator.

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5.5.2.3 Retaining a Cartridge that is Running

While a cartridge is running, if you decide to retain it for further investigation, you can
select the Retain Cartridge After Test Completion check box in the View Results
workspace.
To retain a cartridge that is running:

1. Select the View Another Test icon. This can be selected from any workspace.
Figure 5-45 show the selection occurring on the Xpertise Software Home workspace.
The View Another Test workspace is displayed. See Figure 5-46.
2. In the View Another Test workspace, locate and select the test to be viewed and
select the VIEW RESULTS button (see Figure 5-46). The View Results workspace for
the selected test will be displayed. See Figure 5-47.
3. In the View Results workspace, select the EDIT button.
4. In the View Results workspace, select the Retain Cartridge After Test Completion
check box and then select the SAVE button. See Figure 5-47.
5. Select the CLOSE button. The View Results workspace will close. The initial
workspace will be displayed.
After the test completes, the cartridge will be placed on an accumulator shelf. To retrieve
the cartridge from the accumulator, see Section 10.14, Retrieving Cartridges from the
Accumulator.

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Figure 5-46. View Another Test Workspace

Figure 5-47. View Results Workspace – Retain Cartridge After Test Completion
Figure 5-47. View Results Workspace – Retain Cartridge After Test Completion

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5.5.2.4 Operation in Automation Mode with Kiosk Scanner Not Functioning

If the kiosk scanner is not functioning, call Cepheid Technical Support immediately to correct the
Note problem. This procedure is to be used only until the kiosk scanner is repaired. See the Technical
Assistance section in the Preface for contact information.
If the kiosk scanner is not functioning, the Infinity may still be operated in Automation
mode. In order to operator in this mode, the cartridge barcode information must be
entered using the keyboard. If the barcode scanner is not functioning on startup, the error
message and error icon will be listed in the Message Log (see Figure 5-48). However, the
system will continue to complete the startup sequence the error message will scroll off
the screen.
If the kiosk scanner becomes non-functional after system startup or if the error message
has scrolled off the screen, the error will be indicated by the error icon being displayed
in the dashboard (see Figure 5-49). To confirm the source of the error, select the error
icon to display more information about the error. See Figure 5-50. Hover over the icon to
see more information.
Figure 5-48. Message Log Workspace Showing Kiosk Scanner Error

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Figure 5-49. Error Icon in Dashboard
Select Error Icon to Display Source of Error

Figure 5-50. Source of Error in Dashboard
Hover Over Icon to Display More Information

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To run a test in Automation mode with a non-functioning kiosk barcode scanner:

2. Select the ORDER TEST button. See Figure 5-52.
The ordering process will be demonstrated using a series of workspaces that direct
you to either scan or type in test information.
The following sequence of workspaces will show you how to order a test:
• Type the Patient ID (optional)
• Type in optional patient information (Patient ID 2, Last Name, First Name,
Patient Demographics fields), if needed
• Type the Sample ID
• Select priority – normal or STAT
• Type the cartridge barcode

The Order Test – Patient ID workspace is displayed if Patient ID is enabled. See
Figure 5-53. The Order Test – Sample ID workspace is displayed if Patient ID is not
enabled. See Figure 5-54.

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A. In the Order Test - Patient Information workspace, type in the Patient ID (if the
Patient Information workspace is enabled). See Figure 5-53.
or
down menu.
4. Enter the Sample ID (see Figure 5-54). Select the STAT Priority check box if the
sample needs to be processed quickly. The Order Test – Manual Barcode Entry

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Figure 5-55. Order Test – Manual Barcode Entry Workspace

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5. As shown in Figure 5-55, enter the complete cartridge barcode and select the
CONTINUE button. For additional details about manually entering a cartridge
barcode, see Section 5.6.3.1, Manually Entering the Barcode to Order a Test. For
multiple-test assays, the Order Test – Assay Selection workspace is displayed (see
Figure 5-56). For single-test assays, the Order Test – Test Information workspace is
6. For multiple-test assays only (see Figure 5-56), select the assay to be used for the test
and select the CONTINUE button. The Order Test – Test Information workspace is
7. Enter additional information or notes, if necessary, then select the SUBMIT button or
select the CLEAR ORDER button if you do not want to order a test. The Order Test –
Load Cartridge workspace is displayed. See Figure 5-58.
If Auto Submit is enabled, the Order Test – Test Information workspace will not be displayed. Load
Note the cartridge onto the conveyor. Go to Step 9 to enter the next order. If notes must be entered, they
can be entered on the View Results workspace for the test.

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The conveyor belt moves the cartridge into the system. The gantry places the
cartridge into an available GeneXpert module.

• To enter the next test, enter the information requested in Step 2 and continue the
procedure through Step 11 until all tests have been entered.
or
• If no other tests will be ordered, select the END ORDER TEST button (see
Figure 5-60). If no information has been entered into any of the field in the
Order Test – Patient ID workspace, the Order Test menu will close.
If information has been entered into any of the field in the Order Test – Patient
ID workspace, a confirmation workspace will be displayed to verify that you
want to exit the Order Test menu.
11. In the Order Entry workspace confirmation, select YES to exit the Order Test menu.
Select NO to remain in the Order Test menu and enter additional tests.

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5.5.3 Viewing Test Results

To view the test results for completed tests:
1. In the Xpertise Software Home workspace, select the RESULTS button (see
Figure 5-61). The Results menu will be displayed. See Figure 5-62.
2. In the Results menu (see Figure 5-62), select the VIEW RESULTS button. The View
Results workspace will be displayed. See Figure 5-63.
To view the test results for a test that was recently performed (i.e. since the system was last shut
Note down), the results may be viewed by double-selecting any test listed in the Tests Since Launch
workspace. The View Results workspace will be displayed for the selected test.
The View Results workspace displayed will depend upon the level of the user logged into the
Note system. A basic user will see the workspaces described in Section 5.5.3.1. A detail user or an
administrator will see the workspaces described in Section 5.5.3.2.

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Figure 5-62. Results Menu

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Figure 5-63. View Results Workspace Showing Tabs (Detail User View)
5.5.3.1 Basic User View Results

The View Results workspace shows the test results that a basic user will see. See
Figure 5-64. The buttons available in the basic user View Results workspace are:
• EDIT – Select this button to edit the workspace. This button toggles to a Save button.
During editing, only the Save and Cancel buttons are available.
• REPORT – Select this button to view and print or save the results in a PDF file.
• PREVIOUS TEST – Select this button to view the results of the previous test in the list
of results.
• NEXT TEST – Select this button to view the results of the next test in the list of
results.
• UPLOAD RESULT – Select this button to upload selected results to Host (This button
is present only if host communication is enabled).
• VIEW ANOTHER TEST – When you select this button, a workspace displays a list of
tests (including those that are completed and still running) for you to select a test to
be displayed.
• CLOSE – Closes the workspace.
The View Results workspace allows you to view data associated with either an
in-progress test or completed tests. See Figure 5-63. If host connectivity is enabled, you
can manually upload test results to a host from this workspace.

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As shown in Figure 5-63, the View Results workspace for basic users consists of the
following tabs:
• Test Result
• Errors
• Support
A description of each of the tabs in the View Results workspace is described in the
following subsections.
Test Result Tab

The Test Result tab of the View Results workspace shows the result of a test. See
Figure 5-64.
Figure 5-64. View Results Workspace – Test Result Tab (Basic User View)
Figure 5-64. View Results Workspace – Test Result Tab (Basic User View)
The following test information is available in the Test Result tab of the View Results
• Patient ID – This field is available if the Use Patient ID option is enabled. It is
editable if it did not originate from a host order. If there is an asterisk (*) next to the
field, the Patient ID was scanned.
• Patient ID 2 – This field is available if the Use Patient ID and Patient ID 2 options are
enabled. It is editable if it did not originate from a host order.
• Sample ID – This field is editable if it did not originate from a host order. If there is
an asterisk (*) next to the field, the Sample ID was scanned.
• Assay name and assay version # – Non-editable.

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• Result – Results for this test. It is non-editable.

• Disclaimer – This non-editable disclaimer text is shown after the test result is
available depending on the assay and the result.
• Sample Type – This field is editable, using a drop down list of assay-specific sample
types.
• Other Sample Type – Sample type will contain text entered during the Order Test
process or as a result of editing a test. It is editable if Sample Type is Other;
otherwise, it is non-editable.
• User – This field displays the name of the system operator who performed the test. It
is non-editable.
• Status – The operational status of the test is displayed in this non-editable field. It
will display Done if the test has completed. It may also display RUNNING if the test
has not completed yet, INCOMPLETE if there were problems while running the test or
ABORTED if the test was aborted before it completed.
• Notes – This field displays any notes entered when the test was submitted. If
additional notes are required, select the Edit button and add or change the note
information.
• Upload Status (if host communication is enabled) – If host communication is
enabled, a field will be shown indicating the upload status of the results. This field is
non-editable. If the test has completed, it will display Uploaded if the test results
have been uploaded or it will display Upload-Pending if the test has completed but
the results have not been uploaded yet. If the test is still running, the Upload Status
field will display Run-in-Progress. This field is not displayed if host communication
is not enabled.
Some fields are editable. To edit those fields:
1. Select the EDIT button to activate the workspace.
2. Edit the desired fields.
3. Select the SAVE button to save the changes.
Editable fields are shown on a white background when the workspace is in edit mode. Non-editable
Note
fields have a gray background.

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Errors Tab
The Errors tab of the View Results workspace shows a list of warning or error messages
associated with this test. If there are no errors, then no errors will be displayed on this
tab. See Figure 5-65.
Figure 5-65. View Results Workspace – Errors Tab (Basic User View)
Figure 5-65. View Results Workspace – Errors Tab (Basic User View)
The following information is displayed for each error in the Errors tab of the View
Results workspace (see Figure 5-65):
• # – Sequential number of the errors that occurred during the test. It is not editable.
• Description – A description of the error type is displayed. It is not editable.
• Detail – An error code and additional information is provided about the error (e.g.
Error 5007: Probe check failed......). It is not editable.
• Time – The date and time the error occurred is displayed. It is not editable.

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Support Tab
The Support tab of the View Results workspace provides additional information about a
test. See Figure 5-66.
Figure 5-66. View Results Workspace – Support Tab (Basic User View)
Figure 5-66. View Results Workspace – Support Tab (Basic User View)
The Support tab shows the following additional test information. See Figure 5-66.
• Reagent Lot ID – This non-editable field displays the reagent lot ID. If there is an
asterisk (*) next to the field, the reagent lot ID was scanned from the cartridge.
• Assay Type – This non-editable field displays the type of diagnostic test that was run.
For most tests, it will display In Vitro Diagnostic.
• Cartridge S/N – This non-editable field displays the cartridge serial number. If there
is an asterisk (*) next to the field, the cartridge serial number was scanned from the
cartridge.
• Expiration Date – This non-editable field displays the cartridge expiration date. If
there is an asterisk (*) next to the field, the cartridge expiration date was scanned
from the cartridge.
• Test Type – This editable field displays type of sample that was run. The drop-down
can be set to either Specimen or External Controls.
• Priority – This non-editable field displays the priority of the test that was run. It will
show either Normal or STAT.
• Start Time – This non-editable field displays the test start date and time in the system
configuration format.

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• End Time – This non-editable field displays the test end date and time in the system
configuration format.
• Error Status – This non-editable field indicates if there were any errors during the
test run. No errors are indicated by OK. If an error occurred while the test was
running, the status will be Error.
• S/W Version – This non-editable field displays the software version installed on the
system at the time the test was run.
• Instrument S/N – This non-editable field displays the serial number of the instrument
in which the test was run.
• Module Name – This non-editable field displays the name of the module in which the
test was run (i.e. B2).
• Module S/N – This non-editable field displays the serial number of the module in
which the test was run.
Some fields are editable. To edit those fields:
1. Select the EDIT button to activate the workspace. See Figure 5-66.
2. Edit the desired fields.
3. Select the SAVE button to save the changes.
Editable fields are shown on a white background when the workspace is in edit mode. Non-editable
Note
fields have a gray background.
5.5.3.2 Detail User and Administrative View Results

Detail users and administrators can view additional information about each test. The
View Results workspace shows the test results that a detail or administrative user will
see. See Figure 5-67. The buttons available in the detail user View Results workspace
are:
• EDIT – Select this button to edit the workspace. This button toggles to a Save button.
During editing, only the Save and Cancel buttons are available.
• REPORT – Select this button to view and print or save the results in a PDF file.
• UPLOAD RESULT – Select this button to upload selected results to the host. This
button is present only if host communication is enabled.
• PREVIOUS TEST – Select this button to view the results of the previous test in the list
of results.
• NEXT TEST – Select this button to view the results of the next test in the list of
results.
• VIEW ANOTHER TEST – When you select this button, a workspace displays a list of
tests (including those that are completed and still running) for you to select the test
to be displayed.

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The View Results workspace allows you to view data associated with either an
in-progress test or completed tests. See Figure 5-67. If host connectivity is available, you
may select to manually upload test results to a host from this workspace.
As shown in Figure 5-67, the View Results workspace for a detail user consists of the
following tabs:
• Test Result (same as basic user)
• Analyte Result
• Detail
• Amplification Curve
• Errors (same as basic user)
• History
• Support (same as basic user)
Each of the above tabs is described in the following subsections.
Test Result Tab

The Test Result tab is the same for the detail user as it is for the basic user. See the
description of the Test Result tab for the basic user in Section 5.5.3.1, Basic User View
Results.

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Analyte Result Tab

The Analyte Result tab in the View Results workspace shows non-editable analyte result
Figure 5-68. View Results Workspace – Analyte Result Tab (Detail User View)
Figure 5-68. View Results Workspace – Analyte Result Tab (Detail User View)
The following non-editable analyte result information is available in the Analyte Result
tab:
• Analyte Name – Description of the reference targets that aid in the detection of a
specific assay.
• Ct – The cycle threshold is the first cycle in which the fluorescence reaches a
specified threshold. The Ct is determined by analyzing the amplification curve.
• EndPt – The endpoint is the fluorescence reading for the last cycle of a thermal
cycling protocol.
• Analyte Result – Indicates whether a specific analyte has been detected or not
detected.
• Probe Check Result – Before the start of the PCR reaction, the Infinity system
measures the fluorescence signal from the probes to monitor bead rehydration,
reaction-tube filling, probe integrity and dye stability. Probe Check passes if it meets
the assigned acceptance criteria.
Note There are no editable fields in the Analyte Result tab.

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Detail Tab
The Detail tab in the View Results workspace shows the non-editable miscellaneous data
for the test. See Figure 5-69.
Figure 5-69. View Results Workspace – Detail Tab (Detail User View)
Figure 5-69. View Results Workspace – Detail Tab (Detail User View)
The following non-editable information is available in the Detail tab:
• Analyte Name – Description of the reference targets that aid in the detection of a
specific assay.
• Prb Chk 1 – Probe check 1 data are the results of fluorescent measurements of dye
specific to each analyte.
• Probe Check Result – Before the start of the PCR reaction, the Infinity system
measures the fluorescence signal from the probes to monitor bead rehydration,
reaction-tube filling, probe integrity and dye stability. Probe Check passes if it meets
the assigned acceptance criteria.
• 2nd Deriv Peak Height – The highest peak of the 2nd derivative represents the point
of maximum curvature of the growth curve. The threshold defines only a minimum
peak height for determining Ct. If the 2nd derivative peak is above the threshold, a
Ct is reported. If the peak is below the threshold, no Ct is reported.

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• Curve Fit – Curve fit substitutes the modeled curve fit data to reduce false positives
that may occur due to optical noise, drift or other curve anomalies, by smoothing the
curve. For example a noise spike in a curve could trigger the primary threshold,
indicating a positive whereas an experienced operator would call the result as a
negative.
Note There are no editable fields in the Detail tab.
Amplification Curve Tab

The Amplification Curve tab in the View Results workspace displays the amplification
curve for the test. See Figure 5-70.
Figure 5-70. View Results Workspace – Amplification Curve Tab (Detail User View)
Figure 5-70. View Results Workspace – Amplification Curve Tab (Detail User View)
The Amplification Curve is a graph that plots the number of cycles on the X-axis and the
fluorescence units on the Y-axis for each analyte. The graph reflects the curve analysis
specified in the assay definition. The curve is used to define the cycle threshold.
Note There are no editable fields in the Amplification Curve tab.
To display or hide an analyte graph, select the analyte name in the graph legend to the
right of the graph. In addition, you can change the magnification of the graph in the X or
Y direction by dragging the horizontal or vertical slider next to the X- or Y-axis.
The EXPORT CURVE button is available in the View Results workspace or the
Amplification Curve tab. When you select EXPORT CURVE button, the View Results –
Export Curve workspace is displayed. See Figure 5-71.

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Figure 5-71. View Results Workspace – Export Curve (Detail User View)
Figure 5-71. View Results Workspace – Export Curve (Detail User View)
The buttons in the View Results – Export Curve workspace are described below:
• GENERATE IMAGE – Saves the graph to an image file. The graph image can be saved
on its own or with legend based on your selection. The .jpg file is saved to the report
folder that is defined in the System Configuration.
• GENERATE REPORT FILE – Creates a PDF file containing the graph with basic test
information generated in the report folder. An example of a report file is shown in
Figure 5-73.
• PREVIEW REPORT – When this option is selected, a pdf file is generated and
displayed in Adobe Reader (see Figure 5-72). This file can be saved from Adobe
Reader. An example of a report file is shown in Figure 5-73.

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Figure 5-72. Export Curve Graph Report Shown in Adobe Reader
Figure 5-72. Export Curve Graph Report Shown in Adobe Reader

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Figure 5-73. Export Curve Graph Report
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Errors Tab
The Errors tab is the same for the detail user as it is for the basic user. See the
description of the Errors tab for the basic user in Section 5.5.3.1, Basic User View
Results.
History Tab
The History tab in the View Results workspace shows changes made to the test after it
has been started. A new entry is made for each change. See Figure 5-74.
Figure 5-74. View Results Workspace – History Tab (Detail User View)
Figure 5-74. View Results Workspace – History Tab (Detail User View)
The following information is provided on the History tab:
• Field Name – the field name that was changed.
• WAS – previous entry for the field.
• IS – current entry for the field.
• User – user that made the change.
• Time – date and time at which the change was saved.
Note There are no editable fields in the History tab.
Support Tab
The Support tab is the same for the detail user as it is for the basic user. See the
description of the Support tab for the basic user in Section 5.5.3.1, Basic User View
Results.

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5.5.4 Searching Test Results by Sample ID

You can search the completed test results by Sample ID for single or multiple tests,
using the steps in this section.
1. From the Xpertise Software Home Workspace (see Figure 5-75), select the View
Another Test icon on the dashboard, which will display the View Another Test

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2. In the Sample ID entry area at the top of the workspace, enter (or scan) the Sample
ID for which you’ll be searching. After entering the Sample ID, click the FIND
button.
When performing a search, you can use wild card symbols to aid or narrow your search: Enter the
exact Sample ID, a single-character wildcard (_ [underscore]) combined with exact characters or a
Note multiple-character wildcard (%) with or without exact characters. The Sample ID field limitations will
apply except that the wildcard characters (_ [underscore] and %) are allowed. The Sample ID field
limitations will apply except that the wildcard characters (_ [underscore] and %) are allowed.
3. The View Another Test workspace is updated to display the result(s) of the search
(see Figure 5-77).
4. From this search results workspace, locate the specific test to be viewed, and select
the entry (see Figure 5-77).
5. Select the VIEW RESULTS button to display the results for the specific test selected
(see Figure 5-77).

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Figure 5-77. View Another Test Workspace - Results of Search by Sample ID
Figure 5-77. View Another Test Workspace - Results of Search by Sample ID

Figure 5-78. View Results Workspace - Search Sample ID
Figure 5-78. View Results Workspace - Search Sample ID

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5.5.5 Generating Test Reports

Depending upon the level of detail required, two test reports are available. The basic
user test report shows test results and test information. The administrative and detail user
test report shows test results, test information, analyte results and the amplification curve
(if selected).
• For basic user test reports, see Section 5.5.5.1, Basic User Test Reports.
• For detail and administrative user test reports, see Section 5.5.5.2, Administrative
and Detail User Test Reports.
5.5.5.1 Basic User Test Reports

If analyte results and the amplification curve is required, the test report should be created by a
Note detailed user or an administrative user. See Section 5.5.5.2, Administrative and Detail User Test
Reports.
To generate a basic user test report:

1. From the View Results workspace, select the Report button (see Figure 5-64). The
Test Report workspace appears. See Figure 5-79.
Figure 5-79. Test Report Workspace (Basic User)
Figure 5-79. Test Report Workspace (Basic User)

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2. Select one or more test reports to be generated by using the check boxe(s) in the left-
hand column. See Figure 5-79.
3. When you finish selecting the test report, select one or both of the following buttons:
• GENERATE REPORT FILE – Creates a PDF file and saves it to the location you
specify.
1) Select the GENERATE REPORT FILE button on the Test Report workspace
(see Figure 5-79) to create a PDF file of the test report. The Generate
Report File dialog box will appear, which enables you to save the file to a
specified location. Select SAVE once you have navigated to the location.
2) Optionally, to print the report, go to the saved location, open the test report
and print it. A test report similar to the test report shown in Figure 5-80 will
be printed. The bottom of the test report contains a signature block for
approval of printed test reports.
• PREVIEW PDF – Creates a PDF file and displays the file in Adobe Reader. The
PDF file can be printed and saved from the Adobe Reader software.
4. After the report has been printed or saves, select the Home icon to return to the
Xpertise Software Home workspace or select the CLOSE button to return to the View
Results workspace.

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Figure 5-80. Example of a Test Report (Basic User)
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5.5.5.2 Administrative and Detail User Test Reports

To generate a detail user or administrative user test report:
1. From the View Results workspace, select the Report button (see Figure 5-63). The
Test Report workspace appears. See Figure 5-81.
Figure 5-81. Test Report Workspace (Administrative and Detail Users)
Figure 5-81. Test Report Workspace (Administrative and Detail Users)

2. Select one or more test reports to be generated by using the check boxe(s) in the left-
hand column. See Figure 5-81.
3. If the amplification curve should be included in the test report, select the Include
Amplification Curve check box at the top of the workspace. See Figure 5-81.
4. When you finish selecting the test report, select one or both of the following buttons:
specify.
1) Select the GENERATE REPORT FILE button on the Test Report workspace
(see Figure 5-81) to create a PDF file of the test report. The Generate
Report File dialog box will appear, which enables you to save the file to a
specified location. Select SAVE once you have navigated to the location.
2) Optionally, to print the report, go to the saved location, open the test report
and print it. A test report similar to the test report shown in Figure 5-82 will
be printed. The last page of the test report contains a signature block for
approval of printed test reports.
• PREVIEW PDF – Creates a PDF file and displays the file in Adobe Reader. The
PDF file can be printed and saved from the Adobe Reader software.

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Figure 5-82. Example of a Test Report (Administrative and Detail Users) – Page 1
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5. After the report has been printed or saves, select the Home icon to return to the
Xpertise Software Home workspace or select the CLOSE button to return to the View
Results workspace.
5.5.6 Monitoring a Test in Progress

You can monitor the test progress or other status indicators in the following areas of the
Xpertise Software workspace:
Dashboard Select the View Another Test icon on the dashboard, this will display tests
(in-progress or finished) associated with the Patient ID (optional) and/or Sample ID. You
can select the specific test you want to monitor and select the VIEW RESULTS button. See
Section 10.9.5, View Another Test Icon for more information.
Message Log The Message Log displays the date and time you started the software,
the software version number and any error, information, or warning messages that were
encountered since the software started. See Section 10.11, Message Log for more
information.
5.5.7 Stopping a Test in Progress

To stop a test that is running:
Important Stopping a test in progress will result in no test result for the test(s) being stopped.
1. In the Xpertise Home workspace (see Figure 5-61), select the ORDERS button. The
Order menu workspace will be displayed. See Figure 5-84.
2. Select the STOP TEST button (see Figure 5-84). The Stop Test workspace will be
displayed showing all tests currently running. See Figure 5-85.

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Figure 5-84. Orders Menu Workspace
Figure 5-84. Orders Menu Workspace

Figure 5-85. Stop Test Workspace

3. In the Stop Test workspace, select the test you want to stop. See Figure 5-85.
4. Select the STOP button (see Figure 5-85). The Stop Test confirmation workspace will
be displayed. See Figure 5-86.

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To stop all running tests, select the STOP ALL button. See Figure 5-85. All running tests will begin
Note
the stop test process and the progress bar will be displayed. See Figure 5-87.
5. Select the YES button (see Figure 5-86). The selected test will stop and a progress bar
will be displayed showing the progress of the stop test process. See Figure 5-87.
Select the NO button if you do not want to stop the selected test.
6. After the test is stopped, the Stop Test workspace will be displayed. See Figure 5-85.
Select the CLOSE button.

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Figure 5-87. Stop Test Workspace Showing Progress Bar
Figure 5-87. Stop Test Workspace Showing Progress Bar
5.5.8 Pausing the System

Use the Pause feature to safely open the glass doors to adjust or remove a cartridge or to
clean a spill inside the cabinet. The system automation can be paused after any currently
edited workspace has been saved if it is in Edit mode. When Pause is activated, only the
system automation (gantry, conveyor) is paused. Any tests currently running will
continue to run.
Caution
Pausing the system for a long time can cause tests to expire. Plan to resume from a “pause”
within a short time.
See Section 10.9.12, Pause Icon for detailed description of the Pause command.
5.5.9 EMERGENCY STOP – Stopping and Starting Automation

Push the EMERGENCY STOP button at any time to prevent user injury or instrument
damage. The EMERGENCY STOP button is located just below the monitor display. See
Item 17 on Figure 1-1 for the Infinity-48s or Figure 1-2 for the Infinity-80.
Caution
Stopping the system for a long time can cause tests to expire. Plan to resume from an
emergency stop within a short time.
See Section 8.2, EMERGENCY STOP Button for a detailed description of the emergency
stop.
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5.5.10 Clearing a Test Order in Automation Mode

In some cases, it may be necessary to clear a test order after the automation order test
process has started. Each of the order test workspaces has a CLEAR ORDER button except
for the first order test workspace which has an END ORDER TEST button. To clear a test
order, select the END ORDER TEST or the CLEAR ORDER button on any of these
workspaces. See Figure 5-88 for an example of the CLEAR ORDER button.
To clear a test order:
1. On any automation test order workspace, select the CLEAR ORDER button, (see
Figure 5-88). A confirmation workspace will be displayed to ensure that the test
should be cancelled. See Figure 5-89.
2. Select the YES button to cancel the test order (see Figure 5-89). The initial order test
workspace will be displayed. See Figure 5-61.
Select the NO button to continue with the automation order test entry.
Note that on the initial order test workspace with the END ORDER TEST button, selecting the END
Note
ORDER TEST button will exit the order test process and the Orders menu will be displayed.
Figure 5-88. Order Test – Assay Workspace – Scan Cartridge Barcode
Figure 5-88. Order Test – Assay Workspace – Scan Cartridge Barcode

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Figure 5-89. Order Test – Assay Workspace Confirmation
Figure 5-89. Order Test – Assay Workspace Confirmation
5.6 Ordering a Test in Manual Mode

This section describes procedures for operating the GeneXpert Infinity system in Manual
mode.
5.6.1 Manual Mode Overview

Manual mode can be used when the automated system is not fully functional. The user
can load the cartridge into the GeneXpert module following the manual operation
instructions displayed in the Manual Load workspace.
To start a test in Manual mode:
1. If the system is running in Automation mode, change the operation mode to Manual
mode.
2. Use the kiosk barcode scanner or enter the test information.
A. Scan or enter optional Patient ID.
B. Scan or enter Sample ID.
C. Scan the prepared cartridge barcode.
3. Enter other information, such as sample type and notes, if needed.
4. Select the SUBMIT button in the Order Test workspace.

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5. Place the cartridge into the module that has a flashing green light.
6. Close the module door.
7. After the cartridge has completed the test, open the module door.
8. Remove the processed cartridge.
9. Upon completion of all Manual mode processing, return the system to Automation
mode, if desired.
5.6.2 Changing from Automation Mode to Manual Mode

To change from Automation mode to Manual mode:
button. The Setup menu is displayed. See Figure 5-91.
The Setup menu shown in Figure 5-91 may contain additional buttons if logged in as an
Note
administrator or if the administrator has changed the default privileges.
2. Select the CHANGE OPERATION MODE button (see Figure 5-91). The Change
Operation Mode workspace is displayed. See Figure 5-92.
The Change Operation Mode workspace allows you to change the operation mode.
Two radio buttons are displayed with the current operation mode saved in the
database. See Figure 5-92.
• Automation Mode (Default)
• Manual Mode

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Figure 5-92. Change Operation Mode Workspace

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3. Select EDIT button (see Figure 5-92). The Change Operation Mode workspace is
activated. See Figure 5-93.
4. In the Change Operation Mode workspace, select the Manual Mode radio button and
select the SAVE button (see Figure 5-93). The Change Operation Mode confirmation
workspace for changing to Manual mode is displayed. See Figure 5-94.
5. In the Change Operation Mode confirmation workspace (see Figure 5-94), select the
OK button. The Leaving Automation Mode – Remove Cartridges workspace is
Select the CANCEL button if you do not want to switch to Manual mode.
Any tests that are currently running in the GeneXpert modules will continue to run after the system
switches to Manual mode. These cartridges will need to be removed manually from the GeneXpert
modules after they have finished.
Note Any tests that have been ordered but have not yet started (outstanding orders) will be cancelled
after the change to Manual mode. These tests can be ordered again in Manual mode or they can be
ordered again in Automation mode if they have not expired. If there are outstanding tests that will be
cancelled, the Leaving Automation Mode - Remove Cartridges workspace shown in Figure 5-95 will
be modified to indicate that there are outstanding tests that will be cancelled.
6. Read and perform the instructions provided at the top of the Leaving Automation
Mode – Remove Cartridges workspace (see Figure 5-95) and remove all cartridges
from the accumulator, shuttle, conveyor, and modules.
7. After all cartridges have been removed from the system, select the CARTRIDGE(S)
REMOVED button (see Figure 5-95). The Leaving Automation Mode – Remove
Cartridges confirmation workspace is displayed. See Figure 5-96.

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Figure 5-94. Change Operation Mode Workspace Confirmation
Figure 5-94. Change Operation Mode Workspace Confirmation

Figure 5-95. Leaving Automation Mode – Remove Cartridges Workspace

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8. Verify that all cartridges have been removed from the system with the exception of
modules currently processing cartridges and select the OK button in the Leaving
Automation Mode – Remove Cartridges confirmation workspace (see Figure 5-96).
The Change Operation Mode workspace is displayed (see Figure 5-97) with the
Current Operating Mode changed to Manual Mode, and the Manual Mode icon is
present on the dashboard panel.
9. In the Change Operation Mode workspace, select the CLOSE button (see
Figure 5-97). The Xpertise Software Home workspace is displayed showing the
Setup menu and the Manual Mode icon on the dashboard. See Figure 5-98.
After the system is changed to Manual mode, open all available GeneXpert module doors.
Important Prior to ordering a new test, remove any cartridges that have completed tests and keep the
module doors open.
See Section 5.6.3, Ordering a Test in Manual Mode for details on how to order a test
using the Manual mode.

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Figure 5-97. Change Operation Mode Workspace Indicating Manual Mode
Manual Mode Icon Current Operating Mode

Indicates Manual Mode
Figure 5-97. Change Operation Mode Workspace Indicating Manual Mode

Figure 5-98. Xpertise Home Workspace Showing Manual Mode Icon
Figure 5-98. Xpertise Home Workspace Showing Manual Mode Icon

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5.6.3 Ordering a Test in Manual Mode

This section describes how to order a test in Manual mode. The system must already be
in Manual mode. If it is not in Manual mode, see Section 5.6.2, Changing from
Automation Mode to Manual Mode.
Note When the system is changed to Manual mode, the glass doors are automatically unlatched.
After the system is changed to Manual mode, open all available GeneXpert module doors.
Important Prior to ordering a new test, remove any cartridges that have completed tests and keep the
module doors open.
1. In the Xpertise Software Home workspace, select the ORDERS button (see
Figure 5-99. The Orders workspace will be displayed. See Figure 5-100.
2. Select the ORDER TEST button (see Figure 5-100). The Order Test – Patient ID
workspace is displayed if the Patient ID is enabled. See Figure 5-101. If the Patient
ID is not enabled, the Order Test – Sample ID workspace is displayed. See
Figure 5-102.
A. In the Order Test - Patient Information workspace, type in the Patient ID (if the
Patient Information workspace is enabled). See Figure 5-101.

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or
down menu.

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Select the END ORDER TEST button if you do not want to order a test in manual
mode.
4. On the Order Test – Sample ID workspace, scan or type in the Sample ID and select
the CONTINUE button (see Figure 5-102). The Order Test – Assay workspace is
Select the CLEAR ORDER button if you do not want to order a test in manual mode.
barcode scanner (Item #2). For multiple-test assays, the Order Test – Assay
Selection workspace is displayed (see Figure 5-105). For single-test assays, the
Order Test – Test Information workspace is displayed. See Figure 5-106.
If the kiosk barcode scanner or cartridge barcode is not working, perform the procedure in
Note
Section 5.6.3.1, Manually Entering the Barcode to Order a Test.

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Figure 5-104. Scanning the Cartridge Barcode Using the Kiosk Barcode Scanner
Figure 5-104. Scanning the Cartridge Barcode Using the Kiosk Barcode Scanner
6. For multiple-test assays only (see Figure 5-105), select the assay to be used for the
test and select the CONTINUE button. The Order Test – Test Information workspace
is displayed. See Figure 5-106.

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Figure 5-106. Order Test – Test Information Workspace

Figure 5-107. Order Test – Module Selection Workspace
Figure 5-107. Order Test – Module Selection Workspace

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7. Enter any notes about the test into the Notes field in the Order Test – Test
Information workspace. See Figure 5-106.
8. Select the SUBMIT button (see Figure 5-106). The Order Test – Module Selection
Select the CANCEL ORDER button if you do not want to continue with loading the
cartridge manually.
9. In the Order Test – Module Selection workspace, the Infinity system will suggest an
available module to process the cartridge. Instructions provided on the workspace
are:
Use this module or select another
Select the module to run the test
The drop-down box under the instructions displays the suggested available module.
If this module is acceptable for processing the cartridge, select the CONTINUE
button. If you would like to process the cartridge in another module, use the drop-
down box to select the desired module and select the CONTINUE button (see
Figure 5-107). The Manual Load – Remove Used Cartridge workspace is displayed.
See Figure 5-108.
cartridge manually.
10. In the Manual Load – Remove Used Cartridge workspace, the Infinity system will
provide instruction to remove any used cartridges from the module. Instructions
provided on the workspace are:
Confirm the selected module is empty and leave the door open.
Press CONTINUE to proceed.
Manually, open the module door, remove any used cartridges that may be inside the
module and select the CONTINUE button (see Figure 5-108). The Manual Load –
Module Preparation and Self-Test workspace is displayed. See Figure 5-109.
cartridge manually.

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Figure 5-108. Manual Load – Remove Used Cartridge Workspace
Figure 5-108. Manual Load – Remove Used Cartridge Workspace

11. As instructed in the Manual Load – Module Preparation and Self-Test workspace
(see Figure 5-109), wait while the module is being prepared. The Infinity will run a
series of self-tests to verify the module integrity. After completion of the self-tests,
the Manual Load – Load Cartridge workspace is displayed. See Figure 5-110.
12. As instructed in the Manual Load – Load Cartridge workspace (see Figure 5-110),
load the cartridge into the selected module (see Figure 5-111). The selected module
will have a flashing GREEN light above the module. Manually close the module
door after inserting the cartridge.

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Figure 5-109. Manual Load – Module Preparation and Self-Test Workspace
Figure 5-109. Manual Load – Module Preparation and Self-Test Workspace

Figure 5-110. Manual Load – Load Cartridge Workspace
Figure 5-110. Manual Load – Load Cartridge Workspace

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Figure 5-111. Loading the Cartridge into the GeneXpert Module
Figure 5-111. Loading the Cartridge into the GeneXpert Module

13. After you load the cartridge and close the module door, a progress bar will be
displayed on the Manual Load – Load Cartridge workspace. See Figure 5-112.
The progress bar will not be displayed if the door is not fully closed. If the progress bar does not
Note
appear, check that the module door is fully closed.
After the cartridge loads successfully and the test starts, the Test Start Successful –
Ready For Next Test workspace is displayed. See Figure 5-113.
14. In the Test Start Successful – Ready For Next Test workspace (see Figure 5-113), the
Infinity system will provide instruction to either order another test while the current
test is running or to exit from the Test Start Successful – Ready For Next Test
workspace. Instructions provided on the workspace are:
Press ORDER NEXT TEST to order another test.
Press END ORDER TEST when you are done.
If you want to order another test, select the ORDER NEXT TEST button. The Xpertise
workspace to load another module using Manual mode will be displayed. See
Figure 5-101.
If you do not want to order another test, select the END ORDER TEST button. The
Xpertise Software Home workspace will be displayed. See Figure 5-100.
Monitor test progress in the View Results workspace or in the Tests Since Launch
workspace.
15. After the cartridge has completed the test, manually open the module door.
16. Remove the cartridge from the module and leave the module door open.

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Figure 5-112. Manual Load – Load Cartridge Workspace with Loading Progress Bar
Figure 5-112. Manual Load – Load Cartridge Workspace with Loading Progress Bar
Figure 5-113. Test Start Successful – Ready For Next Test Workspace
Figure 5-113. Test Start Successful – Ready For Next Test Workspace

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5.6.3.1 Manually Entering the Barcode to Order a Test

In some cases, it may be necessary to enter the barcode manually, such as when the
barcode scanner is not operating correctly or when the barcode on the cartridge cannot
be read.
As an alternative to using the MANUAL BARCODE ENTRY button to enter the complete cartridge
Note barcode, the MANUAL ASSAY SELECTION button can be used to display a similar workspace that
will allow entry of the cartridge data in individual fields. See Section 5.6.3.2, Manual Assay Selection.
To enter the barcode manually:

1. In the Order Test – Assay workspace, select the MANUAL BARCODE ENTRY button to
manually select the assay (see Figure 5-114). The Order Test – Manual Barcode
Entry workspace is displayed. See Figure 5-115.
2. As instructed in the workspace, type in the cartridge barcode. The cartridge barcode
numbers are to the left of the actual barcode. A detailed description of the cartridge
barcode is shown in Figure 5-116.
Type in the barcode and then check that it was typed correctly. The test will not run if the
Important
barcode is incorrect.
3. Select the CONTINUE button (see Figure 5-115). The Order Test – Manual Assay
Selection workspace is displayed. See Figure 5-117.

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Reagent Lot ID
Expiration Date
Assay
Cartridge Barcode
(All numbers including
cartridge serial number)
Cartridge Serial Number
Type in the cartridge information accurately. This information will appear on all patient and
Important
results reports.
4. Select the CONTINUE button after entering all of the cartridge information (see
Figure 5-117). For multiple-test assays, the Order Test – Assay Selection workspace
is displayed (see Figure 5-118). For single-test assays, the Order Test – Test
Information workspace is displayed. See Figure 5-119.

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Figure 5-117. Order Test – Manual Assay Selection Workspace with Information Entered
Figure 5-117. Order Test – Manual Assay Selection Workspace with Information Entered

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5. Enter any notes about the test into the Notes field in the Order Test – Test
Information workspace. See Figure 5-119.
6. In the Order Test – Test Information workspace, verify that all information is correct.
If all information is correct, select the SUBMIT button (see Figure 5-119). The Order
Test – Module Selection workspace is displayed. See Figure 5-107.
If any information is not correct, select the CANCEL ORDER button and begin the
manual test entry process again.
7. Continue with the manual test by performing Step 8 through Step 15 in
Section 5.6.3, Ordering a Test in Manual Mode.
5.6.3.2 Manual Assay Selection

In some cases, it may be easier to enter the cartridge barcode information as separate
fields. To enter the barcode information as individual fields:
1. In the Order Test – Assay workspace or the Order Test – Manual Barcode Entry
workspace, select the MANUAL ASSAY SELECTION button. (see Figure 5-114 or
Figure 5-115). The Order Test – Manual Assay Selection workspace will be
2. Enter the cartridge information for each field from the cartridge. See Figure 5-116
for details about the cartridge barcode.
3. After all cartridge information has been entered and verified, select the CONTINUE
button. The Order Test – Test Information workspace is displayed. See
Figure 5-119.
Select the CLEAR ORDER button to cancel entry of the barcode information.

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Figure 5-120. Order Test – Manual Assay Selection Workspace
Figure 5-120. Order Test – Manual Assay Selection Workspace
5.6.3.3 Manual Mode Load Errors

In Manual mode, if a module fails to start a test, a workspace that provides error
handling instructions is displayed. The following paragraphs provide examples of how
the Manual mode workspace indicates to you when there are module errors. The
workspace also provides instructions on what you should do next.
If there is a load error after you close the module door in the Manual Load – Load
Cartridge workspace, a red light will flash above the module with the error and the
Manual Load – Cartridge Load Error workspace will appear, indicating that there is an
error with the module (see Figure 5-121). The workspace instructs you to:
Remove the cartridge from the module with the RED light. (in this case, module A4).
Press ORDER NEXT TEST to order another test.
The specific error message is displayed at the bottom of the workspace in the messages
area.

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Figure 5-121. Manual Load – Cartridge Load Error Workspace
Figure 5-121. Manual Load – Cartridge Load Error Workspace
5.6.4 Changing from Manual Mode to Automation Mode

Caution Remove used cartridges by following the procedure in Section 10.14, Retrieving Cartridges
from the Accumulator before changing to Automation Mode to avoid collisions. Collisions
can cause damage to the GeneXpert modules and automation system, and results in spilled
cartridges inside the system.
To change Manual mode to Automation mode:

button. The Setup menu is displayed. See Figure 5-123.
2. Select the CHANGE OPERATION MODE button (see Figure 5-123). The Change
Operation Mode workspace is displayed. See Figure 5-124.
The Change Operation Mode workspace allows you to change the operation mode.
Two radio buttons are displayed with the current operation mode saved in the
database. See Figure 5-124.
• Automation Mode
• Manual Mode

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Figure 5-123. Xpertise Software Home Workspace Setup Menu
Figure 5-123. Xpertise Software Home Workspace Setup Menu

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3. Select EDIT button (see Figure 5-124). The Change Operation Mode workspace is
activated. See Figure 5-125.
4. In the Change Operation Mode workspace, select the Automation Mode radio button
and select the SAVE button (see Figure 5-125).
When there is a test in progress, the Change Operation Mode workspace will appear
as shown in Figure 5-126; otherwise, it will appear as shown in Figure 5-127.
• If a test is in progress (see Figure 5-126), select OK to display the software Exit
confirmation (see Figure 5-128) and restart the software. After the Xpertise
software is restarted, it will be in Automation mode.
It is not recommended that the software be stopped before all tests have completed. Tests
Important that are currently running will be stopped and the test results will be lost. Wait to restart the
software until all tests have completed.
If you do not want to exit and restart the software now, select CANCEL to
continue editing.

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Figure 5-126. Change Operation Mode Workspace Confirmation When a Test is in Progress
Figure 5-126. Change Operation Mode Workspace Confirmation When a Test is in Progress

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Figure 5-127. Change Operation Mode Workspace Confirmation When No Test is in Progress
Figure 5-127. Change Operation Mode Workspace Confirmation When No Test is in Progress
• If no test is in progress (see Figure 5-127), select OK to display the software Exit
confirmation (see Figure 5-128) and restart the software immediately or select
CONTINUE to save the new operation mode but the new operation mode will not
be effective until after the Xpertise software is restarted.
For the system to actually change to Automation mode, you must restart the Xpertise
Important software. See Section 2.12, Restarting the System. After the Xpertise software is restarted, it
will be in Automation mode.
5. During the software exit process, there may be messages regarding database
management and archiving if these process are due. For more information on these
processes, see Section 5.2.8, Shutting the System Down.
6. To restart the Xpertise software, double-select the Xpertise software icon on the
desktop. See Section 5.2.4, Starting the Xpertise Software. When the software is
restarted, the system will be in Automation mode.

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Figure 5-128. Xpertise Software Exit Confirmation
Figure 5-128. Xpertise Software Exit Confirmation
5.6.5 Clearing a Test Order in Manual Mode

In some cases, it may be necessary to clear a test order after the manual test order
process has started. Each of the test order workspaces has a CLEAR ORDER button. To
clear a test order, select the CLEAR ORDER button on any of these workspaces. See
Figure 5-88 for an example of the CLEAR ORDER button.
To clear a test order:
1. On any manual test order workspace, select the CLEAR ORDER button. (see
Figure 5-129). The Order Test – Test Information Confirmation workspace will be
2. Select the YES button to cancel the test order (see Figure 5-130). The Xpertise
Software Home workspace will be displayed. See Figure 5-122.
Select the NO button to continue with the manual order test entry.

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Figure 5-130. Order Test – Test Information Confirmation Workspace
Figure 5-130. Order Test – Test Information Confirmation Workspace

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5.7 Managing Test Results Data

The GeneXpert Infinity system includes a database that stores all of the saved test
results. The following information is included in this section:
• Section 5.7.1, Archiving the Tests
• Section 5.7.2, Retrieving Tests from an Archive File
• Section 5.7.3, Backing Up the Database
• Section 5.7.4, Restoring the Database
• Section 5.7.5, Compacting the Database
• Section 5.7.6, Checking the Integrity of the Database
The GeneXpert Infinity system administrator specifies whether you have the permissions
for the data management tasks. See Section 2.6.2. See your GeneXpert Infinity system
administrator to adjust the permissions to meet your requirements. For this section of the
manual, the default user permissions will be listed for each data management function.

All data management functions are available in the Data Management menu. To access
the Data Management menu, select the DATA MANAGEMENT button in the Xpertise
Software Home workspace. (see Figure 5-131). The Data Management menu is displayed
See Figure 5-132.

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5.7.1 Archiving the Tests

Archiving tests allows you to copy your test data and, if desired, purge test data to free
up space in the main system database. You can archive multiple tests at a time. In
addition to serving as a safe-keeping mechanism, you can provide the archive files to
Cepheid for analysis if you need help with troubleshooting. The archive process creates a
copy of the test and saves the data in a .gxx file.
Some e-mail filters may block files with .gxx extensions. Adjust your email filter, if possible, or
Note
change the extensions, if required.
All user levels typically have permission to archive tests. To archive tests:
1. In Data Management menu, select the ARCHIVE TEST button (see Figure 5-132). The
Archive Test workspace is displayed. See Figure 5-133.
Figure 5-132. Data Management Menu

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Figure 5-133. Archive Test Workspace Showing Test Selection
Cloak IDs Check Box

Purge Selected Tests from List After Archiving
(Recommended Monthly) Check Box
Figure 5-133. Archive Test Workspace Showing Test Selection

2. Select the check box that is adjacent to each test you want to archive. See
Figure 5-133. You can select the individual tests one-by-one, or select a large number
of tests by selecting one of the following buttons at the bottom of the Archive Test
workspace:
• SELECT ALL – Selects all of the tests in the table.
• SELECT HIGHLIGHTED – Selects the tests you highlighted.
• SELECT NEW ARCHIVE – Selects only the tests that have not been archived
before.
You can also hold the Shift or Ctrl keys to highlight continuous and discontinuous multiple tests in
Note
the Archive Test workspace.
After selecting tests in the Archive Test workspace, select one of the following
buttons to deselect some or all tests:
• DESELECT ALL – Clears all of the test selections in the window.
• DESELECT HIGHLIGHTED – Clears all of the highlighted test selections.
In addition to selecting the tests to archive, there are two check boxes located near
the top of the Archive Test workspace that may need to be selected:

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• Purge Selected Tests from List After Archiving (Recommended Monthly) – Select
this check box to free up space on the computer. After the selected tests have
been successfully archived, they are removed from the database.
• Cloak IDs – Select this check box if you want to send Cepheid Technical
Support data but want to hide patient-sensitive information. See Masking
Patient and Sample IDs During Test Archive for more information.
3. Select the OK button (see Figure 5-133). A confirmation workspace is displayed See
Figure 5-134.
Select the CANCEL button if you do not wish to perform the archive test operation.
4. Select the PROCEED button (see Figure 5-134). The Archive Test Save workspace is
Select the CANCEL button if you do not wish to proceed with the archive test operation.
5. Use the Save In: drop-down to locate and select the folder in which you want to store
the archive (.gxx) file, type a name for the archive file, and then select the SAVE
button. See Figure 5-135.
The default archive location is the export folder which is located on the computer hard drive.
Caution
To guard against loss of data, the files in the export folder should be periodically copied to a
different computer or server. If the GeneXpert Infinity system system is connected to a
network, it is possible to archive files directly to a server. To configure the archive location,
see Section 2.7.2, Folders Workspace.
Select the CANCEL button if you do not wish to proceed with the archive test
operation.
6. After the archive has completed, a confirmation workspace will be displayed
indicating that the tests have been archived and the filename of the archive (see
Figure 5-136). Select the OK button.
7. If the Purge Selected Tests from List After Archiving (Recommended Monthly) option
is selected, a confirmation workspace will appear after a successful archive (see
Figure 5-137). Select the OK button to confirm that you want to purge the tests.
Select the CANCEL button if you do not want to purge the tests.
8. A message is displayed to confirm that the tests you selected have been successfully
purged (see Figure 5-138). Select the OK button to close the confirmation workspace.
The Data Management menu is displayed. See Figure 5-132.
Caution If data is archived and purged from the database, then the archive files will only include the
Patient ID and not the patient demographic data. Therefore, if the archive file is restored in
the future, patient demographic data will not be available in the database for those tests and
cannot be used in future connectivity solutions.
It is important to understand that when tests have been purged, they have not been permanently
deleted from the computer. They have been removed from the main system database and saved to
Note an archive file even when the Purge Selected Tests from List After Archiving (Recommended
Monthly) option has been selected. Tests may be retrieved from the archive file if needed for later
use. See Section 5.7.2, Retrieving Tests from an Archive File.

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Figure 5-134. Archive Test Workspace Confirmation
Figure 5-134. Archive Test Workspace Confirmation

Figure 5-135. Archive Test Workspace Showing Location for Archiving Tests
Figure 5-135. Archive Test Workspace Showing Location for Archiving Tests

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Figure 5-136. Archive Test Workspace – Successful Save Confirmation
Figure 5-136. Archive Test Workspace – Successful Save Confirmation

Figure 5-137. Archive Test Workspace – Purge Confirmation
Figure 5-137. Archive Test Workspace – Purge Confirmation

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Figure 5-138. Archive Test Workspace – Tests Purged Confirmation
Figure 5-138. Archive Test Workspace – Tests Purged Confirmation

9. Select the Home icon to return to the Xpertise Software Home workspace.
Masking Patient and Sample IDs During Test Archive

Masking sample and patient IDs allow customers to send Cepheid Technical Support
some data in question, but hides patient-sensitive information.
When the Cloak IDs check box (see Figure 5-133) is checked, all information about the
Sample ID and Patient ID is masked. Fields that are masked are the Patient ID, Patient
ID 2, Last Name and First Name and Sample ID.
Caution
Once you mask sample and patient ID information for an archived test, if you retrieve the test
information, the sample and patient ID information will still be masked. You should maintain
on-site a copy of the archived test information without the masked information.
5.7.2 Retrieving Tests from an Archive File

Caution
If you retrieve a test that already exists in the current database, the software will overwrite it
with the archive data and the existing data will be lost.
Detail and administrative user levels typically have permission to retrieve tests. To
retrieve test data from an archived file:

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1. In Data Management menu, select the RETRIEVE TEST button (see Figure 5-139).
The Retrieve Test workspace is displayed showing a list of previously archived files.
See Figure 5-140.

Figure 5-140. Retrieve Test Workspace Showing List of Previously Archived Files
Figure 5-140. Retrieve Test Workspace Showing List of Previously Archived Files

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2. Use the Look In: drop-down to locate and select the folder where the archive (.gxx)
file is stored. The default folder is the export folder for the Xpertise software. See
Figure 5-140.
3. Select the file and select the OPEN button (see Figure 5-140). A table of tests in that
archive file is displayed. If any tests in the archive files already exist in the database,
they will be displayed using red text. See Figure 5-141.
Select the CANCEL button if you do not wish to proceed with the retrieve test
operation.
4. Select the check box that is adjacent to each test you want to retrieve. See
Figure 5-141. You can select the individual tests one-by-one, or select a large number
of tests by selecting one of the following buttons at the bottom of the Retrieve Test
workspace:
• SELECT ALL – Selects all of the tests in the table.
• SELECT HIGHLIGHTED – Selects the tests you highlighted.
• SELECT WITH NO DUPLICATE – Selects only the tests that do not exist in the
current database.
Hold the Shift or Ctrl keys to highlight continuous and discontinuous multiple tests in the Retrieve
Note
Test workspace.
Figure 5-141. Retrieve Test Workspace Showing Tests to Select
Figure 5-141. Retrieve Test Workspace Showing Tests to Select

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After selecting tests in the Retrieve Test workspace, select one of the following
buttons to deselect some or all tests:
• DESELECT ALL – Clears all of the test selections in the window.
• DESELECT HIGHLIGHTED – Clears all of the highlighted test selections.
5. Select the OK button (see Figure 5-141). A confirmation message is displayed. See
Figure 5-142.
Select the CANCEL button if you do not wish to proceed with the retrieve test
operation.
6. Select the PROCEED button. For large archives, a Retrieve Test workspace,
displaying a progress bar, indicates the progress of the retrieve test process (see
Figure 5-143). A message will appear to confirm that the tests have been retrieved.
See Figure 5-144.
Select the CANCEL button if you do not want to continue with the retrieve test
operation.
7. When the test retrieval is complete, the Retrieve Test workspace displays a list of
tests that have been retrieved. The tests that already exist in the current database
appear in red text. Select CANCEL to close the Retrieve Test workspace.
Figure 5-142. Retrieve Test Workspace Confirmation
Figure 5-142. Retrieve Test Workspace Confirmation

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Figure 5-143. Retrieve Test Workspace Showing Progress Bar
Figure 5-143. Retrieve Test Workspace Showing Progress Bar

Figure 5-144. Retrieve Test Workspace Showing Retrieve Completed
Figure 5-144. Retrieve Test Workspace Showing Retrieve Completed

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5.7.3 Backing Up the Database

You should back up the entire database periodically and store the backup on a different
computer or on a different storage medium. If the computer fails, you can restore the
entire database using the backup copy.
Opportunities for database operations occur every time the Xpertise software is started
up or shut down. The procedure is the same for both database operations.
All user levels typically have permission to back up the database. To back up the
database:
1. During startup or shutdown of the Xpertise Software, select YES to perform database
management tasks (see Figure 5-145). The Database Management workspace will be
Select the NO button if you do not want to perform database management tasks.
2. In the Database Management workspace, select the DATABASE BACKUP button (see
Figure 5-146). The Database Backup workspace will be displayed. See
Figure 5-147.
Figure 5-145. Database Management Workspace at Software Exit

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If you are logged in as a system administrator, additional buttons may be displayed in the Database
Note
Management workspace.
Figure 5-147. Database Backup Workspace Showing Database Backup Location
Figure 5-147. Database Backup Workspace Showing Database Backup Location

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Figure 5-148. Database Backup Workspace Showing Progress Bar
Figure 5-148. Database Backup Workspace Showing Progress Bar

Figure 5-149. Database Backup Workspace – Backup Completed
Figure 5-149. Database Backup Workspace – Backup Completed

3. Use the Save In: drop-down to locate and select the folder in which to store the
database backup file and then select the SAVE button. See Figure 5-147. The backup
process creates a backup file (.zip) in the location you specified. Depending upon the
amount of data in the database, the backup process may take some time to complete.

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A Database Backup workspace, displaying a progress bar, indicates the progress of

the database backup process. See Figure 5-148.
The default database location is the Backup folder which is located on the computer hard
Caution
drive. To guard against loss of data, the files in the Backup folder should be periodically
copied to a different computer or server. If the GeneXpert Infinity system is connected to a
network, it is possible to back up the files directly to a server. To configure the backup
location, see Section 2.7.2, Folders Workspace.
Select the CANCEL button if you do not wish to proceed with the database backup.
4. When the backup process is finished, a process completion message is displayed.
See Figure 5-149. Select the OK button.
5. After the database backup has completed, the Database Management workspace will
be displayed (see Figure 5-146). Select the CLOSE button the exit the Database
If the database backup was performed during Xpertise software startup, the software
startup process will continue. If the database backup was performed during Xpertise
software shutdown, the Xpertise software will exit.
5.7.4 Restoring the Database

Caution
The database restore process overwrites the data in the current database. Do not restore a
database unless the current database is corrupted or needs to be replaced.
You must be an administrative level user to restore the database unless your system
administrator has set this up for another user level.
You can restore the entire database using the backup database file. Because the restore
process overwrites the data in the current database, you should first archive any test data
you want to retain (see Section 5.7.1), restore the database, and then retrieve the data
from the archive file (see Section 5.7.2).
If you are running C360 Sync on your system, verify that Cepheid Reporter Daemon has stopped
before restoring the GeneXpert database. See the Restoring a GeneXpert Database under the
Note
Tests tab in the C360 Sync Quick Reference Guide for detailed instructions about how to stop the
Cepheid Reporter Daemon.
To restore the database:

1. During startup or shutdown of the Xpertise Software, log into the software with
administrator privileges.
2. Select YES to perform database management tasks (see Figure 5-145). The Database
Management workspace will be displayed. See Figure 5-150.
3. In the Database Management workspace, select the DATABASE RESTORE button (see
Figure 5-150). The Database Restore confirmation workspace will be displayed. See
Figure 5-151.

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Figure 5-151. Database Restore Workspace Confirmation

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Figure 5-152. Database Restore Workspace Confirmation to Back Up Current Database
Figure 5-152. Database Restore Workspace Confirmation to Back Up Current Database

4. Select the PROCEED button (see Figure 5-151). The Database Backup workspace is
Select the CANCEL button if you do not wish to proceed with the restore database
operation.
5. Select the YES button to create a backup of the existing database (see Figure 5-152).
The Database Backup workspace is displayed. See Figure 5-153.
A. Use the Save In: drop-down to locate and select the folder in which you want to
store the database backup file and then select the SAVE button. See
Figure 5-153. The backup process creates a backup file (.zip) in the location you
specified. Depending upon the amount of data in the database, the backup
process may take some time to complete.
B. A Database Backup workspace, displaying a progress bar, indicates the
progress of the database backup process. When the backup process is finished, a
process completion message is displayed and the database restore operation will
begin.
6. Use the Look In: drop-down to locate and select the folder in which the database
backup (.zip) file is stored.See Figure 5-154.
7. Select the file and select the OPEN button (see Figure 5-154).
Select the CANCEL button if you do not wish to proceed with the database restore
operation.

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Figure 5-153. Database Backup Workspace Showing Backup File Location
Figure 5-153. Database Backup Workspace Showing Backup File Location

Figure 5-154. Database Restore Showing File Selection
Figure 5-154. Database Restore Showing File Selection

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8. A Database Restore workspace, displaying a progress bar, indicates the progress of
the database restore process. Depending upon the amount of data in the database, the
restore process may take some time to complete. When the restore process is
finished, a process completion message is displayed. See Figure 5-155.
9. Upon completion of the database restore, select the OK button to close the Xpertise
software application. See Figure 5-155.
10. If desired, restart the Xpertise software application. For details on starting the
software, see Section 5.4, Starting the GeneXpert Infinity System.
5.7.5 Compacting the Database

You must be an administrative level user to compact the database unless your system
You can compact the database periodically to ensure efficient use of the space in the
database and to save hard disk space.
To compact the database:
1. During startup or shutdown of the Xpertise Software, select YES to perform database

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2. In the Database Management workspace, select the COMPACT DATABASE button
(see Figure 5-156). A Compact Database Confirmation workspace will be displayed.
See Figure 5-157.
3. On the Compact Database Confirmation workspace (see Figure 5-157), select the
PROCEED button. The Xpertise software will compact the database.
4. After the database has been compacted, the Compact Database workspace
completion workspace (see Figure 5-158) will be displayed indicating that the
database has been compacted.
6. After the database has been compacted, the Database Management workspace will
be displayed (see Figure 5-156). Select the CLOSE button to exit the Database
In addition to compacting the database, you can also save space by purging data after archiving.
Note
For details on purging archived tests, See Section 5.7.1, Archiving the Tests.

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Figure 5-157. Compact Database Workspace Confirmation
Figure 5-157. Compact Database Workspace Confirmation

Figure 5-158. Compact Database Workspace – Compact Database Complete
Figure 5-158. Compact Database Workspace – Compact Database Complete

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5.7.6 Checking the Integrity of the Database

The software automatically checks the integrity of the database during start-up of the
Xpertise software. If you want to manually check the integrity of the database, perform
the following steps in the Data Management menu of the Xpertise software. Only an
administrative level user to can check the integrity of the database unless the system
1. During shutdown of the Xpertise Software, select YES to perform database
Checking the integrity of the database can only be done during shutdown of the Xpertise software.
Note
The DATABASE INTEGRITY CHECK button is disabled during startup of the software.
2. In the Database Management workspace, select the DATABASE INTEGRITY CHECK

button (see Figure 5-160). The Database Integrity Check workspace will be
Figure 5-159. Database Management Workspace Confirmation
Figure 5-159. Database Management Workspace Confirmation

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Figure 5-161. Database Integrity Check Workspace
Figure 5-161. Database Integrity Check Workspace

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Figure 5-162. Database Integrity Check Workspace Completed Confirmation
Figure 5-162. Database Integrity Check Workspace Completed Confirmation

3. Select the PROCEED button (see Figure 5-161). The software will check the integrity
of the database. If the software finds integrity errors, a message will alert you.
Select the CANCEL button if you do not want to check the integrity of the database.
4. If errors are found, select the PROCEED button to repair the database. Upon
completion of the database integrity check, the Database Integrity Check workspace
will indicate that the integrity check has been completed. See Figure 5-162.
6. After the database integrity has been checked, the Database Management workspace
will be displayed (see Figure 5-156). Select the CLOSE button the exit the Database
Management workspace. The Xpertise software will close.
You have successfully completed the integrity check of the database.

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5.8 Operating with Host Connectivity

This section provides instructions on how to use the GeneXpert Laboratory Information
System (LIS) or Host interface:
• Section 5.8.1, Ordering a Test with Host Connectivity
• Section 5.8.2, Aborting a Query
• Section 5.8.3, Canceling a Host Downloaded Test Order
• Section 5.8.4, Uploading Test Results to Host
Cepheid recommends to always confirm that LIS uploaded results match GeneXpert test
results after any changes to the GeneXpert or host system, including (but not limited to)
changes to the following:
Caution
• GeneXpert Assay Definition version
• LIS software or configuration settings
5.8.1 Ordering a Test with Host Connectivity

When the host connectivity is enabled, test orders can be automatically downloaded from
the host by:
• The GeneXpert system periodically requesting new orders
• Manual queries by GeneXpert user of new orders from the Manage Host Orders
workspace
• Scanning or entering the Sample ID to perform a host query for orders for a specific
Sample ID
The workflow in your laboratory will determine how you will order a test.
Select the Manage Host Orders icon to display the Manage Host Orders workspace panel.
See Figure 5-163.
The Manage Host Orders icon will be white if no orders are downloaded or green when host orders
Note
are downloaded.

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Figure 5-163. Manage Host Orders Workspace
Host Test Order Table
1
2
3
4
5
6
7
Host Download Status Field
Figure 5-163. Manage Host Orders Workspace

The content and menu buttons in the Manage Host Orders workspace are:
• Host Test Order Table – New orders are shown in the table which can be sorted by
selecting the header. The table contains:
• Patient ID (optional) – Patient ID for each test order.
• Patient ID 2 (optional) – Additional Patient ID for each test order.
• Patient Name (optional) – Patient name for each test order.
• Sample ID – Sample ID for each test order.
• Assay – Assay name and version number for each test order.
• Priority – Indicates whether it is STAT priority or Normal priority.
• Host Order Time – Time the order was created on the host.
• Host Download Status field – Located at the bottom of the workspace, displays the
status of the most recent query for new orders.
Buttons are located on the right side of the Manage Host Orders workspace (see
Figure 5-163) and are described in Table 5-2.

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Table 5-2. Manage Host Orders Workspace Buttons
Item Button Name Description

1 ORDER TEST Begins the Order Test process described in Section 5.8.1.1 of this manual.
2 MANUAL QUERY Queries the host for any available new orders.
3 CANCEL SELECTED Cancels one or more downloaded test orders by selecting the corresponding
ORDERS check boxes and selecting the CANCEL SELECTED ORDERS button. A
confirmation message is shown.
If you confirm to cancel, the test order is deleted from the host order list with
notification provided to the host regardless of the Automatic Upload setting in the
System Configuration workspace. The Xpertise software does not wait for
confirmation of this notification.
If you fail to confirm, the test order remains in the host order list.
4 CLEAR STATUS Clears the Host Download Status field.
5 DELETE CANCELLED Deletes cancelled orders. This is useful to remove redundant orders during host
ORDERS communication testing.
6 EXPIRE RESULTS Allows the user to change all tests with Upload-Pending status or Review status
to be changed to Expired status. This button is only available to users who have
System Configuration privileges.
7 RESET Caution Do not use Reset Communication Buffer during normal
COMMUNICATION operation; otherwise, you will have to re-download orders and
re-upload results.
BUFFER
Clears the data between the GeneXpert system and the host. This is useful to
remove data during host communication testing.
8 CLOSE Closes the Manage Host Orders workspace.
To accept an order from the host, the result test codes for the assays must be set up by the host
Note
administrator. See Section 2.7.5 for details.

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Figure 5-164. Manage Host Orders Workspace Showing Pending Host Orders
Figure 5-164. Manage Host Orders Workspace Showing Pending Host Orders
5.8.1.1 Ordering a Test by Selecting from a List of Test Orders Downloaded

Automatically by the Host
To order a test by selecting from a list of test orders downloaded automatically by the
host:
1. Select the Manage Host Orders icon to display the Manage Host Orders workspace
panel. See Figure 5-164.
When a test order has been downloaded, the Manage Host Orders icon, located in the
upper left corner of the Xpertise Software workspace, changes to the color green,
indicating new orders to be filled.
2. Select a downloaded test order by selecting the check box.
3. Select the ORDER TEST button.
The Order Test – Scan Cartridge Barcode workspace is displayed. See Figure 5-165.
Select the Clear Order button if you do not want to run this test.
Even though the patient demographics fields are displayed in the host workspaces, data cannot be
Note
entered into the fields.
barcode scanner (Item #2). The Order Test workspace is displayed. See
Figure 5-167.

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Figure 5-165. Order Test – Scan Cartridge Barcode Workspace – Scan the Cartridge Barcode
Figure 5-165. Order Test – Scan Cartridge Barcode Workspace – Scan the Cartridge Barcode

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5. Enter additional information or notes, if necessary, then select the SUBMIT button.
The Order Test–Load Cartridge workspace is displayed. See Figure 5-168.
You cannot change the Patient ID (if enabled), Sample ID or the assay if it is selected from a host
Note
downloaded test order.

8. Select the OK button to start the test. See Figure 5-168.
5.8.1.2 Ordering a Test by Manually Requesting Test Orders and Selecting

from a List of Test Orders
You can manually request new test orders from the host by selecting the MANUAL
QUERY button (see Figure 5-164) to list all test orders that are currently in the host. After
orders are downloaded from the host, proceed as instructed in Section 5.8.1.1.

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5.8.1.3 Ordering a Test by Querying the Host with Optional Patient ID and
Sample ID
You can query the host for tests for a specific patient ID (optional) and sample ID:
1. In the Xpertise Software Home workspace (see Figure 5-170), select the ORDERS
button. The Orders menu is displayed. See Figure 5-171.

2. Select the ORDER TEST button (see Figure 5-171). The Order Test – Patient ID
workspace is displayed if Patient ID is enabled (see Figure 5-172). The Order Test –
Sample ID workspace is displayed if Patient ID is not enabled. See Figure 5-173.
3. Scan the Patient ID barcode using the kiosk barcode scanner or type in the patient
ID. See Figure 5-172. The Order Test – Sample ID workspace is displayed. See
Figure 5-173.
If you scan in the Patient ID, then you do not have to select the CONTINUE button. The workspace
Note
will automatically continue to the next workspace.

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4. Scan the Sample ID barcode using the kiosk barcode scanner or type in the sample
ID. See Figure 5-173.
If you scan in the Sample ID, then you do not have to select the CONTINUE button. The workspace
Note
will automatically continue to the next workspace.
• If only one test order matches the Patient ID and Sample ID, perform the steps
on page 5-147, When One Test Order Matches the Patient ID and Sample ID.
• If multiple test orders match the same Patient ID and Sample ID, perform the
steps on page 5-149, When Multiple Test Orders Match the Same Patient ID and
Sample ID.

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When One Test Order Matches the Patient ID and Sample ID

When only one test order matches the Patient ID and Sample ID, the Order Test –
Scan Cartridge Barcode workspace is displayed. See Figure 5-174.
Figure 5-174. Order Test – Scan Cartridge Barcode Workspace
Figure 5-174. Order Test – Scan Cartridge Barcode Workspace

barcode scanner (Item #2). The Order Test – Test Information workspace is

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3. If required, login to start the test.
4. As shown in Figure 5-177, load (or place) the cartridge (item #1) in the loading zone
on the conveyor (item #3), outside the yellow and black lines (item #4). Make sure
you place the cartridge on the conveyor with the label (item #2) facing you.
The conveyor belt moves the cartridge into the system. The gantry places the cartridge
into an available GeneXpert module or onto an accumulator shelf if a module is not
available.

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When Multiple Test Orders Match the Same Patient ID and Sample ID
When multiple test orders match the same Patient ID and Sample ID, the Order Test
– Host Order Selection workspace is displayed. See Figure 5-178.
Figure 5-178. Order Test – Host Order Selection Workspace – Select Host Order
Figure 5-178. Order Test – Host Order Selection Workspace – Select Host Order

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1. Select the order to be processed (see Figure 5-178) and select the CONTINUE button.
The Order Test – Scan Cartridge Barcode workspace is displayed. See Figure 5-179.
barcode scanner (Item #2). The Order Test – Test Information workspace is
Figure 5-179. Order Test – Scan Cartridge Barcode Workspace – Scan Cartridge Barcode
Figure 5-179. Order Test – Scan Cartridge Barcode Workspace – Scan Cartridge Barcode

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4. If required, login to start the test.
5. As shown in Figure 5-182, place the cartridge (item #1) in the loading zone on the
conveyor (item #3), outside the yellow and black lines (item #4). Make sure you
The conveyor belt moves the cartridge into the system. The gantry places the cartridge
into an available GeneXpert module or onto an accumulator shelf if a module is not
available.

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5.8.2 Aborting a Query

During the Manual Query described in Section 5.8.1.2 or Host Query described in
Section 5.8.1.3, the MANUAL QUERY button becomes the ABORT QUERY button See
Figure 5-183.
To start a test or close the workspace, wait until the query is completed or select the
ABORT QUERY button to cancel the operation.
Figure 5-183. Order Test – Host Order Selection Workspace – Waiting for Host Test Order Query
Figure 5-183. Order Test – Host Order Selection Workspace – Waiting for Host Test Order Query

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5.8.3 Canceling a Host Downloaded Test Order

Occasionally, you may need to cancel an order downloaded from the host.
1. Select the Manage Host Orders icon to display the Manage Host Orders workspace
panel. See Figure 5-184.
2. In the Host Test Order Table, select one or more orders to cancel by selecting the
check box.
3. Select the CANCEL SELECTED ORDERS button (see Figure 5-184). A confirmation
workspace is displayed in the Manage Host Orders workspace to request
confirmation that you want to cancel the selected order(s). See Figure 5-185.
4. Select the YES button to confirm the cancellation. the test order will be removed
from the table and the host notified of the test cancellation.
Select the NO button if you do not want to cancel the test order.
Figure 5-184. Manage Host Orders Workspace – Canceling a Test
Figure 5-184. Manage Host Orders Workspace – Canceling a Test

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Figure 5-185. Manage Host Orders Workspace – Cancel Test Confirmation
Figure 5-185. Manage Host Orders Workspace – Cancel Test Confirmation
5.8.4 Uploading Test Results to Host

Test results can be uploaded to the host either automatically or manually. Automatic
uploading of test results is set up in the system configuration (see Section 2.7.4, Host
Communication Settings Workspace and Section 2.7.4.2, Configuring Host
Communications for Cepheid Link). Manual uploading of test results is done from the
Upload Result workspace.
If your host connectivity is enabled, the Upload Result workspace can be used to select
test(s) for manually uploading to the host and the UPLOAD RESULT button is used to
manually upload the test results. See Figure 5-186.

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Figure 5-186. Upload Result Workspace Showing Test Selection
Figure 5-186. Upload Result Workspace Showing Test Selection

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5.8.4.1 Automatic Upload of Test Results to the Host

After the test is completed, the result will be automatically uploaded if the Automatic
Result Upload box is checked in the Host Communication Settings workspace (see
Section 2.7.4, Host Communication Settings Workspace and Section 2.7.4.2, Configuring
Host Communications for Cepheid Link). The Upload Status is shown in the Test Result
tab of the View Results workspace See Figure 5-187.
Figure 5-187. View Results Workspace – Test Result Tab Showing Host Upload Status
Figure 5-187. View Results Workspace – Test Result Tab Showing Host Upload Status
5.8.4.2 Manual Upload of Test Results to the Host

The Upload Result workspace can be used to select test(s) for manually uploading to the
host and the UPLOAD RESULT button is used to manually upload the test results. To
upload test results manually:
1. In the View Results workspace, select the UPLOAD RESULT button (see
Figure 5-188). The Upload Result workspace is displayed that shows a list of
completed tests. See Figure 5-189.

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Figure 5-188. View Results Workspace Showing Upload Pending
Test Results Have Not

Been Uploaded
Figure 5-188. View Results Workspace Showing Upload Pending
There are seven possible types of host upload status results shown in the Upload
Status column:
• Run-in-Progress – The test has been started and is still running. The result is not
available yet.
• Upload Pending – This result has not been uploaded.
• Uploading – This result is in the process of being uploaded.
• Re-Uploading – This result has been uploaded previously and is currently being
uploaded again.
• Uploaded – This result has been uploaded to the host.
• Review – This is an external control and the test results should be reviewed
before manually uploading the results to the host. See Section 5.8.4.3.
• Expired – The test result has not been uploaded. The upload time has run out;
therefore, the test will not be automatically uploaded. Manually upload the test
result to the host.
If you attempt to exit the software with results in the Upload Pending, Uploading or Re-Uploading
Note
status, the software will remind you to let the upload complete before exiting.

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Figure 5-189. Upload Result Workspace Showing Completed Tests Ready to be Uploaded to the Host
Figure 5-189. Upload Result Workspace Showing Completed Tests Ready to be Uploaded to the Host
2. Select the test(s) you want to upload by checking the corresponding check box(es).
You can select the individual tests one-by-one or select a large number of tests by
selecting one of the following:
• Select All – Selects all of the tests in the table.
• Deselect All – Clears all of the test selections in the table.
• Select Highlighted – Selects the tests you have highlighted in the table.
• Deselect Highlighted – Clears all of the highlighted test selections.
• Select All Pending – Selects all of the tests with Upload Pending status.
3. Select the UPLOAD RESULT button to upload the selected test results to the host. See
Figure 5-189.
Select the CLOSE button if you do not want to manually upload the test results to the
host.
5.8.4.3 Upload of an External Control Result to the Host

Regardless of the setting for Automatic Result Upload, an external control result must be
manually uploaded. See Section 5.8.4.2, Manual Upload of Test Results to the Host.

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5.9 Operating with Cepheid Link Connectivity

This section provides instructions on how to use Cepheid Link to scan samples and
cartridges and to run the tests on the GeneXpert Infinity system. The workflow for using
Cepheid Link is that the test order is entered into the institution’s LIS system. The
Cepheid Link scanner is used to scan the samples and cartridges either near the
GeneXpert Infinity system or remotely. The cartridges are then transported to the
GeneXpert Infinity system to run the tests. Test results are uploaded to the institution’s
LIS system.
Once the system has been configured for Cepheid Link, it cannot be used for non-LIS
originated test orders or for running external controls without disabling Cepheid Link.
Important Cepheid Link may be enabled again after running non-LIS originated test orders or external
controls. Configuration for Cepheid Link is described in Section 2.7.4.2, Configuring Host
Communications for Cepheid Link.
• Section 5.9.1, Scanning a Sample and Cartridge using Cepheid Link

• Section 5.9.2, Running Cartridges Scanned from Cepheid Link
Cepheid recommends to always confirm that LIS uploaded results match GeneXpert test
results after any changes to the GeneXpert or host system, including (but not limited to)
changes to the following:
Caution
• GeneXpert Assay Definition version
• LIS software or configuration settings
5.9.1 Scanning a Sample and Cartridge using Cepheid Link

After an order is entered into the LIS, system, use the Cepheid Link scanner to scan the
sample and cartridge. This procedure assumes that the Cepheid Link scanner has been
set up following the instructions in the Cepheid Link User Guide and the scanner has
already been powered on.
In order to scan a sample and cartridge, an order for the test must have been previously
Important
entered into the institution’s LIS system.
1. Remove the scanner from the docking station.

2. If the scanner screen is locked, swipe the screen vertically to unlock the screen.
3. Log into the Cepheid Link scanner using your assigned user name and password (see
Figure 5-190). The Scan Sample screen will be displayed. See Figure 5-191.

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Figure 5-190. Cepheid Link Scanner Login Screen
Figure 5-190. Cepheid Link Scanner Login Screen

4. Enter the sample ID into the scanner:
• To scan the sample ID:
1) Press the scanner button (located on either side of the barcode scanner) to
scan the sample barcode. The sample barcode will be scanned and Cepheid
Link will check to see if there is a test order for the sample.
2) If an order was found, the Success screen (green check mark) will be
displayed for a very short time (see Figure 5-192) and the Scan Cartridge
screen will be displayed. See Figure 5-195.
3) If an order was not found, the Error screen (Order Not Found (red X)) will
be displayed (see Figure 5-193). Touch the Ok button to return to the Scan
Sample screen.
• If a sample barcode is not available, to enter the sample ID manually:
1) Touch the Barcode area of the screen (see Figure 5-191). A keyboard will
be displayed (see Figure 5-194) to enter the sample ID manually.
2) Manually enter the sample ID using the keyboard.
3) Press the Submit button to submit the sample ID.
4) If an order was found, the Success screen (green check mark) will be
displayed for a very short time (see Figure 5-192) and the Scan Cartridge

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5) If an order was not found, the Error screen (Order Not Found (red X)) will
be displayed (see Figure 5-193). Touch the Ok button to return to the Scan
Sample screen.
Figure 5-191. Cepheid Link Scan Sample Screen
Touch Here to Display

Scanner Menu
Touch Here to Manually

Enter Sample ID
Figure 5-191. Cepheid Link Scan Sample Screen

Figure 5-192. Cepheid Link Scanner Success (Green Check Mark) Screen
Figure 5-192. Cepheid Link Scanner Success (Green Check Mark) Screen

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Figure 5-193. Cepheid Link Scanner Error (Order Not Found (Red X)) Screen
Figure 5-193. Cepheid Link Scanner Error (Order Not Found (Red X)) Screen
Figure 5-194. Sample ID Manual Barcode Entry
Touch Submit Button

After Entering Sample ID
Figure 5-194. Sample ID Manual Barcode Entry

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Figure 5-195. Cepheid Link Scan Cartridge Screen
Touch Start Over to

Return to the Scan
Sample Screen
Figure 5-195. Cepheid Link Scan Cartridge Screen

5. Scan the cartridge barcode:
• Press the scanner button (located on either side of the barcode scanner) to scan
the cartridge barcode. After the cartridge barcode has been successfully
scanned, Cepheid Link will pair the cartridge with the sample. The scanner will
momentarily display the scanned cartridge information (see Figure 5-196).
If the cartridge is successfully paired with the sample, the Success screen (green
check mark) will be displayed for a very short time (see Figure 5-192).
• If the cartridge is not successfully paired with the sample, the Error (Red X)
screen will be displayed along with the error message (see Figure 5-197) for an
example. Touch the Ok button to return to the Scan Cartridge screen. The
scanner will return to the Scan Sample screen (see Figure 5-191).
• If aliquots are to be scanned, the Scan Aliquot screen will be displayed (see
Figure 5-198).
• The scanner will display the Confirmation screen (see Figure 5-199), if aliquots
are not required and if Confirmation is enabled, or will return to the Scan
Sample screen (see Figure 5-191).
• Touch Start Over to not scan the aliquot and return to the Scan Sample screen.
See Figure 5-191. A confirmation screen will be displayed after touching the
Start Over button.

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6. (Optional) If the sample requires an aliquot to be scanned, the Scan Aliquot screen
will be displayed (see Figure 5-198).
• Press the scanner button (located on either side of the barcode scanner) to scan
the aliquot barcode. The aliquot barcode will be scanned.
• If the aliquot is successfully scanned, the Success screen (green check mark)
will be displayed for a very short time (see Figure 5-192).
• If the assay is set up for aliquots but the sample has not been divided into
aliquots, touch Skip to skip scanning an aliquot. The scanner will display the
Confirmation screen (see Figure 5-199), if aliquots are not required and if
Confirmation is enabled, or will return to the Scan Sample screen (see
Figure 5-191).
• If aliquots are to scanned, the Scan Aliquot screen will be displayed (see
Figure 5-198).
• Touch Start Over to not scan the aliquot and return to the Scan Sample screen.
See Figure 5-191. A confirmation screen will be displayed after touching the
Start Over button.
7. (Optional) The scanner will display the Confirmation screen (see Figure 5-199), if
enabled, or will return to the Scan Sample screen (see Figure 5-191).
8. If the Confirmation screen is displayed, touch Start Over to go to the Scan Sample
screen. See Figure 5-191.
Figure 5-196. Cepheid Link Scanned Cartridge Information Screen
Figure 5-196. Cepheid Link Scanned Cartridge Information Screen

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Figure 5-197. Cepheid Link Scanned Cartridge Error Screen
Figure 5-197. Cepheid Link Scanned Cartridge Error Screen

Figure 5-198. Cepheid Link Scan Aliquot Screen
Figure 5-198. Cepheid Link Scan Aliquot Screen

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Figure 5-199. Cepheid Link Confirmation Screen
Figure 5-199. Cepheid Link Confirmation Screen

9. To scan additional samples and cartridges, go to Step 4.
10. When all samples and cartridges have been scanned, log off the Cepheid Link.
Access the scanner menu by touching the Menu icon in the drop down menu (see
Figure 5-191). The scanner menu will be displayed. See Figure 5-200.
11. On the scanner menu, touch Logout. The logout dialog will be displayed at the
bottom of the screen. See Figure 5-201.
12. On the logout dialog, touch OK to log off the scanner (see Figure 5-201). The scanner
Login screen will be displayed. See Figure 5-190.
Select Cancel if you do not want to log off the scanner.
13. Return the scanner to the docking station.

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Figure 5-200. Cepheid Link Scanner Drop Down Menu
Touch Logout to Display

the Logout Dialog
Figure 5-200. Cepheid Link Scanner Drop Down Menu

Figure 5-201. Cepheid Link Scanner Logout Dialog
Touch OK to Log Off

the Scanner
Figure 5-201. Cepheid Link Scanner Logout Dialog

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5.9.2 Running Cartridges Scanned from Cepheid Link

After cartridges have been scanned using Cepheid Link, they are transported to the
GeneXpert Infinity system to run the tests.
The system must be configured for Cepheid Link before running tests using this procedure.
Important Configuration for Cepheid Link is described in Section 2.7.4.2, Configuring Host
Communications for Cepheid Link.
The ordering process will be demonstrated using a series of workspace screenshots that
direct you to either scan or type in test information.
To run tests on the GeneXpert Infinity system:
2. Select the ORDER TEST button. The Order Test – Assay workspace is displayed to
scan the cartridge barcode. See Figure 5-204.
Select the END ORDER TEST button if you do not want to run a test.
Even though the patient demographics fields are displayed in the host workspaces, data cannot be
Note
entered into the fields.

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barcode scanner (Item #2). The GeneXpert Infinity system will query the Cepheid
Link system to verify that the order exists on the system. If the order exists, the order
will be downloaded to the GeneXpert Infinity system.
• If Auto Submit Order is enabled in the Automation workspace, the Order Test –
Assay workspace will be displayed to scan the next cartridge (see
Figure 5-204). Load (or place) the cartridge onto the conveyor. See
Figure 5-208.
• If Auto Submit Order is not enabled in the Automation workspace, the Order
Test – Test Information workspace will be displayed. See Figure 5-206.
4. In the Order Test – Test Information workspace (see Figure 5-206), review the order.
Enter additional information or notes, if necessary, then select the SUBMIT button.
The Order Test – Load Cartridge workspace is displayed. See Figure 5-207.
You cannot change the patient information (if enabled), Sample ID, patient demographics
Note
information or the assay if it is downloaded from a Link test order.

6. On the Order Test – Load Cartridge workspace, select the OK button (see
Figure 5-207). The Order Test – Assay workspace will be displayed to scan another
cartridge. See Figure 5-204.
The Order Test – Load Cartridge workspace will automatically advance to the Order Test – Assay
Note
workspace after several seconds to scan another cartridge if the OK button is not selected.

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8. Continue scanning cartridges for testing by repeating Step 3 through Step 7 until all
cartridges have been processed. When all cartridges have been processed, select END
ORDER TEST on the Order Test – Assay workspace. See Figure 5-204.

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6 Calibration Procedures
This chapter describes the following:

• Section 6.1, Calibration
• Section 6.2, Quality Control
• Section 6.3, External Quality Control
• Section 6.4, Control Trend Reports
• Section 6.4.1, Qualitative Assays vs. Quantitative Assays
• Section 6.4.2, Running Control Trend Reports
6.1 Calibration
Calibration of the GeneXpert instrument is not required during the initial system setup.
Cepheid performs all of the necessary calibrations before the system is shipped.
However, Cepheid recommends that the system be checked for proper calibration on an
annual basis from the point of initial use. Based upon the usage and care of each system,
calibration checks may be recommended more frequently. The system is designed to
measure module performance with the internal assay controls. In the event of a module
replacement, the replacement module provided will have been calibrated prior to
shipment.
A GeneXpert operator or Field Service Engineer with Administrator user permissions
can perform calibration checks during annual maintenance. Contact Cepheid Technical
Support for information about calibration checks. See the Technical Assistance section in
the Preface for contact information.
6.2 Quality Control

Quality control is an important part of diagnostic testing because it ensures you are
performing the tests correctly and that your GeneXpert Infinity system is working
properly. System control checks the optics, temperature of the module, and mechanical
integrity of each cartridge. If the system controls fail, an ERROR test result will be
reported. The GeneXpert cartridge automatically performs internal quality control for
each cartridge run. During each test, the system uses one or more of the following
controls:

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Calibration Procedures
• Sample-Processing Control (SPC) – Ensures the sample was processed correctly.

The SPC verifies that sample processing is adequate. Additionally, this control
detects sample-associated inhibition of the real-time PCR assay, ensures the PCR
reaction conditions (temperature and time) are appropriate for the amplification
reaction, and that the PCR reagents are functional. The SPC should be positive in a
negative sample and can be negative or positive in a positive sample. The SPC
passes if it meets the assigned acceptance criteria.
• Probe Check Control (PCC) – Before the start of the PCR reaction, the GeneXpert
System measures the fluorescence signal from the probes to monitor bead
rehydration, reaction tube filling, probe integrity, and dye stability. The PCC passes
if it meets the assigned acceptance criteria.
• Internal Control (IC) – Helps verify the performance of the PCR reagents and
prevent a false negative result. The internal control PCR assay assesses if there is
any inhibition, possibly by components in the sample. The internal control is
provided in the cartridge and should be positive in a negative sample.
• Endogenous Control (EC) – a control gene from the sample that normalizes targets
and/or helps ensure that sufficient sample is used in the test.
6.3 External Quality Control

External controls may be used in accordance with local, state or federal accrediting
organizations, as applicable. External controls can be identified as control tests by
selecting a control under the test type. See Section 5.5.2, Ordering a Test in Automation
Mode. For additional information, see the quality label or package insert for the specific
assay. During Order Test, select the appropriate Test Type for controls being tested.
6.4 Control Trend Reports

6.4.1 Qualitative Assays vs. Quantitative Assays
The Control Trend Report may be generated for both qualitative assays and quantitative
assays. After selecting the assay, to trend quantitative assay results, check the Use
Quantitative Data check box. For qualitative assays, the Use Quantitative Data check box
is grayed out.
It is possible to trend qualitative assay results on an assay that uses quantitative data. Do not check
Note
the Use Quantitative Data check box.

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6.4.2 Running Control Trend Reports

Control Trend reports can be used to monitor the performance of quality control
materials and observe trends in system, reagents or specimens over time in response to
contamination or reagent degradation.
The procedure below shows how to perform both qualitative assay control trend reports and
Note
quantitative assay control trend reports.
To view the control trends:

1. In the Xpertise Software Home workspace, press the RESULTS button (see
Figure 6-1). The Results menu is displayed. See Figure 6-2.

302-1288, April 2019

2. Press the CONTROL TREND REPORT button (see Figure 6-2). The Control Trend
Report Workspace is displayed. See Figure 6-3 for qualitative assay selection and
Figure 6-5 for quantitative assay selection.
3. Under the Date Range, select All to include all of the tests or the Select button to
select tests in a specific date range.
4. Select an assay to generate the Control Trend Report. See Figure 6-3 for qualitative
assay selection and Figure 6-5 for quantitative assay selection.
Note Control trending is not available for % Ratio quantitative assays.
5. Select the Use Quantitative Data check box, if applicable. If the assay selected is a
qualitative assay, the Use Quantitative Data check box will be grayed out (see
Figure 6-3). If the assay selected is a quantitative assay, the Use Quantitative Data
check box will be available (see Figure 6-5). Check the Use Quantitative Data check
box to generate the Control Trend Report using quantitative data.
6. If the assay contains multiple reagent lot numbers, select the lot number to use for
the Control Trend Report using the Reagent Lot Number drop down or select All
(default) to use all reagent lot numbers for the report.
7. Press the CONTINUE button to continue to the next Control Trend workspace where
additional criteria will be selected for qualitative and quantitative assays. See
Figure 6-4 for qualitative assay trends and Figure 6-6 for quantitative assay trends.
Press the CLOSE button to exit the Control Trend Report workspace.
8. Specify the following criteria on the second page of the Control Trend workspace:
• Qualitative Assay Options (see Figure 6-4):

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• Test Types – Select the external control types to be trended. For the
example in this chapter, Negative Control 1 was selected. Test types support
are Positive Control, Negative Control and Specimen test types.
• Select Analyte(s) – Select the analytes. For the example in this chapter, SPC
and Toxin B were selected.
• Data Type – Select the data type. For this example, the Cycle Threshold and
End Point data are selected to be trended. Data types will vary between
assays.
• Other Criteria – Select any other criteria desired for trending. For the
example in this chapter, Exclude tests in which any target analyte is positive
was not selected. This selection will exclude any tests from the graph if the
target analyte is positive.
• Quantitative Assay Options (see Figure 6-6):
• Test Types – Select the external-control types to be trended. For the
example in this chapter, Positive Control 1 was selected.
• Plot Data Format – Select the format of the data to be plotted. If the box is
checked, the data will be plotted in log format. If the box is unchecked, the
data will be plotted in scientific notation format. For the example in this
chapter, Plot quantitative value in log format was selected.
• Customize Graph Limits – Select the data limits to be used for plotting the
data. For this example, the Target was set to 200, the Lower Limit was set to
96 and the Upper Limit was set to 991. Lower and upper limits are defined in
the assay.
Figure 6-3. Control Trend Report Workspace Showing Qualitative Assay Selected
Figure 6-3. Control Trend Report Workspace Showing Qualitative Assay Selected

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Figure 6-4. Control Trend Report Workspace for Qualitative Options
Figure 6-4. Control Trend Report Workspace for Qualitative Options

Figure 6-5. Control Trend Report Workspace Showing Quantitative Assay Selected
Figure 6-5. Control Trend Report Workspace Showing Quantitative Assay Selected

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Figure 6-6. Control Trend Report Workspace for Quantitative Options
Figure 6-6. Control Trend Report Workspace for Quantitative Options

9. After selecting the options, generate the report to save or preview:
• GENERATE REPORT FILE – Creates a PDF file and saves it to a specified
location (see Figure 6-4 for qualitative assay trends and Figure 6-6 for
quantitative assay trends). The Generate Report File dialog box (see Figure 6-7)
enables you to save the file to a specified location.
Select the SAVE button once you have navigated to the specific location. To
view the Control Trend Report, go to the specified report location, open the
report and print it.
Note The default location for saving the Control Trend Report is report folder.
• PREVIEW PDF – Creates a PDF file and displays the file in the Adobe Reader
window. Select the PREVIEW PDF button on the Control Trend Report
workspace (see Figure 6-4 for qualitative assay trends and Figure 6-6 for
quantitative assay trends) to create the PDF file of the report. You can save and
print the PDF file from the Adobe Reader software. The Control Trend Report
pdf file may be saved in the GeneXpert Reports folder or saved on another
device.
The number of pages in the Control Trend Report will vary depending on the amount of data
Note
selected for the report. Figure 6-8 shows only the first page of the report.
CLOSE – Select the CLOSE button if you do not wish to generate a Control Trend
report and to close the Control Trend workspace.

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Figure 6-7. Generate Report File Workspace

Figure 6-8. Example Control Trend Report in the Adobe Reader Window
Figure 6-8. Example Control Trend Report in the Adobe Reader Window
A sample control trend report for a qualitative assay (Xpert C. difficile G2) is shown in
Figure 6-9 and Figure 6-10. A sample control trend report for a quantitative assay (Xpert
HIV-1 Viral Load) is shown in Figure 6-11.

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Figure 6-9. Control Trend Report Qualitative Assay Example (Xpert C. difficile G2), Page 1
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302-1288, April 2019
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302-1288, Rev. A April 2019
Figure 6-11. Control Trend Report Quantitative Assay Example (Xpert HIV-1 Viral Load), Page 1
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302-1288, April 2019

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7 Operational Precautions and Limitations
This chapter describes the operational precautions and limitations to be aware of when
using the GeneXpert Infinity systems. It is imperative that you follow the precautions in
this chapter for safe operation. The topics are as follows:
• Section 7.1, General Safety Precautions
• Section 7.2, Moving the System
• Section 7.3, Electrical Safety
• Section 7.4, Chemical Safety Precautions
• Section 7.5, Biological Hazard Safety Precautions
• Section 7.6, Precautions and Limitations
• Section 7.6.1, Security Precautions
• Section 7.6.2, Anti-Virus Software
• Section 7.6.3, Laboratory
• Section 7.6.4, Hardware and Software
• Section 7.6.5, Software
• Section 7.6.6, Cartridge
• Section 7.6.7, Assay
7.1 General Safety Precautions

Before you start to use the GeneXpert Infinity system, make sure you read the safety
information in this operator manual and additional sections in this manual related to your
job function. Ensure that you have the proper training required for operation of the
GeneXpert Infinity systems.
Using controls, making adjustments or performing procedures other than those specified
in this manual can result in exposure to hazards that can cause injury to personnel or
damage to the system.
Two sets of interlocks, on the glass doors, are provided to pause all movement of the
gantry and conveyor if any of the cabinet doors are opened.

302-1288, Rev. A April 2019
Operational Precautions and Limitations
7.2 Moving the System

Because of the GeneXpert Infinity system’s weight, do not attempt to lift the system. See
the system weight in Table 4-2 (for the Infinity-48s) or Table 4-5 (for the Infinity-80) in
Chapter 4, Performance Characteristics and Specifications.
Warning
Lifting or moving the system without proper training and assistance can cause personal
injury, damage the system and void your warranty. Do not climb or stand on any instrument
surface at any time. This could create a tipping hazard.
7.3 Electrical Safety

Warning
Do not attempt to open or remove the instrument covers. Doing so can expose you to
electrical hazards and cause injuries.
The GeneXpert Infinity system enclosure is designed to protect you from electrical
shock hazards. Under normal operating conditions, you are protected from electrical
shock hazards by the GeneXpert Infinity system enclosure.
If maintenance procedures require the system to be turned off and unplugged, a lockout
device may be installed on the power cord to prevent accidental operation until the
procedure is completed. See Figure 7-1.
If the system is locked out, do not attempt to use the system. Contact your system
administrator to determine when the system will be available.
Figure 7-1. Lockout Device Installed on Power Plug
Power Cord
Unplugged and
Lockout Device
Installed
Figure 7-1. Lockout Device Installed on Power Plug
Warning
Do not attempt to remove a lockout device and start the system. Doing so can expose you to
electrical hazards and cause injuries or equipment damage.

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7.4 Chemical Safety Precautions

Biological specimens, transfer devices, and used cartridges should be considered capable
! of transmitting infectious agents requiring standard precautions. Follow your institution’s
environmental waste procedures for proper disposal of used cartridges and unused
reagents. These materials may exhibit characteristics of chemical hazardous waste
requiring specific disposal. If country or regional regulations do not provide clear
direction on proper disposal, biological specimens and used cartridges should be
disposed per WHO [World Health Organization] medical waste handling and disposal
guidelines.
7.5 Biological Hazard Safety Precautions

Treat all biological specimens, including used cartridges, as if capable of transmitting
infectious agents. Because it is often impossible to know which might be infectious, all
biological specimens should be treated with standard precautions. Guidelines for
specimen handling are available from the U.S. Centers for Disease Control and
Prevention and the Clinical and Laboratory Standards Institute.
7.6 Precautions and Limitations

Be aware of the following system precautions and limitations to ensure proper operation
and results:
• Section 7.6.1, Security Precautions
• Section 7.6.2, Anti-Virus Software
• Section 7.6.2.2, Windows 10 Anti-Virus Software
• Section 7.6.4, Hardware and Software
• Section 7.6.5, Software
• Section 7.6.6, Cartridge
• Section 7.6.7, Assay

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7.6.1 Security Precautions

User data stored in the system may contain personal health information of patients, such
as name, patient ID and test results. Cepheid strongly recommends that you implement
physical, technical and administrative safeguards to protect the privacy and integrity of
patient data. Such measures may include but are not limited to restricting network and
system access, enforcing user authentication practices, maintaining antiviral software as
necessary for HIPAA compliance or any other protection required to comply with patient
privacy laws outside the United States. In particular, unique, strong passwords should be
maintained for all system users and should not be disabled. Consult your facilities
security officer to ensure internal compliance with all applicable regulations.
7.6.2 Anti-Virus Software

• For Windows 7, see Section •, For Windows 10, see Section 7.6.2.2, Windows 10
Anti-Virus Software.
• For Windows 10, see Section 7.6.2.2, Windows 10 Anti-Virus Software.
7.6.2.1 Windows 7 Anti-Virus Software

In order to protect the Windows 7 based GeneXpert Infinity system workstation
computer from malware that could cause data corruption or disrupt normal functionality,
Cepheid strongly recommends installing and maintaining an updated anti-virus program.
Computer viruses can be introduced by connecting the computer to a local or wide area
network or from extracting data using external memory devices.
Cepheid has validated several commercially available off-the-shelf solutions from
Symantec Corporation and McAfee Inc.
If the software is purchased from a commercial supplier, install the software by
following the instructions in the user documentation provided with the selected software
program chosen. Activation of the anti-virus software is usually accomplished by
connecting to the Internet. Follow the specific activation instructions in the software
dialog screens or documentation.
The computer usually must be connected to the Internet to activate the anti-virus software. Be sure
Note
any updating is scheduled when no data is being collected.
If your institution requires the use of another type of anti-virus software other than the
programs listed above, the institution is responsible for validating the solutions
compatibility with Cepheid product offerings.
Maintain an active anti-virus subscription and download updates regularly. If you have used
Important the Infinity computer to access the Internet, run anti-virus software before resuming Infinity
software and confirm results from the system match results output to any connected LIS.

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Caution
The Infinity workstation computer is set up to use Windows® Firewall so the firewall can
remain turned on. Do not turn on or use other non-Windows firewall products. Doing so can
prevent data collection or instrument malfunction.
Caution Cepheid tests and qualifies our system components to provide optimal performance. Do not
alter the computer settings, preinstalled software or other system components unless
instructed by Cepheid. Do not install non-approved software. Do not replace the system
network connection.
7.6.2.2 Windows 10 Anti-Virus Software

The GeneXpert Infinity system computer running Windows 10 ships with Windows
Defender Antivirus to protect against malware that could cause data corruption or disrupt
normal functionality. Because Windows Defender Antivirus comes bundled with
Windows 10 and is updated and maintained automatically with the operating system,
Cepheid does not recommend using third-party anti-virus software for the GeneXpert
Infinity system computer running Windows 10.
If Bitlocker is enabled, it is the customer’s responsibility to maintain the encryption key if it

Important
is forgotten or misplaced. For more information, visit https://www.microsoft.com.
7.6.3 Laboratory
Before you install the GeneXpert Infinity system, make sure your laboratory meets the
electrical specifications and environmental requirements specified in Chapter 4,
Performance Characteristics and Specifications.
7.6.4 Hardware and Software

Be sure to do the following:
• Place the GeneXpert Infinity system in a sheltered environment because it is
designed for indoor use only.
• Provide at least 32 inches (81.28 cm) of clearance on the backside of the instrument
to ensure adequate ventilation and serviceability.
• Do not place the GeneXpert Infinity system close to the vents of other instruments or
air handling units.
• Connect the GeneXpert Infinity system to a Synergy II series UPS and a properly
grounded AC circuit. See Section 4.3 for the electrical requirements.
• Use the GeneXpert Infinity system for diagnostic applications only.

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While a test is in progress:

• Do not move the system.
• Do not run other software.
• Do not change the date and time.
Cepheid has tested and qualified the GeneXpert Infinity system components to provide
optimal performance.
Do not alter the computer settings, preinstalled software and other system components
Caution
unless Cepheid instructs you to do so. Do not install non-approved software. Do not replace
system parts without assistance from Cepheid. Altering computer settings, preinstalled
software or other system components without guidance from Cepheid can result in the loss
of data, impact system performance, damage the instrument and void your warranty.
7.6.5 Software
Microsoft® Windows® 7 or Windows® 10 has been installed and activated on the
GeneXpert Infinity system computer. Other software supplied with the system include
CD-ROMs or DVD-ROMs containing Xpertise software, GeneXpert Infinity System
Operator Manual (in various languages) and possibly other software.
Store the media in a safe place in the original packaging. If the software needs to be
reinstalled by Cepheid Field Service, the original media will be required. In addition, to
Important
reactivate the software, the product key (located on the Certificate of Authenticity that is on
the installation media packaging) will also be required.
7.6.6 Cartridge
The GeneXpert cartridges are designed to process one test. Do not reuse spent cartridges.
7.6.7 Assay
Specific precautions and limitations for each assay are provided in the assay-specific
package insert.

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8 Hazards
This chapter describes the possible safety hazards found in the GeneXpert Infinity
systems. It is imperative that you follow the precautions in this chapter for safe
operation. The topics are as follows:
• Section 8.1, Safety Labels on the System
• Section 8.2, EMERGENCY STOP Button
8.1 Safety Labels on the System

This type of warning label indicates that the area contains a Class 1 laser and is located
on the shuttle. See Figure 8-1. The shuttle area contains a visible Class 1 laser. Class 1
lasers are safe under reasonably foreseeable conditions of operation, including the use of
optical instruments for intra-beam viewing.
Do not stare into the laser beam.
This type of warning label indicates a potential biological risk hazard. There is a
biological risk label located inside the kiosk near the waste container. See Figure 8-2.
Biological risk labels are also located on the serial number label on the side of the
monitor (Infinity-48s shown in Figure 8-3 or Infinity-80 shown in Figure 8-4). Biological
samples such as tissues, body fluids and blood of humans and/or animals have the
potential to transmit infectious diseases. Follow your local, state/provincial and national
safety regulations for handling and disposing the samples.
This type of warning label indicates that hazardous high voltages are present in the
electrical system in the GeneXpert Infinity system. Labels are located on each of the rear
system panels. See Figure 8-3 and Figure 8-4.
Do not operate the system with any rear panels removed. If you operate the system with
panels removed, you may be exposed to line voltage as well as several DC voltages.

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Hazards
Figure 8-1. Location of Class 1 Laser Label on Shuttle
Figure 8-1. Location of Class 1 Laser Label on Shuttle

Figure 8-2. Location of Biological Risk Label Inside the Waste Container Housing
Figure 8-2. Location of Biological Risk Label Inside the Waste Container Housing

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Hazards
Figure 8-3. GeneXpert Infinity-48s Rear Panels Showing Hazard Labels
Serial Number Label
Biological
Risk Label
High Voltage
Labels
Nameplate Label
Figure 8-3. GeneXpert Infinity-48s Rear Panels Showing Hazard Labels

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Hazards
Figure 8-4. GeneXpert Infinity-80 Rear Panels Showing Hazard Labels
Serial Number Label
Biological
Risk Label
High Voltage
Labels
Nameplate Label
Figure 8-4. GeneXpert Infinity-80 Rear Panels Showing Hazard Labels

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Hazards
8.2 EMERGENCY STOP Button

When the hardware EMERGENCY STOP button is pressed, power to the automation
system is removed immediately. The Xpertise software will indicate that the system is in
emergency stop mode. The EMERGENCY STOP button is located near the bottom of the
monitor on the front of the system. See Figure 8-5.
Figure 8-5. EMERGENCY STOP Button Location
Figure 8-5. EMERGENCY STOP Button Location

During emergency stop, the following actions occur:
• All cartridge transfer functions are suspended.
• All user interface features are suspended.
Remove all cartridges from the conveyor before resuming the system from an emergency
Important stop. The cartridges in the modules will continue running. The cartridges removed from the
conveyor can be reprocessed.
Caution
Do not move or add cartridges to other areas in the system under any circumstances.
Caution
Using the EMERGENCY STOP button may cause cartridges to be unusable. Please use the
Pause icon in non-emergency situations.

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Hazards
If there is a situation that requires an immediate stop of the system automation:

1. Press the EMERGENCY STOP button located on the lower portion of the monitor (see
Figure 8-5). The Emergency Stop workspace is displayed with instructions about
how to proceed. See Figure 8-6.
2. Select the UNLATCH GLASS DOORS button on the Emergency Stop workspace. See
Figure 8-6. The glass doors will unlatch and the next Emergency Stop workspace
3. Open the glass doors and remove stuck or fallen cartridges and/or clean up any
spills.
4. Remove all cartridges from the conveyor.
5. After removing cartridges from the conveyor, untwist the EMERGENCY STOP button
(see Figure 8-5).
6. Select the RESUME button in the Emergency Stop workspace (see Figure 8-7). The
Emergency Stop workspace will display instructions to close and latch the glass
doors. See Figure 8-8.
Figure 8-6. Emergency Stop Workspace with Cartridge Removal Instructions
Figure 8-6. Emergency Stop Workspace with Cartridge Removal Instructions

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Hazards
Figure 8-7. Emergency Stop Workspace after Completion of Cartridge Operations
Figure 8-7. Emergency Stop Workspace after Completion of Cartridge Operations

Figure 8-8. Emergency Stop Workspace to Close Glass Doors
Figure 8-8. Emergency Stop Workspace to Close Glass Doors

7. Close the glass doors and select the LATCH GLASS DOORS button on the Emergency
Stop workspace (see Figure 8-8). The Emergency Stop workspace displays
instructions to resume operation. See Figure 8-9.

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Hazards
Figure 8-9. Emergency Stop Workspace with Instructions to Resume Operation
Figure 8-9. Emergency Stop Workspace with Instructions to Resume Operation

Figure 8-10. Emergency Stop Workspace Completion Message
Figure 8-10. Emergency Stop Workspace Completion Message

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Hazards
8. In the Emergency Stop workspace, select the RESUME button (see Figure 8-9). The
Emergency Stop workspace indicates that the system has returned to normal
operation. See Figure 8-10.
9. In the Emergency Stop workspace, select the CLOSE button (see Figure 8-10). The
Emergency Stop workspace will close and the workspace will be displayed that was
previously active before the EMERGENCY STOP button was pressed.

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Hazards

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9 Service and Maintenance
This chapter describes the basic maintenance procedures for the GeneXpert Infinity
systems, and lists the possible problems or error messages you might encounter.
This chapter is organized as follows:
• Section 9.1, Maintenance Tasks
• Section 9.2, Maintenance Log
• Section 9.3, Guidelines for Cleaning and Disinfecting
• Section 9.4, Cleaning the Infinity Systems
• Section 9.4.1, Cleaning the Kiosk Table Top, Monitor, Mouse and Keyboard
• Section 9.4.2, Cleaning the Kiosk Scanner
• Section 9.4.3, Cleaning the Instrument Surfaces
• Section 9.5, Cleaning the Conveyor Belt
• Section 9.5.1, Weekly Quick Cleaning of the Conveyor Belt
• Section 9.5.2, Quarterly Cleaning of the Conveyor Belt
• Section 9.6, Vacuuming the Rear Fan Filters
• Section 9.6.1, Before You Start
• Section 9.6.2, Setting Up the Vacuum Cleaner
• Section 9.6.3, Vacuuming the Rear Fan Filters
• Section 9.7, Replacing/Cleaning the Fan Filters
• Section 9.7.1, Determining if Fan Filters can be Replaced/Cleaned
• Section 9.7.2, Replacing/Cleaning Fan Filters
• Section 9.7.3, Cleaning Fan Filters
• Section 9.8, Cleaning the Cartridge Bays and Plunger Rods
• Section 9.9, Replacing the Waste Container Bag
• Section 9.9.1, Replacing the Waste Container Bag of Cartridges
• Section 9.9.2, Assembling the Waste Container
• Section 9.10, Checking and Replacing Batteries in the Keyboard and Mouse
• Section 9.10.1, Checking Battery Levels in the Keyboard and Mouse
• Section 9.10.2, Replacing Batteries in the Keyboard and Mouse
• Section 9.11, Annual Instrument Maintenance

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Service and Maintenance
• Section 9.12, Generating Reports for Troubleshooting

• Section 9.12.1, Module Report
• Section 9.12.2, System Log Report
• Section 9.13, Performing a Manual Self-Test
• Section 9.14, Excluding Modules from Test
• Section 9.15, Repairing the System
• Section 9.16, Hardware Problems
• Section 9.17, Error Messages
• Section 9.17.1, Run-time Errors
• Section 9.17.2, Operation Terminated Errors
• Section 9.17.3, Cartridge Loading Errors
• Section 9.17.4, Self-Test Errors
• Section 9.17.5, Post-Run Amplification Curve Analysis Errors
• Section 9.17.6, Automation Errors
• Section 9.18, Troubleshooting Host Connectivity
• Section 9.18.1, Host Connectivity Indication
• Section 9.18.2, Host Communication Buffer
• Section 9.19, Export Log Files
• Section 9.20, Export Host Settings
• Section 9.21, Clearing Failed Automation Locations
• Section 9.22, Failure Handling
• Section 9.22.1, Failure Locations
• Section 9.22.2, Return an Affected Cartridge
• Section 9.22.3, Disable New Test Orders
• Section 9.22.4, Prompt User for Non-Accessible Module
• Section 9.22.5, Prompts to Fix a Specific Failure
• Section 9.22.6, Prompt User to Switch to Manual Mode or Reboot the
Instrument
• Section 9.22.7, Prompt User to Contact Technical Support due to Repetitive
Failures
• Section 9.22.8, Prompt for Technical Support
• Section 9.23, Decontamination for Shipping

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9.1 Maintenance Tasks

The system is designed to be low-maintenance. However, Cepheid recommends periodic
system checks and cleaning as a preventive measure. Table 9-1 lists the basic
maintenance tasks you can perform.
Table 9-1. Maintenance Tasks and Frequency
Task Frequency Section

Clean the kiosk table top, keyboard and Weekly Section 9.4.1
monitor
Quick clean the conveyor belt Weekly Section 9.5.1
Perform system shutdown Weekly Section 5.2.8
Vacuum the rear fan filters Monthly Section 9.6
Archive / Purge tests Monthly Section 5.7.1
Clean the kiosk scanner Quarterly Section 9.4.2
Clean the conveyor belt Quarterly Section 9.5.2
Clean the cartridge bays and plunger rods Quarterly Section 9.8
Clean instrument surfaces Quarterly Section 9.4.3.1
Replace or clean rear fan filters, if Quarterly Section 9.7
applicable
Check the instrument calibration Annually Section 9.11
Print module report As required Section 9.12
Print system log report As required Section 9.12.2
Empty / replace waste container As required Section 9.9
Back up system database As required Section 5.7.3
Clean the instrument surfaces In case of a spill Section 9.4.3.2
The maintenance functions, which can be access through the maintenance menu (see
Figure 9-1), allow you to perform various instrument housekeeping tasks, such as
cleaning instrument parts and exporting software log files for troubleshooting.

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To improve efficiency, the suggested monthly and quarterly workflows are described
below:
Infinity Monthly Maintenance Workflow

1. Archive/Purge tests. See Section 5.7.1, Archiving the Tests.
2. Shut down the system. See Section 5.2.8, Shutting the System Down.
3. Vacuum the rear fan filters. Section 9.6.3, Vacuuming the Rear Fan Filters.
4. Restart the system. See Section 5.2.1, Turning the System On and Section 5.2.4,
Starting the Xpertise Software.
Infinity Quarterly Maintenance Workflow

1. Perform cartridge bay and plunger rod maintenance. See Section 9.8, Cleaning the
Cartridge Bays and Plunger Rods.
2. Shut down the system. See Section 5.2.8, Shutting the System Down.
3. Replace and clean the rear fan filters, if possible. See Section 9.7, Replacing/
Cleaning the Fan Filters.
4. Clean the instrument surfaces:
A. Clean the kiosk table top, monitor, mouse and keyboard. Section 9.4.1,
Cleaning the Kiosk Table Top, Monitor, Mouse and Keyboard.
B. Clean the kiosk scanner. See Section 9.4.2, Cleaning the Kiosk Scanner.
C. Clean the instrument floor, gantry rails and door rails. See Section 9.4.3,
Cleaning the Instrument Surfaces.
5. Restart the system. See Section 5.2.1, Turning the System On and Section 5.2.4,
Starting the Xpertise Software.
6. Clean the conveyor belt. See Section 9.5.2, Quarterly Cleaning of the Conveyor
Belt.

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Figure 9-1. Maintenance Menu Map
GX Maintenance Menu
Generates Module
Report
Maintenance Menu
Opens Plunger
Maintenance
Workspace
Opens Perform Self-

Test Workspace
Excludes Modules
Main Menu from Being Used
for Tests
Creates System Log

Report
Exports System Log File
Exports Host Settings File
Opens Automation Failed

Location Workspace
(Admin. User Only)
Opens Clean Conveyor -

Confirmation Workspace
Displays Information
About the Xpertise
Software
Figure 9-1. Maintenance Menu Map

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9.2 Maintenance Log

Complete the maintenance log shown in Figure 9-2 daily or whenever maintenance tasks
are performed on the system. You may make copies of this monthly log to use, as
required. There is an electronic version of this file on the GeneXpert Infinity system
Operator Manual CDROM that can be copied and used for monthly records. The
electronic version of this file is a pdf file that can be filled in and saved using Adobe
Reader or Adobe Acrobat.
9.3 Guidelines for Cleaning and Disinfecting

Cleaning and disinfecting system components is crucial for proper system maintenance.
Disinfection is a chemical reaction. As a chemical reaction it is affected by many factors
including the concentration of the disinfectant, contact time, temperature, nature of the
microbes present, amount of organic residue, surface properties, etc. With any
disinfectant it is crucial that the entire area to be disinfected be in contact with the
disinfecting solution.
General guidelines for routine surface cleaning are:
• Use only 70% ethanol or denatured ethanol (70% ethanol containing 5% methanol
and 5% isopropanol).
• Use only deionized water or bleach with a deionized water rinse for cleaning the
conveyor belt. Never use an ethanol solution for cleaning the conveyor belt.
General guidelines for cleaning combined with disinfection are:
• Bleach solution: use a 0.5% final active chlorine concentration or a 1:10 dilution
factor of household chlorine bleach prepared within one day of use.
• Use sufficient disinfectant (bleach solution) and spread the disinfectant evenly. The
entire surface should be wet to completely disinfect the surface.
• Allow a minimum of two minutes contact time. More than five minutes is not
recommended.
• Remove remaining bleach residue with deionized (DI) water or 70% ethanol or
denatured ethanol (70% ethanol containing 5% methanol and 5% isopropanol).
Caution
Failure to remove bleach solution residue from the system may cause damage to the
instrument components. Always perform a wipe down with deionized water or ethanol after
using the bleach solution.
• Except for the conveyor belt, repeat the cleaning and disinfection with the bleach
solution three times (two minutes contact time for each bleach application) followed
by a final wipe with ethanol to remove bleach solution residue.

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Figure 9-2. GeneXpert Infinity Systems Maintenance Log
Figure 9-2. GeneXpert Infinity Systems Maintenance Log

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9.4 Cleaning the Infinity Systems

There are several procedures to be used to clean the GeneXpert Infinity systems. Some
procedures are to be performed at regular intervals and some are to be performed as
needed (such as in the event of a spill).
9.4.1 Cleaning the Kiosk Table Top, Monitor, Mouse and

Keyboard
Clean and disinfect the kiosk table top, monitor, mouse and keyboard weekly or in the
event of a spill. The materials required for this procedure are:
• Bleach solution: A 0.5% final active chlorine concentration or a 1:10 dilution factor
of household chlorine bleach prepared within one day of use
• 70% ethanol or denatured ethanol (70% ethanol containing 5% isopropanol and 5%
methanol)
Caution
Do not use 70% isopropyl alcohol for cleaning the kiosk table top, monitor, mouse and
keyboard. Isopropyl alcohol can degrade polycarbonate plastics.
• Deionized water
• Lint-free wipes or paper towels
• Disposable gloves
• Eye protection
Biological Risks Wear disposable gloves, eye protection and other personal protective equipment mandated
by your institution’s safety policies while performing this cleaning procedure. Wearing
personal protective equipment prevents exposure to chemical and biologically hazardous
materials.
To clean the kiosk table top, monitor, mouse and keyboard (see Figure 9-3):
1. Remove the mouse and all other items from the kiosk table top.
2. Thoroughly moisten a lint-free wipe or paper towel with the bleach solution.
3. Wipe the table top surface thoroughly with the lint-free wipe or paper towel. Use
additional lint-free wipes or paper towels, as needed, to ensure adequate coverage.
Allow the bleach solution to remain on the surface a minimum of two minutes.
4. Discard the used lint-free wipe according to your standard laboratory procedure.

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Figure 9-3. Kiosk Table Top
Monitor
Kiosk Table Top
Mouse
Keyboard
Figure 9-3. Kiosk Table Top

5. Thoroughly moisten a lint-free wipe or paper towel with the 70% ethanol solution.
6. Wipe the table top, keyboard, mouse and monitor thoroughly with the lint-free wipe
or paper towel. Use additional lint-free wipes or paper towels, as needed.
7. Discard the used lint-free wipes or paper towels according to your standard
laboratory procedure.
9.4.2 Cleaning the Kiosk Scanner

Clean the kiosk scanner every three months (quarterly). The materials required for this
procedure are:
methanol)
Caution
Do not use 70% isopropyl alcohol for cleaning the kiosk scanner. Isopropyl alcohol can
degrade polycarbonate plastics.

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• Lint-free wipes
• Eye protection
materials.
To clean the kiosk scanner (see Figure 9-4):

1. Thoroughly moisten a lint-free wipe with the 70% ethanol solution.
2. Wipe the lens of the kiosk scanner.
4. Wipe the scanner lens with a dry lint-free wipe to dry the lens and remove any
residue on the lens.
Figure 9-4. Cleaning the Kiosk Scanner
Figure 9-4. Cleaning the Kiosk Scanner

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9.4.3 Cleaning the Instrument Surfaces

9.4.3.1 Quarterly Maintenance
Clean the floor of the instrument, tracks of the gantry and doors every three months. The
materials required for this procedure are:
For the quarterly cleaning procedure, do not use a bleach solution. A bleach solution is to be
Important
used only in the event of a spill.

methanol)
Caution
Do not use 70% isopropyl alcohol for cleaning the instrument surfaces. Isopropyl alcohol
can degrade components inside the system.

• Eye protection
materials.
Warning
The GeneXpert Infinity system must be completely shut down when cleaning the instrument
surfaces.
Do not use a vacuum cleaner inside the instrument at any time. Remove debris from
Important instrument surfaces using lint-free wipes or paper towels moistened with ethanol or a bleach
solution as described in the following procedure.
When cleaning the rails and floor in the following procedure, only short sections can be cleaned at
one time due to limited reach between the instrument doors. Clean a small section within reach,
Note
move the instrument doors and clean the small section within reach. Repeat until the rails and floor
have been cleaned for the entire instrument.
To clean the instrument surfaces (see Figure 9-5):

1. Shut down the GeneXpert Infinity system following the procedure in Section 5.2.8,
Shutting the System Down.
3. Wipe the gantry rail cover. Change lint-free wipes or towels frequently while
wiping.
4. Wipe the tracks of the door rail. Change lint-free wipes or towels frequently while
wiping.

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5. Wipe the floor of the instrument. Change lint-free wipes or paper towels frequently
while wiping.
6. Discard the used lint-free wipe or paper towel according to your standard laboratory
procedure.
7. After the instrument surfaces have been cleaned, restart the system following the
procedure in Section 5.2.1, Turning the System On and Section 5.2.4, Starting the
Xpertise Software.
Figure 9-5. Cleaning the Instrument Surfaces for Quarterly Maintenance
Clean Gantry Rail Covers Clean Door Rail
Clean Instrument Floor

Figure 9-5. Cleaning the Instrument Surfaces for Quarterly Maintenance

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9.4.3.2 In Case of Spill

Clean affected instrument surfaces in the event of a spill. All surfaces within the
instrument housing should be cleaned including the ceiling, floor, sides, metal vertical
and horizontal surfaces, gantry, door rails, accumulator shelves and outside door of
modules.
The materials required for this procedure are:
methanol)
Caution
Do not use 70% isopropyl alcohol for cleaning the instrument surfaces. Isopropyl alcohol
can degrade components inside the system.

• Eye protection
materials.
Warning
The GeneXpert Infinity system must be completely shut down when cleaning the instrument
surfaces.
Do not use a vacuum cleaner inside the instrument at any time. Remove debris from
Important instrument surfaces using lint-free wipes or paper towels moistened with ethanol or a bleach
solution as described in the following procedure.
To clean the affected instrument surfaces (see Figure 9-6 for potentially affected
surfaces):
1. Shut down the GeneXpert Infinity system following the procedure in Section 5.2.8,
Shutting the System Down.
2. Thoroughly moisten a lint-free wipe or paper towel with the bleach solution.
3. Wipe affected surfaces inside the instrument. Change lint-free wipes or paper towels
frequently while wiping.
4. Allow the bleach solution to remain on the surfaces at least two minutes but no
longer than five minutes.
5. Repeat Step 1 through Step 4 two more times for a total of three times.

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Figure 9-6. Cleaning the Potentially Affected Instrument Surfaces
Ceiling
Accumulator
Shelves
Gantry
Sides
Module
Doors
Floor
Door Rails (Top

and Bottom)
Figure 9-6. Cleaning the Potentially Affected Instrument Surfaces

7. Wipe affected surfaces inside the instrument. Change lint-free wipes or paper towels
frequently while wiping.
8. Discard the used lint-free wipe or paper towel according to your standard laboratory
procedure.
9. After the instrument surfaces have been cleaned, restart the system following the
procedure in Section 5.2.1, Turning the System On and Section 5.2.4, Starting the
Xpertise Software.

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9.5 Cleaning the Conveyor Belt

9.5.1 Weekly Quick Cleaning of the Conveyor Belt
A quick clean of the conveyor belt with the kiosk table top in place should be performed
weekly with deionized water to remove particulate debris. The Clean Conveyor
workspace allows the user to clean the conveyor in Automation mode.
• Deionized water
• Eye protection
materials.
Biological Risks
If a spill occurs on the kiosk or conveyor belt, press the EMERGENCY STOP button to
reduce the possibility of spreading the spill to other areas of the system.
Caution
Before performing this procedure, ensure that there are no cartridges to be processed on the
conveyor belt.
Caution
Do not use alcohol to clean the conveyor belt. Alcohol can damage the conveyor belt
material.
To clean the conveyor belt:

1. Check the conveyor to verify that there are no cartridges on the conveyor. If there are
cartridges on the conveyor, let the system finish processing cartridges before
performing this procedure.
Caution
It is possible to pinch your fingers when cleaning the conveyor belt. To prevent injury, do not
place your fingers along the edges of the conveyor belt.
2. Thoroughly moisten a lint-free wipe or paper towel with deionized water.

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Figure 9-7. Quick Cleaning Conveyor Belt from Top of Kiosk
Figure 9-7. Quick Cleaning Conveyor Belt from Top of Kiosk

3. Hold the lint-free wipe or paper towel tightly (to avoid it being pulled from your
hand) against the exposed surface of the conveyor belt for two rotations of the belt
(approximately two minutes). See Figure 9-7.
The conveyor belt will stop before it has rotated for two minutes. When the belt stops, lift the wipe or
Note
paper towels off the conveyor to restart it and then continue wiping.
4. Dry the belt using a new lint-free wipe or paper towel. Hold the lint-free wipe or
paper towel tightly (to avoid it being pulled from your hand) against the exposed
surface of the conveyor belt for two rotations of the belt (approximately two
minutes). See Figure 9-7.
This completes the procedures for quick cleaning the conveyor belt.

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9.5.2 Quarterly Cleaning of the Conveyor Belt

The conveyor belt should be cleaned and disinfected quarterly or in the event of a spill.
The Clean Conveyor workspace allows the user to clean the conveyor in Automation
mode.
• Deionized water
• Eye protection
Biological Risks
Make sure you wear disposable gloves and eye protection for the cleaning procedure.
Wearing gloves and eye protection prevents you from being exposed to chemical and
biologically hazardous materials.
Biological Risks
If a spill occurs on the kiosk or conveyor belt, press the EMERGENCY STOP button to reduce
the possibility of spreading the spill to other areas of the system.
Caution
Do not use alcohol or ethanol to clean the conveyor belt. Alcohol or ethanol can damage the
conveyor belt material.
To clean the conveyor belt:

1. In the Xpertise Software Home workspace, select the MAINTENANCE button (see
Figure 9-8). The Maintenance menu is displayed. See Figure 9-9.
2. Select the CLEAN CONVEYOR button (see Figure 9-9). The Clean Conveyor –
Confirmation workspace is displayed. See Figure 9-10.
3. Read the instructions shown in the Clean Conveyor – Confirmation workspace (see
Figure 9-10). Select the CONFIRM button to continue. The Clean Conveyor –
Preparing Conveyor workspace appears. See Figure 9-11.
Select the CANCEL button to exit the Clean Conveyor workspace.
4. The system will process any cartridges on the conveyor while the Clean Conveyor –
Preparing Conveyor workspace is displayed (see Figure 9-11). While this screen is
displayed, you may select the CANCEL button to exit the Clean Conveyor
workspace, if desired. The system with automatically display the Clean Conveyor –
Confirm Empty workspace when the conveyor has no cartridges present. See
Figure 9-12.

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Figure 9-9. Maintenance Menu

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Figure 9-10. Clean Conveyor Confirmation Workspace
Figure 9-10. Clean Conveyor Confirmation Workspace

Figure 9-11. Clean Conveyor – Preparing Conveyor Workspace
Figure 9-11. Clean Conveyor – Preparing Conveyor Workspace

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Figure 9-12. Clean Conveyor – Confirm Empty Workspace
Figure 9-12. Clean Conveyor – Confirm Empty Workspace

Figure 9-13. Clean Conveyor Workspace

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5. Check the conveyor to verify that there are no cartridges on the conveyor. If there are
no cartridges on the conveyor, select the EMPTY button (see Figure 9-12). The Clean
Conveyor workspace is displayed. See Figure 9-13.
If there are still cartridges on the conveyor, select the CANCEL button to exit the
Clean Conveyor – Confirm Empty workspace.
Make sure that the Clean Conveyor – Confirm Empty workspace (see Figure 9-12) is displayed and
Note you have verified that there are no cartridges on the conveyor belt before cleaning the conveyor
belt.
6. Remove the kiosk table top:

A. Remove all objects from the kiosk table top including the mouse.
B. Pull out the keyboard drawer, push the keyboard to the back of the keyboard
drawer and place the mouse in the front, right corner of the drawer. See
Figure 9-14.
Caution
It is possible to pinch your fingers when removing the kiosk table top. To avoid pinching
your fingers, perform the following steps exactly as instructed.
Figure 9-14. Place the Keyboard and Mouse into the Keyboard Drawer
A B
Figure 9-14. Place the Keyboard and Mouse into the Keyboard Drawer
C. With the keyboard drawer still open, put grip the front corner of the kiosk table
top (near the keyboard) with one hand and grip the back corner of the kiosk
table top with the other hand. See Figure 9-15A.
Newer Infinity systems have a cutout for your hands on the back of the kiosk frame for gripping the
Note
kiosk top plate. Older systems do not have a cutout for your hands.
D. Lift the end of the kiosk table top off the mounting pins using both hands. See
Figure 9-15B.
E. With both hands, pull or slide the kiosk table top away from the system’s
chassis wall. See Figure 9-15C.

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F. Lift and remove the kiosk table top and place it in a secure location. See
Figure 9-15D. The conveyor belt is accessible for cleaning. See Figure 9-16.
Warning
The kiosk table top may be heavy. On older Infinity-80 systems, the kiosk table top weighs
approximately 9 kg. (20 lbs.) Use correct lifting procedures.
7. Follow the instructions provided in the Clean Conveyor workspace (see

Figure 9-13), and then perform the following steps:
A. Select the ON button in the Clean Conveyor workspace (see Figure 9-13) to start
the conveyor belt. The conveyor belt starts to move.
B. Dampen a lint-free wipe or paper towel with the bleach solution.
C. Hold the dampened lint-free wipe or paper towel tightly (to avoid it being
pulled from your hand) on top of the accessible portion of the conveyor belt for
30 seconds or until the conveyor belt seam reappears. See Figure 9-16. Allow
the bleach solution to remain on the belt for a minimum of two minutes.
Figure 9-15. Removing the Kiosk Table Top
A B
C D
Figure 9-15. Removing the Kiosk Table Top

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D. Dampen another lint-free wipe or paper towel with the bleach solution, wipe the
belt again and leave the bleach solution on the belt for two minutes. Perform
this step two times.
E. Dampen another lint-free wipe or paper towel with deionized water.
F. Hold the dampened lint-free wipe or paper towel tightly (to avoid it being
pulled from your hand) on top of the accessible portion of the conveyor belt for
about 30 seconds or until the conveyor belt seam reappears. See Figure 9-16.
8. Select the OFF button in the Clean Conveyor workspace (see Figure 9-17) to stop the
conveyor belt. The conveyor belt stops.
9. Select COMPLETE button to close the workspace. See Figure 9-13.
11. Discard all wipes according to the laboratory disposal policies.
Figure 9-16. Wiping the Conveyor Belt
Figure 9-16. Wiping the Conveyor Belt

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Figure 9-18. Installing the Kiosk Table Top
A B
C D
Figure 9-18. Installing the Kiosk Table Top

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Caution
It is possible to pinch your fingers when installing the kiosk table top. To avoid pinching your
fingers, perform the following steps exactly as instructed.
12. Reinstall the kiosk table top:

A. Place the kiosk table top over the kiosk. See Figure 9-18A.
B. Align the conveyor with the slot in the kiosk table top and slide the kiosk table
top in until it is against the system’s chassis wall. See Figure 9-18B.
C. Align the kiosk table top so the holes in the table top align with the mounting
pins on the frame of the kiosk. See Figure 9-18C.
D. With both hands on the top of the kiosk table top, press down on the table top
until the pins on the kiosk frame are inside the holes in the table top. See
Figure 9-18D.
Make sure that the kiosk table top is all the way down. If it sticks up or is not positioned
Important
correctly, cartridges will not feed properly.
This completes the procedures for cleaning the conveyor belt.
9.6 Vacuuming the Rear Fan Filters

The Infinity rear fan filters should be vacuumed monthly.
In the United States, a vacuum cleaner is shipped with the GeneXpert Infinity system.
Instructions for using the vacuum cleaner are provided in the following sections. For
GeneXpert Infinity systems shipped outside the United States, no vacuum cleaner is
provided. A vacuum cleaner should be purchased locally for vacuuming the filters.
Important Use a vacuum cleaner with 5 HP or less to avoid damage to the filters.
This section is organized as follows:

• Section 9.6.1, Before You Start
• Section 9.6.2, Setting Up the Vacuum Cleaner
• Section 9.6.3, Vacuuming the Rear Fan Filters

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9.6.1 Before You Start

Completely shut down the GeneXpert Infinity system by following the procedure in
Section 5.2.8, Shutting the System Down in this manual.
Warning
The GeneXpert Infinity system must be completely shut down during vacuum procedures.
9.6.2 Setting Up the Vacuum Cleaner

The Eureka® 71B Handheld Vacuum Cleaner and its accompanying Shop-Vac®
attachments tool kit are shown in Figure 9-19.
Note Not all of the attachments shown in Figure 9-19 are used for cleaning the Infinity fans.
Figure 9-19. vVacuum Cleaner and Attachments
Cepheid Part No. 850-0263 Cepheid Part No. 850-0264

Eureka 71B Handheld Vacuum Cleaner Shop-Vac 801-89-62 Micro Tool Kit
Figure 9-19. Vacuum Cleaner and Attachments

1. Remove the hose from the hose adapter. See Figure 9-20.
2. Assemble the hose attachments. See Figure 9-21.
A. Insert the curved wand into the hose adapter.
B. Insert the round brush into the curved wand.

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Figure 9-20. Disconnect Hose from Hose Adapter
Hose Hose Adapter
Figure 9-20. Disconnect Hose from Hose Adapter

Figure 9-21. Connect Hose to Hose Attachments
Hose Adapter Curved Wand Round Brush
Figure 9-21. Connect Hose to Hose Attachments

3. Connect the hose attachments to the vacuum cleaner hose.

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9.6.3 Vacuuming the Rear Fan Filters

The rear fan filters should be vacuumed monthly to remove dust and particulates from
the filters.
• Distilled water
• Vacuum cleaner and attachments
• Eye protection Warning
Warning
The GeneXpert Infinity system must be completely shut down during this vacuum procedure.
materials.
Biological Risks
Always soak the vacuum attachment in the bleach solution for five minutes after vacuuming
the Infinity system to prevent contamination, then rinse the vacuum attachment with distilled
water. Allow the attachments to dry.
Caution
If you are not using the Eureka 71B vacuum, use a vacuum cleaner with a rating of 5 HP
(horsepower) or less.
During installation of the Infinity system, the system should have been installed at least 50 cm
Note
(18 inches) away from the wall to allow access to the fan filters.
To vacuum the rear fans/filters:

1. Attach a brush tip or crevice tool to the hose of the vacuum cleaner as shown in
Figure 9-21.
2. Gently brush the vacuum cleaner’s brush tip or crevice tool over each filter. See
Figure 9-22.
Caution
Be careful not to press too hard against the filter because the filter may dislodge.

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Figure 9-22. Vacuuming the Rear Fan Filters
Fan/Filter
Vacuum
Attachment
Figure 9-22. Vacuuming the Rear Fan Filters

3. After cleaning the fan filters, soak the vacuum cleaner attachments in the bleach
solution.
4. Rinse the vacuum cleaner attachments with distilled water.
5. Thoroughly allow the vacuum cleaner attachments to dry before using them again.
9.7 Replacing/Cleaning the Fan Filters

9.7.1 Determining if Fan Filters can be Replaced/Cleaned
There are two fan filters on each 8-pack assembly on the Infinity systems. If the Infinity
system has a rear panel that has larger openings, the fan filters can be replaced as part of
the customer maintenance procedures. If the rear panel has smaller openings, the fan
filters must be replaced by a Cepheid Field Service Engineer. See Figure 9-23 to
determine if you can replace the fan filters.
If you can replace the fan filters, perform the procedure in Section 9.7.2, Replacing/
Cleaning Fan Filters. If you cannot replace the fan filters, then vacuum the fan filters
following the procedures in Section 9.6.3, Vacuuming the Rear Fan Filters and request
your Cepheid Field Service Engineer to replace the fan filters on his next service call for
the system.

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Figure 9-23. Determining if Fan Filters can be Replaced
Fan Filter NOT to be Replaced by Fan Filter to be Replaced by Customer

Customer
Not Enough Space
to Remove Filter
Figure 9-23. Determining if Fan Filters can be Replaced
9.7.2 Replacing/Cleaning Fan Filters

Warning
The GeneXpert Infinity system must be completely shut down during this cleaning
procedure.
In order to minimize system downtime, Cepheid recommends that you have a complete set of fan
Note filters available to replace all of the fan filters on the system. After replacing the fan filters, the dirty
fan filters may be cleaned and used the next time that the fan filters are replaced.
If you can replace/clean the fan filters, they should be cleaned every 3 months
(quarterly) and replaced yearly. The recommended filter replacement process is to have a
second set of filters available and use those filters as replacement filters when the dirty
filters are removed. Then, clean the dirty filters to use the next time the filters need to be
replaced. The fan filters are located on the back of each 8-pack module on the Infinity
system.
The materials you need for this procedure are:
• Replacement Fan Filters – 5 filters per package (Cepheid Part No. 001-1537)
• Lint-free wipes
• Water
Each fan filter is attached to the Infinity system using a fan filter retainer. The fan filter
retainer grips the edges of the fan using four grips. See Figure 9-24.

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Figure 9-24. Fan Guard Grips
Fan Filter
Retainer Grips
(4 Places)
Figure 9-24. Fan Guard Grips

To replace the rear fan filters:
1. Exit the Xpertise software and power down the Infinity system.
When powering down the Infinity system, always use the shutdown utility and wait a
Important
minimum of two minutes before turning off the power to the system.
2. Vacuum the fan filters to remove excess dust. See Section 9.6.3, Vacuuming the
Rear Fan Filters.
3. On the back of the system, grip the fan filter retainer on the bottom edge and gently
pull it toward you. See Figure 9-25.
4. Grip the fan filter retainer on the right edge and gently pull it toward you. See
Figure 9-25.
5. Gently continue pulling on the fan filter retainer until all four grips have been
released and the fan filter retainer and filter have been removed from the system.
6. Remove the dirty filter from the fan filter retainer and install a replacement filter in
the fan filter retainer. See Figure 9-26.
7. Install the fan filter assembly back onto the 8-pack assembly. See Figure 9-27.
A. Holding the clean fan filter in place, place the fan filter and fan filter retainer
against the fan.
B. Press on the top of the fan filter retainer until the grip snaps into place over the
fan.
C. Press on the sides of the fan filter retainer until the grips on each side of the fan
filter retainer snap into place over the fan.
D. Press on the bottom of the fan filter retainer until the grip snaps into place over
the fan.

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Figure 9-25. Removing the Fan Filter and Filter Retainer
Grip the bottom edge of the fan

filter retainer and pull it toward
you until the bottom grip releases.
Grip the right edge of the fan filter

retainer and pull it toward you until
the right grip releases. Continue
gently pulling on the fan guard
until all grips have been released.
Fan Filter and Filter Retainer

Removed
Figure 9-25. Removing the Fan Filter and Filter Retainer

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Figure 9-26. Remove Dirty Filter from Fan Filter Retainer
Lift the Fan Filter

from the Fan Guard
Figure 9-26. Remove Dirty Filter from Fan Filter Retainer

8. Repeat Step 3 through Step 7 for each fan on each of the 8-pack assemblies.
9. Turn on power to the Infinity system.
10. Verify that each of the fans are functioning by placing your hand against the fan
filter and feeling that air is flowing into the fan or by placing a sheet of paper against
each fan and verifying that the paper sticks to the fan indicating proper air flow.
Important Check the airflow on each fan one fan at a time. Do not leave the paper on the fans.
This completes the cleaning/replacement of the fan filters for the unit. Cepheid
recommends that the dirty filters be cleaned and stored until the next fan filter cleaning.
See Section 9.7.3, Cleaning Fan Filters.
9.7.3 Cleaning Fan Filters

To clean the dirty fan filters, gently brush the filters with a dry lint-free wipe to remove
dust, wash the dirty fan filters in water and then place them between two lint-free wipes
to dry. After the filters are dry, save them to use when you replace the fan filters again.
Caution
Never wash the fan filters and then put them back onto the system immediately. The fan
filters must be completely dry before installing them onto the system.

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Figure 9-27. Installing the Fan Filter and Guard
Hold the filter inside the fan filter

retainer and place the fan filter retainer
against the fan.
Press the top of the fan filter retainer

until the grip snaps into place on the
fan.
Press the sides of the fan filter retainer

until the side grips snap into place on the
fan.
Press the bottom of the fan filter

retainer until the grip snaps into place
on the fan.
Figure 9-27. Installing the Fan Filter and Guard

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9.8 Cleaning the Cartridge Bays and Plunger Rods

Clean and disinfect the cartridge bays and plunger rods quarterly (every three months),
in the event of a spill or if a negative control yields a positive result.
Before cleaning the plunger rods and cartridge bays, read Section 9.3, Guidelines for
Cleaning and Disinfecting.
• A final concentration of 1:10 dilution of household chlorine bleach (used within 1
day of preparation)
Perform the bleach wipe-down three separate times on the interior surfaces of the cartridge
bay, allowing the bleach to remain on the surfaces for two minutes after each wipe. After the
Important
final two minutes, remove the bleach residue by thoroughly wiping the cartridge bay and
plunger rod with ethanol.

methanol)
• Soft lint-free wipes
Caution
Do not use 70% isopropanol alcohol for cleaning the cartridge bay and plunger rod.
Isopropanol alcohol can degrade plastics.
• Eye protection
Biological Risks
Wear disposable gloves, eye protection and other personal protective equipment (PPE)
mandated by your institution’s safety policies while performing this cleaning procedure.
Wearing PPE prevents exposure to chemical and biologically hazardous materials.
Important No tests can be running in the GeneXpert Infinity system during these procedures.
Caution
Do not sit or lean on any part of the instrument while cleaning.
To clean the cartridge bays and plunger rods:

1. If cartridges are in the modules, remove them through the Pause function (see
Section 10.9.12.2). Ensure that all removed cartridges are scanned out of the system.
Figure 9-28). The Maintenance Menu is displayed. See Figure 9-29.
3. Select the GX MAINTENANCE button (see Figure 9-29). The GX Maintenance menu

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The GX Maintenance button will not be available (grayed out) if there are any cartridges inside any
Note
of the modules or if there are unavailable modules.


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Figure 9-30. GX Maintenance Menu

Figure 9-31. Plunger Rod Maintenance Workspace

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4. Select the PLUNGER ROD MAINTENANCE button (see Figure 9-30). The Plunger Rod
Maintenance workspace is displayed. See Figure 9-31.
Note For efficient cleaning of the cartridge bays and plunger rods, clean them in groups of four modules.
5. In the Plunger Rod Maintenance workspace, select the check box that is adjacent to
each module you want to clean the plunger on. See Figure 9-31. You can select the
modules one-by-one, or select a large number of modules by selecting one of the
following buttons at the bottom of the Plunger Maintenance workspace:
• SELECT ALL – Selects all of the modules in the system.
• SELECT HIGHLIGHTED – Selects the modules you highlighted.
You can also hold the Shift or Ctrl keys to highlight continuous and discontinuous multiple modules
Note
in the Plunger Maintenance workspace.
After selecting tests in the Plunger Rod Maintenance workspace, select one of the
following buttons to deselect some or all modules:
• DESELECT ALL – Clears all of the module selections in the window.
• DESELECT HIGHLIGHTED – Clear the modules you highlighted.
6. Select the CLEAN button (see Figure 9-31). The second Plunger Rod Maintenance
workspace is displayed along with instructions. See Figure 9-32.
7. Verify that the modules selected are correct (see Figure 9-32).
8. Open the glass doors and open the module doors to clean the plungers for each
selected module. Remove any cartridges present in the modules.
9. Select the CONTINUE button. The screen shown in Figure 9-33 will be displayed
while the plungers are lowered. After the plungers have been lowered, the screen
will automatically change to the screen shown in Figure 9-34.
The plunger rod(s) in the selected module(s) are lowered into the cartridge bay(s)
(see Figure 9-35) and the glass doors unlatch for access to the module(s).

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Figure 9-33. Plunger Rod Maintenance Workspace Indicating Plungers Being Lowered
Figure 9-33. Plunger Rod Maintenance Workspace Indicating Plungers Being Lowered

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Figure 9-35. Plunger Rod Lowered into Cartridge Bay
Cartridge Bay
Plunger Rod (Lowered)
Slit for I-CORE Module
Instrument Module Door (Opened)
Figure 9-35. Plunger Rod Lowered into Cartridge Bay

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Caution
Getting liquid inside the I-CORE module can damage the module. Do not touch the slit on the
I-CORE module where the cartridge reaction tube is inserted. See Figure 9-35.
Caution
Do not allow the bleach solution to remain on any surface for more than eight minutes.
Perform the bleach wipe-down three separate times on the interior surfaces of the cartridge
bay, allowing the bleach to remain on the surfaces for two minutes after each wipe. After the
Important
final two minutes, remove the bleach residue by thoroughly wiping the cartridge bay and
plunger rod with ethanol.
10. Working with a set of four modules, clean each cartridge bay and plunger rod as
follows:
A. Thoroughly moisten a lint-free wipe with a 1:10 solution of household chlorine
bleach.
B. Vigorously wipe the plunger rod with the lint-free wipe. Wipe hard enough to
remove the black debris that accumulates on the plunger rod.
Using the same lint-free wipe, wipe the walls, ceiling, corners and edges of the
cartridge bay, then wipe the inside of the door and the top lip of the door and
discard the lint-free wipe
C. Wait 2 minutes after wiping with the bleach solution.
D. Using another new lint-free wipe thoroughly moistened with the 1:10 bleach
solution, wipe the plunger rod, walls, ceiling, corners and edges of the cartridge
bay. Wipe the inside of the door and the top lip of the door and discard the lint-
free wipe.
E. Wait 2 minutes after wiping with the bleach solution.
F. Using another new lint-free wipe thoroughly moistened with the 1:10 bleach
solution, wipe the plunger rod, walls, ceiling, corners and edges of the cartridge
bay. Wipe the inside of the door and the top lip of the door and discard the lint-
free wipe.
G. Wait 2 minutes after wiping with the bleach solution.
H. Thoroughly moisten a lint-free wipe with the 70% ethanol solution.
I. Use the lint-free wipe with the 70% ethanol solution to remove all residual
bleach. Wipe the plunger rod, walls, ceiling, corners and edges of the cartridge
bay, then wipe the inside of the door and the top lip of the door and discard the
lint-free wipe. Use a fresh lint-free wipe for each module. This ethanol “rinse”
is necessary to remove residual bleach solution which can harm the instrument
materials.
J. Repeat Step A through Step I for the next group of four modules until all
modules have been cleaned.

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11. Close all of the module doors.

12. Close the glass doors.
Figure 9-36. Plunger Rod Maintenance Workspace - Completed
Figure 9-36. Plunger Rod Maintenance Workspace - Completed

Figure 9-37. Plunger Rod Maintenance Workspace Indicating Plungers Being Raised
Figure 9-37. Plunger Rod Maintenance Workspace Indicating Plungers Being Raised

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Figure 9-38. Plunger Rod Maintenance Workspace Indicating Completion of Maintenance
Figure 9-38. Plunger Rod Maintenance Workspace Indicating Completion of Maintenance

13. In the Plunger Rod Maintenance workspace, select the COMPLETED button (see
Figure 9-34). The plunger rod(s) move back up to their normal position. The screen
shown in Figure 9-37 is displayed while the plungers are being raised. After the
plunger rod(s) have been raised, the Plunger Rod Maintenance workspace will
indicate that maintenance has been completed (see Figure 9-38).
14. Select the OK button (see Figure 9-38). The initial Plunger Rod Maintenance
This completes the procedures for cleaning the cartridge bays and plunger rods.

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9.9 Replacing the Waste Container Bag

Replace the waste container bag of cartridges whenever the bag is full or as needed.
• Eye protection
• Heavy-duty 4.2-mil plastic bag – 50 bags per package (Cepheid Part No. 300-9639)
or equivalent 4.2-mil biohazard bag
Warning
A bag filled with cartridges is very heavy (approximately 17 kg (38 lbs.)). Use proper lifting
techniques when lifting the waste container and bags with cartridges.
by your institution’s safety policies while replacing the waste container bag. Wearing
personal protective equipment prevents exposure to chemical and biological hazardous
materials.
9.9.1 Replacing the Waste Container Bag of Cartridges

The system will provide a warning when the Waste Container Almost Full Cartridge Count
reaches the specified number of cartridges. The default value for the Waste Container
Almost Full Cartridge Count is 350 cartridges. This value is set in the Automation
Configuration workspace (see Section 2.8.). The system will stop processing when the
cartridge count is 400 cartridges.
The Infinity system can process tests while you empty the waste container; however, it is
Note
recommended that you do not empty the waste container while testing is in progress.
To remove the waste container:

1. On the dashboard, select the Waste Container icon (see Figure 9-39). The Waste
Container workspace is displayed showing the Disposed Cartridge Count. See
Figure 9-40.
2. Select the UNLATCH DOOR button (see Figure 9-40). A progress bar may be
displayed briefly and then a second Waste Container workspace is displayed with
instructions to empty the waste container. See Figure 9-41.
The system unlocks the waste access door and the waste access door workspace is
displayed (see Figure 9-41). Also, the Waste Container Unlock icon is displayed in
the dashboard of the workspace.
Select the CLOSE button if you do not want to empty the waste container.
3. Follow the instructions provided in the workspace (see Figure 9-41) to open the
access door and empty the waste container.

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Waste Container Icon

Figure 9-40. Waste Container Workspace

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Figure 9-41. Waste Container Workspace – Open Waste Container Door
Waste Container Unlock Icon
Figure 9-41. Waste Container Workspace – Open Waste Container Door

Figure 9-42. Waste Container Workspace – Empty Waste Container and Close Waste Container Door
Figure 9-42. Waste Container Workspace – Empty Waste Container and Close Waste Container Door

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4. Empty the waste container.

A. Open the access door (see Figure 9-43A). The Waste Container workspace
changes to the workspace shown in Figure 9-42.
B. Grab the handle of the waste container and remove it from the container
housing until it is resting on the floor. See Figure 9-43B and Figure 9-43C.
C. Grab the other handle of the waste container and carefully lift it away from the
system. See Figure 9-43D.
D. Remove the waste container bag from the waste container and dispose of the
bag of used cartridges.
Biological Risks
Remove the waste container bag carefully to avoid puncturing of the bag by the cartridges. If
the bag punctures, liquid from the cartridges may leak.
Biological specimens, transfer devices, and used cartridges should be considered capable
of transmitting infectious agents requiring standard precautions. Follow your institution’s
Biological Risks
environmental waste procedures for proper disposal of used cartridges and unused
reagents. These materials may exhibit characteristics of chemical hazardous waste requiring
specific disposal. If country or regional regulations do not provide clear direction on proper
disposal, biological specimens and used cartridges should be disposed per WHO [World
Health Organization] medical waste handling and disposal guidelines.
Warning
A bag filled with cartridges is very heavy (approximately 17 kg (38 lbs.)). Use proper lifting
techniques when lifting the waste container and bags with cartridges.
Caution
Be careful not to damage the metal latch that protrudes from the door while removing the
waste container. See Figure 9-46.

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Figure 9-43. Removing the Waste Container
A B
C D
Figure 9-43. Removing the Waste Container

5. Inspect inside of the waste container. It should not contain liquids and should not be
damaged or worn. If it does contain liquids or is damaged, it must be replaced. See
Section 9.9.2 for instructions to assemble the waste container box.

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6. Obtain a new waste container bag and place it into the waste container:
A. Place the bag into the waste container. See Figure 9-44A.
B. Push the bottom of the bag to the bottom of the waste container. See
Figure 9-44B.
C. Fold the top of the waste container bag over each of the four corners of the
container. See Figure 9-44C.
Smooth the waste container bag against all four inner walls of the waste container. Any
Important
bulges in the bag may be detected as an overflow by the waste container overflow sensor.
Figure 9-44. Placing the Bag into the Waste Container
C
Figure 9-44. Placing the Bag into the Waste Container

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7. Place the waste container back into its housing with the FRONT label facing forward.
See Figure 9-45.
8. Slide the waste container all the way back against the back wall so that the container
breaks the optical beam.
The waste container must break the beam in order for the system to detect that the container is in
Note
place.
9. Close the waste access door. The Waste Container workspace empty confirmation
screen is displayed. See Figure 9-47.
10. Select the YES button (see Figure 9-47). The waste container workspace shows the
Disposed Cartridge count in the container reset to zero. See Figure 9-48.
Caution Do not indicate that the waste container is empty if it contains cartridges. The waste container
counter must match the quantity of cartridges in the waste container. Failure to maintain the correct
count will cause damage to the instrument and may cause chemicals and biological materials to be
spilled inside the instrument if the waste container overflows.
11. Select the CLOSE button to close the Waste Container workspace. See Figure 9-48.
This completes the replacement of the waste container bag.
Figure 9-45. Installing the Waste Container
FRONT Facing
Forward
Figure 9-45. Installing the Waste Container

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Figure 9-46. Metal Latch on Waste Container Door
Do Not Damage
Metal Door Latch
Figure 9-46. Metal Latch on Waste Container Door

Figure 9-47. Waste Container Workspace Empty Confirmation Screen
Figure 9-47. Waste Container Workspace Empty Confirmation Screen

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Figure 9-48. Waste Container Workspace Showing Cartridge Count Reset to Zero
Figure 9-48. Waste Container Workspace Showing Cartridge Count Reset to Zero
9.9.2 Assembling the Waste Container

The waste container is part of a Waste Container 10-Pack Kit (Part No.300-9520). The
cardboard waste container has to be assembled before it can be used.
The kit contains the following items shown in Figure 9-49 and Table 9-2:

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Figure 9-49. Waste Container Kit
1 2 3
Figure 9-49. Waste Container Kit
Table 9-2. Contents of Waste Container Kit
Item No. Description Quantity

1 Handle 10
2 Absorbent Sheet 10
3 Waste Container Box 10

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To assemble the waste container:

1. Open the box (Part No. 300-9520) that contains the waste container boxes and other
components. See Figure 9-50A.
2. Take one of the folded waste containers out of the box. See Figure 9-50B.
3. Open up the waste container and set it on the floor. See Figure 9-50C and
Figure 9-50D.
Figure 9-50. Assembling the Waste Container (Part 1)
A B
C D
4. Press on the bottom of the waste container until it is flat on the floor.
5. Take an absorbent sheet from the box and place it on the bottom of the waste
container box. See Figure 9-51A. Ensure it is covers the bottom of the waste
container box.

302-1288, Rev. A April 2019
A B
C D
6. Open the transparent plastic bag that contains the handles and remove two handle
pieces from the bag. See Figure 9-51B. The outside handle piece contains the handle
and the inside handle piece screws onto the front handle piece through round hole in
the box.
7. Attach one handle to the front of the waste container box (see Figure 9-51C) and one
handle to the back of the waste container box (see Figure 9-51D) by inserting the
outer handle piece into the inner handle piece and screwing the inner handle piece
into the outer handle piece.
This completes the assembly of the waste container box.

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9.10 Checking and Replacing Batteries in the Keyboard

and Mouse
Occasionally, the batteries will need to be replaced in the wireless keyboard and mouse.
The keyboard has up to three years of battery life and the mouse has up to one year of
life. This section provides information about checking the battery levels in both the
keyboard and mouse and also how to replace the battery in both these devices.
Your keyboard and mouse go into sleep mode after you stop using them for a few minutes. This
Note feature helps limit battery usage and eliminates the need to keep switching your devices on and off.
Both your keyboard and mouse are up and running immediately once you begin using them again.
9.10.1 Checking Battery Levels in the Keyboard and Mouse

9.10.1.1 Checking the Keyboard Battery Level
Press and hold the function (FN) key, then press the F12 key. If the battery LED glows
green, the batteries are good. If the LED glows red, the battery level has dropped to 10%
and you have only a few days of battery power left. You can also turn the keyboard off
then back on using the On/Off switch on top of the keyboard (See Figure 9-52).
Figure 9-52. Keyboard (Partial) Showing the Function Keys and the Battery Level LED
Battery LED
Figure 9-52. Keyboard (Partial) Showing the Function Keys and the Battery Level LED

302-1288, Rev. A April 2019
9.10.1.2 Checking the Mouse Battery Level

Using Figure 9-53 as a guide, turn the mouse off, then back on, using the On/Off switch
on the bottom of the mouse, while observing the LED on the top of the mouse. If the
LED glows green for 10 seconds, the battery is good. If the LED blinks red, the battery
level has dropped to 10% and you have only a few days of battery power left.
Figure 9-53. Mouse, Top and Bottom Views
Mouse On/Off Switch
Mouse LED
Figure 9-53. Mouse, Top and Bottom Views
9.10.2 Replacing Batteries in the Keyboard and Mouse

9.10.2.1 Replacing the Keyboard Batteries
The batteries in the keyboard will need to be replaced occasionally. The batteries are a
AA-size alkaline (Duracell Alkaline LR6 1.5v, or equivalent). There are two batteries per
keyboard. The batteries can be obtained commercially.
The batteries should be changed every three years or if the battery LED glows red when
the battery check is performed, indicating that the batteries need to be replaced. Both
batteries (2) be replaced at the same time in the keyboard. Figure 9-54 shows the battery
locations.

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To replace the batteries in the keyboard:

1. Obtain the two replacement batteries.
2. Turn the keyboard over, with the bottom facing up. Use your fingers to open the
battery compartment door (see Figure 9-54).
Figure 9-54. Keyboard Battery Compartment, Opened
Keyboard Batteries (2)
Battery Compartment Door
Figure 9-54. Keyboard Battery Compartment, Opened

3. Remove the old batteries.
4. Insert the new batteries into the keyboard, observing the correct polarity.
5. Reinstall the battery compartment door.
6. Test the batteries by performing the battery check in Section 9.10.1.1.
7. Dispose of the old batteries according to your institution’s policies and procedures
for hazardous waste.
This completes the replacement of the keyboard batteries.
9.10.2.2 Replacing the Mouse Battery

The battery in the mouse will need to be replaced occasionally. The battery is a AA-size
alkaline (Duracell Alkaline LR6 1.5v, or equivalent). The battery can be obtained
commercially.
The battery should be changed every year, or if the battery LED blinks red when the
battery check is performed, indicating that the battery needs to be replaced. See
Figure 9-55 shows the battery location.
To replace the battery in the mouse:
1. Obtain the replacement battery.
2. Turn the mouse over, with the bottom facing up. Use your fingers to slide open the
battery compartment (see Figure 9-55).

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Figure 9-55. Mouse Battery Compartment, Opened
Battery Compartment
Door being Opened
Press and Slide to Open

Battery Compartment
Mouse Battery
Figure 9-55. Mouse Battery Compartment, Opened

3. Remove the old battery.
4. Insert the battery into the mouse, observing the correct polarity.
5. Slide the battery compartment door closed, until it latches.
6. Test the battery by performing the battery check in Section 9.10.1.2.
7. Dispose of the old battery according to your institution’s policies and procedures for
hazardous waste.
This completes the replacement of the mouse battery.

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9.11 Annual Instrument Maintenance

Calibration of the GeneXpert instrument is not required during the initial system setup.
Cepheid performs all of the necessary calibrations before the system is shipped.
However, Cepheid recommends that the system be checked for proper calibration on an
annual basis from the point of initial use. Based upon the usage and care of each system,
calibration checks may be recommended more frequently. The system is designed to
measure module performance with the internal assay controls. In the event of a module
replacement, the replacement module provided will have been calibrated prior to
shipment.
A GeneXpert operator or Field Service Engineer with Administrator user permissions
can perform calibration checks during annual maintenance. Contact Cepheid Technical
Support for information about calibration checks. See the Technical Assistance section in
the Preface for contact information.
9.12 Generating Reports for Troubleshooting

There are reports that can be generated for troubleshooting the GeneXpert Infinity
system. These reports are:
• Module Report
• System Log Report
9.12.1 Module Report

No tests can be running in the GeneXpert Infinity system when generating the Module
Important
Report.
Cepheid Technical Support may ask you to use the Module Report feature when
investigating the source of possible calibration-related problems. It provides calibration
information and other data. See Figure 9-60.
To view the Module Report:
The GX MAINTENANCE button will not be available (grayed out) if there are any cartridges inside
Note
any of the modules or if there are unavailable modules.
2. In the Maintenance menu, select the GX MAINTENANCE button (see Figure 9-57).
The GX Maintenance menu is displayed. See Figure 9-58.
3. In the GX Maintenance menu, select the MODULE REPORT button (see Figure 9-58).
The Module Report is displayed in Adobe Reader. See Figure 9-58. The PDF file
can be printed and saved from the Adobe Reader software. See Figure 9-60 for an
example of a printed Module Report.

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4. After viewing and/or saving the Module Report, select the BACK button to close the
GX Maintenance menu. See Figure 9-58. The Maintenance menu is displayed.

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5. Select the BACK button to close the Maintenance menu (see Figure 9-57). The
Xpertise Main Software Home workspace is displayed. See Figure 9-56.
This completes the Module Report.
Figure 9-59. Module Report Shown in Adobe Reader
Figure 9-59. Module Report Shown in Adobe Reader

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Figure 9-60. Module Report Example (Page 1 Shown)
GeneXpert PC 03/05/19 14:23:47
Module Report
Instrument S/N: 805034
Module Module I-CORE Gateway Ambient I-CORE

Name S/N S/N S/N Temp (º C) Starts
Since Cal
A1 642969 546456 712374 28.2 112
Reporter Name Calibration Status Concentration

TxR Valid 400
Alx532 Valid 200
CF1 Valid 800
Alx647 Valid 200
FAM-2 Valid 300
CF6 Valid 400

Since Cal
A2 642999 546462 712374 28.7 112

TxR Valid 400
Alx532 Valid 200
CF1 Valid 800
Alx647 Valid 200
FAM-2 Valid 300
CF6 Valid 400

Since Cal
A3 643030 546464 712374 28.6 111

TxR Valid 400
Alx532 Valid 200
CF1 Valid 800
Alx647 Valid 200
FAM-2 Valid 300
CF6 Valid 400
GeneXpert® Infinity Xpertise Software Version 6.8 Page 1 of 6
Figure 9-60. Module Report Example (Page 1 Shown)

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9.12.2 System Log Report

You can use the System Log report to review self-test data and system errors that may be
related to a module failure. The System Log report will provide a detailed list of all
errors that have been logged for each module in the system.
To view and generate a System Log Report:
2. In the Maintenance menu, select the SYSTEM LOG button (see Figure 9-57). The
System Log Report workspace is displayed. See Figure 9-61.
Figure 9-61. System Log Report Workspace
Figure 9-61. System Log Report Workspace

3. Specify the following criteria to view the trends you want to include in the report:
You can select the individual tests one-by-one, or select a large number of tests by
selecting one of the following buttons at the bottom of the Archive Test workspace:
• Date Range:
• All – Select to include all dates. This is the default option.
• Select – Select to filter the records by specifying a range of dates. Entries
older than 1 year are automatically deleted from the system.

302-1288, Rev. A April 2019
• Modules:
• Currently Connected Modules – Displays modules that are connected to the
system. This is the default option.
• All Logged Modules – Displays all modules which have self-test or error
entries in the system database within the last 1 year. This allows Technical
Support to obtain self-test/error entries for a module that is no longer
connected to the system.
• Select Modules from Table – A list of modules is displayed in the table.
Select the module(s) to be included in the System Log Report. Select the
individual modules one-by-one by checking the boxes in the Select column
or by using one of the following buttons:
• SELECT ALL – Selects every module in the table by checking all of the
check boxes.
• SELECT HIGHLIGHTED – Selects the module(s) you highlighted.
You can also hold the Shift or Ctrl keys to highlight continuous and discontinuous modules in the
Note
System Log Report workspace.
After selecting modules in the System Log Report workspace, select one of
the following buttons to deselect some or all tests:
• DESELECT ALL – Deselects all of the module selections in the window
by unchecking all of the check boxes.
• DESELECT HIGHLIGHTED – De-selects the modules you highlighted by
unchecking the check boxes.
• Show:
• Errors Only – Displays only error entries in the report.
• All Entries – Displays all self-test entries and error entries in the report.
4. When you finish selecting the log criteria, select one or both of the following
buttons:
specify.
Select the GENERATE REPORT FILE button on the System Log Report
workspace (see Figure 9-61) to create the PDF file of the report. The Generate
Report File dialog box is displayed (see Figure 9-63), which enables you to
save the file to a specified location.
Note The default location for saving the Control Trend Report is the report folder.

302-1288, April 2019
window. You can save and print the PDF file from the Reader software. See
Figure 9-62.
• Select the CLOSE button if you do not wish to generate a system log report.
5. After viewing and/or saving the System Log Report, select the CLOSE button to
close the System Log Report workspace (see Figure 9-61). The Maintenance menu
This completes the generation of the System Log Report.
Figure 9-62. System Log Report Shown in Adobe Reader
Figure 9-62. System Log Report Shown in Adobe Reader

302-1288, Rev. A April 2019

302-1288, April 2019
Figure 9-64. System Log Report Example (Page 1)
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302-1288, Rev. A April 2019
9.13 Performing a Manual Self-Test

Important No tests can be running in the GeneXpert Infinity system when performing a manual self-test.
The GeneXpert Infinity system automatically performs a self-test during startup.

However, you can initiate a self-test manually on any of the modules to reset and check
for hardware failures.
To start the self-test:
The GX Maintenance button will not be available (grayed out) if there are any cartridges inside any
Note
of the modules or if there are unavailable modules.
3. In the GX Maintenance menu, select the PERFORM SELF-TEST button (see
Figure 9-58). The Perform Self-Test workspace is displayed. See Figure 9-65.
4. Select the check box that is adjacent to each module you want to perform self-test
on. See Figure 9-65. You can select the modules one-by-one, or select a large
number of modules by selecting one of the following buttons at the bottom of the
Perform Self Test workspace:
• SELECT ALL – Selects all of the modules in the table.
• SELECT HIGHLIGHTED – Selects the modules you highlighted.
You can also hold the Shift or Ctrl keys to highlight continuous and discontinuous multiple modules
Note
in the Perform Self Test workspace.
After selecting modules in the Perform Self Test workspace, select one of the
following buttons to deselect some or all modules, if needed:
• DESELECT ALL – Clears all of the module selections in the window.
• DESELECT HIGHLIGHTED – Clears the modules you highlighted.
5. Select the SELF-TEST button. The self-test begins and the modules being tested are
shown in green with a status of Self-Test.
When the self-test finishes, the software changes the status to Available, indicating
the self-test passed. If the message indicates the self-test failed, contact Cepheid
Technical Support. See the Technical Assistance section in the Preface for the
contact information.
Select the CLOSE button if you do not wish to perform a self-test of the system
modules.

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Figure 9-65. Perform Self-Test Workspace
Figure 9-65. Perform Self-Test Workspace

Figure 9-66. Perform Self-Test Workspace During Test
Figure 9-66. Perform Self-Test Workspace During Test

6. After completion of the self-test, select the CLOSE button to close the Perform Self-
Test workspace (see Figure 9-66). The GX Maintenance menu is displayed. See
Figure 9-58.

302-1288, Rev. A April 2019
7. Select the BACK button to close the GX Maintenance menu. See Figure 9-58. The
Maintenance menu is displayed.
This completes the Perform Self-Test procedure.
9.14 Excluding Modules from Test

Use the Exclude Modules From Test workspace to prevent one or more modules from
being used for testing.
Modules that are excluded will be listed as Disabled in the Module Status section of the
workspace, and will not be used by the system to run tests.
To exclude modules from testing:
1. In the Xpertise Software Home workspace (see Figure 9-56), select the
MAINTENANCE button. The Maintenance menu is displayed. See Figure 9-57.
3. In the GX Maintenance menu, select the EXCLUDE MODULES FROM TEST button
(see Figure 9-58) to display the Exclude Modules From Test workspace. See
Figure 9-67.
Figure 9-67. Exclude Modules From Test Workspace

302-1288, April 2019

4. In the Exclude Modules From Test workspace, select the EDIT button (see
Figure 9-67). The Exclude Modules From Test workspace is now activated and may
be edited as shown in Figure 9-68.
5. By default, no modules are excluded. To exclude a module, select the check box
adjacent to the module in the Module Name column. To select more than one module
or a large number of modules, select the following:
• SELECT ALL – Selects all modules in the system.
• DESELECT ALL – Deselects all modules in the system.
• SELECT HIGHLIGHTED – Highlight modules you want to exclude and then select
the SELECT HIGHLIGHTED button.
• DESELECT HIGHLIGHTED – Highlight modules you want to include for testing
and then select the DESELECT HIGHLIGHTED button.
6. After selecting or deselecting modules in the Exclude Modules From Test
workspace, select the SAVE button to save the changes (see Figure 9-68) or select the
CANCEL button to cancel changes.
Any modules that have been disabled will be highlighted in yellow in the Exclude
Modules From Test workspace and in the Module Status section of the workspace.
See Figure 9-69.

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Figure 9-69. Exclude Modules From Test Workspace Showing Disabled Modules
Figure 9-69. Exclude Modules From Test Workspace Showing Disabled Modules
To re-enable modules, follow the same procedure except uncheck the module check
boxes and select SAVE.
9.15 Repairing the System

Warning
Do not attempt to open or remove the instrument covers. Doing so can expose you to
electrical hazards resulting in injuries or death.
Warning
Do not attempt to open or remove the system covers. Do not attempt to modify or repair the
system. Improper repairs and incorrect part replacements can cause injury, damage the
system and void your warranty.
Note The user can open the glass doors for cleaning and maintenance.
To protect your warranty and for proper operation, the GeneXpert Infinity system should
be serviced only by an authorized Cepheid representative. If the system is not working
correctly, call Cepheid Technical Support. See the Technical Assistance section in the
Preface for contact information. When you call Cepheid Technical Support, be prepared
to supply the serial number of your system. You can find the serial number label on the
side of the monitor for all Infinity systems. See Section 8.1 for specific serial number
label locations.

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9.16 Hardware Problems

Table 9-3 lists the possible hardware problems you might encounter. To contact Cepheid
Technical Support, see the Technical Assistance section in the Preface for contact
information.
Table 9-3. Hardware Problems
Problem Possible Causes Possible Solutions

The system does not start. • The instrument is not connected • Check the instrument power
to the power outlet or UPS. connections.
• UPS failure. • Check that the UPS is ON. Press
the UPS power button.
• Check that the circuit breaker in
the facility’s electrical box is ON.
If the error persists, call Cepheid
Technical Support.
The system started up in Manual • System may have been set to 1. Confirm operation mode is set to
Mode instead of Automation Mode. operate in Manual mode. Automation mode.
• One or more glass doors are 2. Check that all glass doors are
open. closed and securely latched.
Confirm that they cannot be
pulled open.
3. Restart the system, waiting two
minutes before logging into
Windows. See Section 2.12 for
instructions.
Technical Support.
Module not detected. • Network cable not connected. • Restart the system waiting two
• Computer not recognized. minutes before logging into
• IP Config. is incorrect Windows. See Section 2.12 for
instructions.
• Check the IP Config. Correct, if
necessary.
• Verify that all circuit breakers on
the rear panel are in the ON
position.
Technical Support.
Kiosk Barcode scanner failure. • Symbology used for Patient ID 1. Cepheid supports Code 39,
and Sample ID unsupported. Codabar, Code 128 (A, B and C)
• Scanner barcode cable not linear barcode symbologies and
plugged in. Interleaved 2 of 5.
• Cartridge barcode label 2. Restart the system waiting two
damaged. minutes before logging into
Windows. See Section 2.12 for
instructions.
Technical Support.

302-1288, Rev. A April 2019
Table 9-3. Hardware Problems (Continued)
Problem Possible Causes Possible Solutions

The cartridge is stuck inside the Module mechanical failure. 1. Perform a manual self-test. See
GeneXpert Module. Section 9.13.
2. Perform Plunger Maintenance, if
possible. See Section 9.8.
If the cartridge is still stuck or if the
error persists, call Cepheid Technical
Support.
The instrument module red light is Module mechanical failure. 1. Confirm no cartridge is in the
flashing. module.
2. Perform a manual self-test. See
Section 9.13.
3. Review the message log for any
error messages and refer to the
error message troubleshooting
section in this chapter.
If the error recurs, call Cepheid
Technical Support.
Report is not printed when test is • System configuration is not set to Check:
completed. print after test completes. • System configuration selected to
• Printer off line. print at end of test. See
• Printer out of paper and/or toner. Section 2.7.1.
• Printer on-line.
• Paper present.
• Toner OK.
Order Test button not active. • No user is logged in. 1. Check that you are logged in.
• Waste container full. 2. Empty waste container.
• Modules not available. 3. Check Module Status
• Module not calibrated for workspace.
reporters used in assay.
4. Calibrate system.
Unable to start test. Reporters out of calibration. 5. Check that reporters are present
for the assay in the Module
Report.
9.17 Error Messages

This section lists the error messages and provides possible causes and solutions. The
error messages are grouped into the following categories:
• Section 9.17.1, Run-time Errors – Errors that occurred during a test that has not been
aborted.
• Section 9.17.2, Operation Terminated Errors – Errors that aborted a test.
• Section 9.17.3, Cartridge Loading Errors – Errors that occurred while loading a
cartridge.
• Section 9.17.4, Self-Test Errors – Errors that occurred during a manual self-test or
during the self-test at start-up.

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• Section 9.17.5, Post-Run Amplification Curve Analysis Errors – Errors that

occurred during the data reduction process.
• Section 9.17.6, Automation Errors – Errors that occurred in the Infinity automation
system.
All of the errors are displayed in the Message Log workspace. See Figure 9-70. The
following buttons are available in the Message Log workspace:
window. You can save and print the PDF file from the Reader software. See
Figure 9-71.
• Select the CLOSE button if you do not wish to generate a system log report and
close the Message Log workspace.
Figure 9-70. Message Log Workspace Showing Messages
Select to Expand and Collapse the

Message Log
Figure 9-70. Message Log Workspace Showing Messages

302-1288, Rev. A April 2019
Figure 9-71. Message Log Report in Adobe Reader
Figure 9-71. Message Log Report in Adobe Reader

Details for test-specific errors are also shown in the Error tab of the View Results
workspace. See Figure 9-72. If the system is displaying an error message, have the error
message information available when contacting Cepheid Technical Support.
Figure 9-72. View Results Workspace – Errors Tab Showing Error Messages
Figure 9-72. View Results Workspace – Errors Tab Showing Error Messages

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9.17.1 Run-time Errors

Table 9-4 lists errors that might appear during a test that has not been aborted. Although
the system was able to finish the test and save the results, some non-critical errors
occurred and require your attention. These error messages appear in the Error tab of the
View Results workspace. See Figure 9-72. To contact Cepheid Technical Support, see the
Technical Assistance section in the Preface for contact information. If the system is
displaying an error message, have the error message information available when
contacting Cepheid Technical Support.
Table 9-4. Run-time Error Codes
Error
Code Error Message Possible Causes Possible Solution(s)
1001 The actual temperature n °C has A heater component or a related 1. Rerun the test in the same
drifted too far away from the component failed. module to determine if the
setpoint of m °C. problem is in the module.
(n and m are temperature values 2. If the error recurs, rerun the
that the software displays. The test in a different module to
values can vary.) determine if the problem is in
the test or test procedures.
Technical Support.
1002 The temperature difference of n The difference between the 1. Rerun the test in the same
°C exceeds the limit of m °C. The temperatures of the two module to determine if the
temperatures for heaters A and B thermistors has exceeded the problem is in the module.
are p °C and q °C. acceptable difference of 5 °C. 2. If the error recurs, rerun the
(n, m, p, and q are temperature test in a different module to
values that the software displays. determine if the problem is in
The values can vary.) the test or test procedures.
Technical Support.
1004 The internal instrument One or more of the following Check the following:
temperature n °C was out of might have caused the error: 1. The laboratory environmental
range of m1 °C to m2 °C. • The ambient temperature is conditions meet the
(n, m1, and m2 are temperature not within the required requirements specified in
values that the software displays. range. Chapter 4.
The values can vary.) • The environmental 2. Check that all fans are clean
conditions do not meet the and operating.
requirements. If the instrument meets all the
• The ambient temperature requirements and the error
sensor failed. persists, call Cepheid Technical
• Broken or dirty fan(s). Support.
1005 Optic signal of n from detector One or more of the following Rerun the test using a different
#m using LED #p exceeded the might have caused the error: cartridge.
limit of q. • The signal from the reporter If the error recurs, call Cepheid
(n, m, p, and q are values that is too high. Technical Support.
the software displays. The values • A hardware component
can vary.) failed.

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Table 9-4. Run-time Error Codes (Continued)
Error
1006 Detector #n dark signal of m The detector or the electronics Call Cepheid Technical Support.
exceeded the limit of p. failed.
(n, m, and p are values that the
software displays. The values
can vary.)
1007 The n V power supply was The power supply voltage is out Call Cepheid Technical Support.
detected to be m V. of range.
(n and m are voltage values that
the software displays. The values
can vary.)
1011 The actual time nnn ms taken to The detector or the electronics Call Cepheid Technical Support.
read the optics was longer than 2 failed.
seconds.
1017 The measured temperature of One or more of the following Rerun the test using a different
the optical system was n °C might have caused the error: cartridge.
which was not within the • The optical block thermistor If the error recurs, call Cepheid
acceptable range of m1 °C to m2 failed. Technical Support.
°C.
• The ambient temperature is
(n, m1, and m2 are temperature too high.
values that the software displays.
The values can vary.)
1018 A valve positioning error of n A valve component failed. 1. Perform self-test.
count(s) was detected at the end 2. Rerun the test. Use a new
of the run. cartridge or follow the retest
(n is a value that the software procedure in the package
displays. The value can vary.) insert.
Technical Support.
1032 Module [site name] cannot start One or more of the following Check the following:
test due to internal temperature might have caused the error: 1. The laboratory environmental
at f.f degree C above threshold of • The ambient temperature is conditions meet the
f.f at [date]. not within the required requirements specified in
(f.f, are temperature values that range. Chapter 4.
the software displays. The values • The environmental 2. Check that all fans are clean
can vary. Site name can vary.) conditions do not meet the and operating.
requirements. If the instrument meets all the
• The ambient temperature requirements and the error
sensor failed. persists, call Cepheid Technical
• Broken or dirty fan(s). Support.
1035 Module [site name]: Requires The module has had too many Run plunger rod maintenance. See
Cleaning (nn tests since syringe test starts since the last plunger Section 9.8.
was last cleaned). rod maintenance. If the error recurs, call Cepheid
(nn is a values indicating number Technical Support.
of test starts. The value can vary.
Site name can vary.)

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Table 9-4. Run-time Error Codes (Continued)
Error
1096 Proceeded to Next Step #1: n, m, Assay specific cause. This code For more information on the code
p, q. is reported as maximum number (message) contact
(n, m, p and q values are assay- pressure was reached in the Cepheid Technical Support.
specific) assay. The high pressure leads
the program to move to the next
step. This will not influence the
performance of the assay or the
assay result.
1097 Proceeded to Next Step #2: n, m, Assay-specific cause. For more information on the code
p, q. number (message) contact
(n, m, p and q values are assay- Cepheid Technical Support.
specific)
1098 Proceeded to Next Step #3: n, m, ADF-specific cause, used during Rerun the test.
p, q. assay development only. If the error recurs, call Cepheid
(n, m, p and q values are assay- Reported as “Proceeded to Next Technical Support.
specific) Step” in assay results stream.
1125 Possible Insufficient Volume Possible insufficient volume. Rerun the test.
Error: n, m, p, q. If the error recurs, call Cepheid
(n, m, p and q values are assay- Technical Support.
specific)

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9.17.2 Operation Terminated Errors

Table 9-5 lists errors that might appear during a test that is aborted. The operation
terminated error messages appear in the Error tab of the View Results workspace. See
Figure 9-72. To contact Cepheid Technical Support, see the Technical Assistance section
in the Preface for contact information. If the system is displaying an error message, have
the error message information available when contacting Cepheid Technical Support.
Table 9-5. Operation Terminated Error Codes
Error
2003 Module is already running a test Software communication failed. Call Cepheid Technical Support.
with ID n while performing
command ID.
(n is an ID number that the
software displays. The number
can vary.)
2005 Motion of the syringe drive was • A syringe stall was detected Try one or more of the following
not detected. Detected motion (module issue. solutions:
started at position n ul and • Cartridge issue (Note if there • Use a new cartridge.
transferred m ul at valve position is a time-sequence ‘pattern’ • Restart the system. See
p with pressure q PSI. for the error). Section 2.12 for instructions.
(n, m, p, and q are values that • Cartridge lid was not • Check for crystallization in the
the software displays. The values opened. module and if required clean
can vary.) module per Operation Manual
instructions. Monitor for one
weak after cleaning.
• If cartridge suspected, then
note the Assay Name,
Cartridge Serial Number, and
Cartridge Lot Number.
Technical Support.
2006 Valve motion was not detected. One or more of the following Try one or more of the following
Valve started at position n. Last causes might have caused the solutions:
detected at position m. error: • Rerun the test. Use a new
(n and m are values that the • The valve drive failed. cartridge or follow the retest
software displays. The values • Improper interface between procedure in the package
can vary.) cartridge and valve body. insert.
• Perform self-test, if possible.
See Section 9.13.
Technical Support.

302-1288, April 2019
Table 9-5. Operation Terminated Error Codes (Continued)
Error
2008 Syringe pressure reading of n One or more of the following Try one or more of the following
PSI exceeds the protocol limit of causes might have caused the solutions:
m PSI, command #. error: • Retest sample per the
(n and m are pressure values • The filter is clogged by package insert using a new
that the software displays. The debris in sample. cartridge.
values can vary; the command • Pressure sensor failed. • Run a new cartridge with
line number in the ADF is matrix only [no patient sample
displayed.).) added](e.g., add to cartridge
only
• ‘Sample Reagent’ or ‘Samples
Transport Medium’ - if
applicable).
Technical Support. If possible, note
the Assay Name, Cartridge Lot
Number, Sample Type, Cartridge
Serial Number and Collection
information for troubleshooting.
2009 Syringe pressure reading of n The filter is clogged. Try one or more of the following
PSI is below the protocol limit of solutions:
m PSI, command #. • Rerun the test. Use a new
(n and m are pressure values cartridge or follow the retest
that the software displays. The procedure in the package
values can vary; the command insert.
line number in the ADF is • Run a cartridge containing
displayed.).) buffer only.
Technical Support.
2011 Unable to initialize pressure Unable to tune the force sensor Try one or more of the following
sensor to nnn. Sensor value of during the pre-cartridge load solutions:
nnn was obtained. operation. Possible cause is • Restart the test.
(nnn is the pressure value that force sensor is broken.
• Rerun the test using a new
the software displays. The value cartridge.
can vary.) If the error persists, call Cepheid
Technical Support.
2012 An inaccurate valve move to A component of the valve drive Rerun the test. Use a new
position n was detected. The failed. cartridge or follow the retest
valve was detected to stop at procedure in the package insert.
position m. If the error persists, call Cepheid
(n and m are values that the Technical Support.
can vary.)

302-1288, Rev. A April 2019
Error
2014 The digital temperature reading The heater A / heater B / Check the following:
of n for Thermistor A / Thermistor module’s optical block thermistor • Check that all fans are clean
B / Ambient Thermistor / Optic failed. and operating.
Thermistor was not within the
• The ambient temperature
acceptable range of m1 to m2.
• The laboratory environmental
(n, m1, and m2 are temperature conditions meet the
values that the software displays. requirements specified in
The values can vary.) Chapter 4.
If the ambient and internal
temperatures are within the
acceptable range and you continue
to see the error message, call
Cepheid Technical Support.
2016 The system was unable to find The valve position sensor failed. • Perform a self-test, if possible.
the valve home position. • Call Cepheid Technical
Support.
2017 The door latch sensor is still on One or more of the following Perform a self-test, if possible.
after a cartridge eject operation. might have caused the error: If the error persists, call Cepheid
• A syringe component failed. Technical Support.
• The door or a related
component failed.
• The door sensor failed.
2022 Failed to get to desired Environmental temperature is Check the following:
temperature of n °C. The above or below the acceptable • Check that all fans are clean
temperature reached m °C. range. and operating.
(n and m are temperature values • The ambient temperature
that the software displays. The • The laboratory environmental
values can vary.) conditions meet the
requirements specified in
Chapter 4.
2024 An ultrasonic horn failure The ultrasonic horn failed. Perform a self-test, if possible.
occurred with n% duty cycle, m If the error persists, call Cepheid
Hz and actual p% amplitude. Technical Support.
Setpoint amplitude was q%.
(n, m, p, and q are values that
can vary.)
2026 The ultrasonic horn current was The ultrasonic horn failed. Perform a self-test, if possible.
detected to be out of the normal If the error persists, call Cepheid
range. Technical Support.

302-1288, April 2019
Error
2032 The ultrasonic horn could not be The ultrasonic horn failed. Rerun the test. Use a new
tuned properly. The tuning cartridge or follow the retest
frequency value was n Hz. procedure in the package insert.
(n is a value the software If the error persists, call Cepheid
displays. The value can vary.) Technical Support.
2034 The optical signal from Detector One or more of the following Rerun the test. Use a new
n / LED n did not reach the might have caused the error: cartridge or follow the retest
expected value. Expected • The LED is not working. procedure in the package insert.
value=m, Actual value=p. If the error persists, call Cepheid
• The detector is not working.
(n, m, and p are values that the • The associated circuit is Technical Support.
software displays. The values experiencing problems.
can vary.)
2035 An ultrasonic failure occurred One or more of the following Clean the module surface and/or
with n% duty cycle, m Hz and might have caused the error: use a new cartridge. See
actual p% amplitude. Setpoint • Cartridge issue Section 9.8.
amplitude was q%. If the problem persists, call
• Dirt on the horn surface
(n, m, p, and q are values that • The ultrasonic horn failed. Cepheid Technical Support.
can vary.)
2096 ADF-specific Termination Error ADF-specific cause. Sample Rerun the test. Ensure correct
#1: n, m, p, q. volume related. sample volume added to new
(n, m, p and q values are assay- Refer to Package Insert for detail cartridge.
specific) of error. In some cases the issue Call Cepheid Technical Support. If
is: possible, note the following
• Cartridge-related information for troubleshooting:
Assay Name, Cartridge Lot,
• Pressure sensor failure
Cartridge Serial Number and
Module Serial Number(s) for the
error(s).
2097 ADF-specific Termination Error ADF-specific cause. Sample Rerun the test. Ensure correct
#2: n, m, p, q. volume related. sample volume added to new
(n, m, p and q values are assay- Refer to Package Insert for detail cartridge.
specific) of error. In some cases, the issue Call Cepheid Technical Support. If
is: possible, note the following
• Cartridge-related information for troubleshooting:
error(s).
2098 ADF-specific Termination Error ADF-specific cause, used during Rerun the test.
#3: n, m, p, q. assay development only. If the error recurs, call Cepheid
(n, m, p and q values are assay- Reported as “FatalCmd” in assay Technical Support.
specific) results stream.

302-1288, Rev. A April 2019
Error
2120 Module X lost communication One or more of the following If the error recurs, restart the
while module was idle. might have caused the error: system. See Section 2.12 for
• Loose or faulty instructions.
communication cable If the error persists, call Cepheid
between the gateway board Technical Support.
and the module.
• Ethernet port on the
instrument.
• Ethernet cable between the
PC and the 8-pack.
• Network connections
disabled.
before module door was latched. might have caused the error: system. See Section 2.12 for
and the module.
instrument.
PC and the 8-pack.
disabled.
while starting test, test aborted. might have caused the error: system. See Section 2.12 for
and the module.
instrument.
PC and the 8-pack.
disabled.

302-1288, April 2019
Error
while test was running. might have caused the error: system. See Section 2.12 for
attempting recovery. • Loose or faulty instructions.
and the module.
instrument.
PC and the 8-pack.
disabled.
2124 Module X communication One or more of the following This message indicates that the
restored. might have caused the error: communication has been restored.
• Communication restored No action is required.
from loose or faulty If the error recurs, call Cepheid
communication cable Technical Support.
between the gateway board
and the module.
• Communication restored to
the Ethernet port on the
instrument.
• Communication restored to
the Ethernet cable between
the PC and the 8-pack.
2125 Termination Error – Insufficient Specified as a “Termination Error Ensure correct volume added to
Volume: n, m, p, q. – Insufficient Volume” in the cartridge. Retest sample per
(n, m, p and q values are assay- command sequence. Package Insert using new
specific) In some cases, the issue is: cartridge.
• Sample volume related Call Cepheid Technical Support. If
possible, note the following
information for troubleshooting:
error(s).
2126 Module X was reset. Communication failure. • Perform a self-test, if possible.
• Check the UPS to see if there
is an alarm condition.
• Restart system. See
Section 2.12.
If problem persists, call Cepheid
Technical Support.

302-1288, Rev. A April 2019
9.17.3 Cartridge Loading Errors

Table 9-6 lists errors that might appear during the cartridge loading process. The
cartridge loading error messages appear in the Message Log workspace. See Figure 9-70.
Because the software performs some self-test procedures during the loading process,
some of the error messages that appear during the loading process are identical to the
self-test error messages. See Section 9.17.4 for the list of those messages. To contact
Cepheid Technical Support, see the Technical Assistance section in the Preface for
contact information. If the system is displaying an error message, have the error message
information available when contacting Cepheid Technical Support.
Table 9-6. Cartridge Loading Error Codes
Error
2011 Unable to initialize pressure Unable to tune the force sensor If the error recurs, restart the
sensor to nnn. Sensor value of during pre-cartridge load system. See Section 2.12 for
nnn was obtained. operation. Possible cause is instructions.
(nnn is the pressure value that force sensor is broken. If the error persists, call Cepheid
the software displays. The value Technical Support.
can vary.)
2018 Attempt to load a cartridge while One of the following might have If the error recurs, restart the
the door is still closed. caused the error: system. See Section 2.12 for
• The valve motor failed. instructions.
• A syringe component failed. If the error persists, call Cepheid
• The door latch sensor failed. Technical Support.
2025 One of the following messages is The plunger components or the To determine if the error is caused
displayed: force sensor failed. by a failed instrument module or a
• The system failed to find the bad cartridge:
plunger home position. 1. If the error recurs, restart the
Plunger moved down test using the same cartridge
looking for ADC = n. ADC but load it into a different
value m was detected and instrument module. If the test
stall occurred. progresses successfully in the
• The system failed to find the new module, the previous
plunger home position. module requires repair. Call
Upward move with minimum Cepheid Technical Support.
force value of n was 2. If the error occurs in the
completed without reaching second instrument module,
force value less than m. restart the test using a new
(n and m are values that the cartridge and load it into the
software displays. The original module. If the test
values can vary.) progresses successfully, the
previous cartridge was bad.
Technical Support.

302-1288, April 2019
Table 9-6. Cartridge Loading Error Codes (Continued)
Error
2037 The cartridge integrity test failed One of the following might have 1. Remove the cartridge and
at valve position <n>. The caused the error: inspect it for damage.
pressure change of f.ff PSI did • The reaction tube is missing 2. Rerun the test using a new
not exceed the requirement of f.ff from the cartridge. cartridge.
PSI. The pressure increased Call Cepheid Technical Support. If
• The cartridge has been
from f.ff PSI to f.ff PSI during the possible, note the Assay Name,
damaged.
test. Cartridge Lot Number, Cartridge
• The cartridge integrity test
failed. Serial Number and Module Serial
Number(s) for the error(s).
• Pressure sensor failure.
9.17.4 Self-Test Errors

Table 9-7 lists errors that might appear during the self-test process. The self-test error
messages appear in the Check Status window. See Figure 9-70. To contact Cepheid
Technical Support, see the Technical Assistance section in the Preface for contact
information. If the system is displaying an error message, have the error message
information available when contacting Cepheid Technical Support.
Table 9-7. Self-Test Error Codes
Error
4001 A problem with the memory of A hardware component failed. Restart the system. See
the I-CORE was detected. Section 2.12 for instructions.
Technical Support.
4002 A problem with the main memory A hardware component failed. Restart the system. See
of the GeneXpert Module was Section 2.12 for instructions.
detected. If the error recurs, call Cepheid
Technical Support.
4003 A problem of the ultrasonic horn The ultrasonic drive circuitry Restart the system. See
system was detected. failed. Section 2.12 for instructions.
Technical Support.
4004 Valve motion was not detected at • A cartridge is ajar in the 1. Remove the cartridge and
position <m> during move <n>. module during self-test. place it into the module again.
(where <m> is the valve position • A component of the valve 2. Perform a self-test, if
at which the valve is stuck and drive failed. possible. See Section 9.13.
<n> is the move number (0 or 1)
3. Remove any cartridges from
that failed to move during valve
the module and restart the
self-test.).
system.
Technical Support.

302-1288, Rev. A April 2019
Table 9-7. Self-Test Error Codes (Continued)
Error
4006 Syringe drive movement was not The stall sensor failed during Restart the system. See
detected. cartridge loading because: Section 2.12 for instructions.
• The cartridge was not If the error recurs, call Cepheid
positioned correctly. Technical Support.
• A component of the syringe
drive failed.
4008 The n-V power supply was The power supply has failed. • Restart the system. See
detected to be m V. Section 2.12 for instructions.
(n and m are voltage values that • Check the UPS to see if there
the software displays. The is an alarm condition
values can vary.) If the error recurs, call Cepheid
Technical Support.
4009 Heater A operation was not A heater A component failed. Check the following:
verified. Measured temperature • Check that all fans are clean
changed from n °C to m °C. and operating.
values can vary.) conditions meet the
Chapter 4.
4010 Cooling fan operation was not A cooling component failed. Check the following:
of n °C exceeded the limit of m and operating.
°C.
• The ambient temperature
(n and m are temperature values • The laboratory environmental
that the software displays. The conditions meet the
values can vary.) requirements specified in
Chapter 4.
4011 The reported dark value of n for The module door was not closed Perform self-test, if possible.
detector m was too high. completely, or a hardware If the error persists, call Cepheid
(n and m are values that the component failed. Technical Support.
can vary.

302-1288, April 2019
Error
4012 Heater B operation was not A heater B component failed. Check the following:
changed from n °C to m °C. and operating.
value can vary.) conditions meet the
Chapter 4.
4013 An inaccurate valve move was A valve error has occurred. 1. Remove any cartridge from
detected. The valve was the module.
programmed to stop at position n 2. Perform a self-test manually.
but stopped at position m. See Section 9.13.
(n and m are position values that If the error recurs, call Cepheid
the software displays. The Technical Support.
values can vary.)
4014 The optical signal from Detector An optics component failed. Rerun the test. Use a new
n/LED n did not reach the cartridge or follow the retest
expected value. Expected value procedure in the package insert.
= m, Actual value = p. Call Cepheid Technical Support.
(n, m, and p are optical signal
4015 The measured temperature of An optical block thermistor failed. 1. Perform a self-test. See
the optical system is n which was Section 9.13.
not within the acceptable range 2. Rerun the test. Use a new
of m1 to m2. cartridge or follow the retest
(n, m1, and m2 are temperature procedure in the package
values that the software displays. insert.
The values can vary.) Call Cepheid Technical Support.
4016 GeneXpert Module program 1. Possible RAM failure Restart the system. See
corruption. Unable to continue 2. Possible EMI Section 2.12 for instructions.
the test. If the error recurs, call Cepheid
3. Firmware defect
Technical Support.
4017 The digital temperature reading The heater A / heater B / If the error recurs, call Cepheid
of n for Thermistor A / Thermistor module’s optical block thermistor Technical Support.
B / Ambient Thermistor / Optic failed.
Thermistor was not within the
acceptable range of m1 to m2.
(n, m1, and m2 are temperature

302-1288, Rev. A April 2019
Error
4019 The optical ramp test for LED n LED is broken. Call Cepheid Technical Support.
resulted in non-monotonic
results at DAC setting of nnn.
The reference detector readings
were nnn and nnn.
9.17.5 Post-Run Amplification Curve Analysis Errors

Table 9-8 lists errors that might appear during the post-run analysis (data reduction)
process. The post-run analysis error messages appear in the Error tab of the View Results
workspace. See Figure 9-72. To contact Cepheid Technical Support, see the Technical
Assistance section in the Preface for contact information. If the system is displaying an
error message, have the error message information available when contacting Cepheid
Technical Support.
Table 9-8. Data Reduction Error Codes
Error
5001 Unable to verify positive analyte • Too much sample was Rerun the test using a new
[analyte name] using curve placed in the cartridge. cartridge and the correct amount of
fitting. f.ff value of <parameter • A component of the sample.
name> * cartridge is defective, If the error recurs, call Cepheid
* Note: With Error ‘5001’, the ‘Test causing the positive Technical Support. If possible, note
Result’ lists “Invalid” and not the word amplification curve to have the following information for
“Error”. an abnormal shape. troubleshooting: Assay Name,
Cartridge Lot Number, Cartridge
Serial Number and Module Serial
5002 Failed to verify valid amplification A component of the cartridge is Rerun the test using a new
curve for reporter. The shape defective, causing the positive cartridge and the correct amount of
factor of n was below the amplification curve to have an sample.
minimum of m. abnormal shape. If the error recurs, call Cepheid
(n and m are values that the Technical Support. If possible, note
software displays. The values the following information for
can vary.) * troubleshooting: Assay Name,
* Note: With Error ‘5002’, the ‘Test Cartridge Lot Number, Cartridge
Result’ lists “Invalid” and not the word Serial Number and Module Serial
“Error”. Number(s) for the error(s).

302-1288, April 2019
Table 9-8. Data Reduction Error Codes (Continued)
Error
curve for reporter. The shape defective, causing the positive cartridge and the correct amount of
factor of n was higher than the amplification curve to have an sample.
maximum of m. abnormal shape. If the error recurs, call Cepheid
curve for reporter. The defective, causing the positive cartridge and the correct amount of
normalized sum of errors of n amplification curve to have an sample.
was greater than the limit of m. abnormal shape. If the error recurs, call Cepheid
curve for reporter. The slope to defective, causing the positive cartridge and the correct amount of
vertical scaling ratio of n was amplification curve to have an sample.
higher than the limit of m. abnormal shape. If the error recurs, call Cepheid
* Note: With Error ‘5005, the ‘Test Cartridge Lot Number, Cartridge
5006 X probe check failed. Probe One or more of the following Check the following:
check value of n for reading might have caused the error: • Reagents are added to the
number m was above the • An incorrect amount of cartridge correctly.
maximum of p. reagent was inserted into • Cartridges were stored
(x is the analyte name, n, m, and the cartridge. correctly.
p are values that the software • The reagent is bad. Rerun the test using a new
displays. The values can vary.) • Fluid transfer failed. cartridge following the Package
• Something in the sample is Insert.
auto-fluorescing. If the error recurs, call Cepheid
• Module related. Technical Support. If possible, note
the following information for
troubleshooting: Assay Name,

302-1288, Rev. A April 2019
Error
check value of n for reading might have caused the error: • Reagents are added to the
number m was below the • An incorrect amount of cartridge correctly.
minimum of p. reagent was inserted into • Cartridges were stored
(x is the analyte name, n, m, and the cartridge. correctly.
p are values that the software • The reagent is defective. Rerun the test using a new
displays. The values can vary.) • Fluid transfer failed. cartridge following the Package
• Something in the sample is Insert.
auto-fluorescing. • If the error persistently recurs:
• The sample was processed Clean module using optical
incorrectly in the cartridge. brush (PN# 300-8330, Lens
• Module related (possibly Cleaning Brush). Refer to
dirty optics or calibration Section 9.4 within “Guidelines
issue. for Cleaning and Disinfecting”
or Package Insert for Xpert
• Sample-specific.
Check (301-4121 or
301-3985).
• If the error recurs, call
Cepheid Technical Support. If
possible, note the following
information for
troubleshooting: Assay Name,
Cartridge Lot Number,
Module Serial Number(s) for
the error(s).
check delta value n between might have caused the error: • Reagents are added to the
reading number m and reading • An incorrect amount of cartridge correctly.
number p was below the reagent was inserted into • Cartridges were stored
minimum of q. the cartridge. correctly.
(x is the analyte name, n, m, and • The reagent is bad. Rerun the test using a fresh
p are values that the software • Fluid transfer failed. sample and cartridge.
displays. The values can vary.)
Technical Support.
check delta value n between might have caused the error: • Reagents are added to the
reading number m and reading • An incorrect amount of cartridge correctly.
number p was above the reagent was inserted into • Cartridges were stored
maximum of q. the cartridge. correctly.
(x is the analyte name, n, m, and • The reagent is bad. Rerun the test using fresh
p are values that the software • Fluid transfer failed. cartridges.
displays. The values can vary.)
Technical Support.

302-1288, April 2019
Error
5010 Unable to verify positive analyte One or more of the following Check the following:
[analyte name] using curve might have caused the error: • Reagents are added to the
fitting. X readings were available, • An incorrect amount of cartridge correctly.
but the minimum number of reagent was inserted into • Cartridges were stored
readings required is Y. the cartridge. correctly.
• The reagent is bad. Rerun the test using fresh
• Fluid transfer failed. cartridges.
Technical Support.
5011 Signal loss detected in the Usually occurs when a Refer to Package Insert for specific
amplification curve for analyte fluorescent signal is so high that re-test procedures.
[analyte name]. f.f decrease in it bleeds into another channel, Rerun the test using a new
signal with f.f% decrease at cycle causing the second signal to go cartridge following the Package
n. into negative curve. Insert.
In addition, the error could be If the error recurs, call Cepheid
due to the following: Technical Support. If possible, note
• Sample related the following information for
• Module related troubleshooting: Assay Name,
• Cartridge related Cartridge Lot Number, Cartridge
5013 Quantitative value for analyte The base quantitative value or If the error recurs, call Cepheid
[analyte name] is beyond the quantitative value is too large to Technical Support.
upper calculation limit. represent using the Double type
in Java or Float type in database.
5014 Quantitative value for analyte The quantitative value is less If the error recurs, call Cepheid
[analyte name] is below the lower than 0.01. Technical Support.
calculation limit.
5015 Failed to verify valid background High slope in optical background Rerun the test using a new
slope for analyte [analyte name]. region. cartridge following the Package
The absolute value of f.f was Insert.
above the maximum of f.f. * If the error recurs, call Cepheid
* Note: With Error ‘5015’, the ‘Test Technical Support. If possible, note
Result’ lists “Invalid” and not the word the following information for
“Error”. troubleshooting: Assay Name,
5016 Failed to verify valid background High RMS error in background Rerun the test using a new
error for analyte [analyte name]. region. cartridge following the Package
The RMS error of f.f was above Insert.
the maximum of f.f. * If the error recurs, call Cepheid
* Note: With Error ‘5016’, the ‘Test Technical Support. If possible, note
Result’ lists “Invalid” and not the word the following information for
“Error”. troubleshooting: Assay Name,

302-1288, Rev. A April 2019
Error
5017 X probe check failed. Probe There is a problem with the Rerun the test using a new
check value of n for reading cartridge. cartridge following the Package
number m was below the valid • Cartridge issue. Insert.
level of p. If the error recurs, call Cepheid
• An incorrect amount of
reagent was inserted into Technical Support. If possible, note
the cartridge. the following information for
• The reagent is defective. troubleshooting: Assay Name,
• Fluid transfer failed.
• The sample was processed Number(s) for the error(s).
incorrectly in the cartridge.
5018 Failed o verify valid probe check There is a problem with the Rerun the test using fresh
ratio for analyte [analyte name]. cartridge. cartridges.
Probe check 1 = m, probe check If the error recurs, call Cepheid
2 = n, ratio = f.ff greater than Technical Support.
maximum f.ff.
5019 Failed o verify valid probe check There is a problem with the Rerun the test using fresh
ratio for analyte [analyte name]. cartridge. cartridges.
Probe check 1 = m, probe check If the error recurs, call Cepheid
2 = n, ratio = f.ff less than Technical Support.
minimum f.ff.
9.17.6 Automation Errors

The automation error messages are grouped according to subsystem. Table 9-9 lists the
automation subsystem error messages from the Xpertise software.
To contact Cepheid Technical Support, see the Technical Assistance section in the
Preface for contact information. If the system is displaying an error message, have the
error message information available when contacting Cepheid Technical Support.
Table 9-9. Automation Subsystem Error Codes
Error
Code Subsystem User Interface Message Possible Causes Possible Solution(s)
6001 Infinity Server Unable to Connect To • The embedded PC is Restart the system. See
Infinity Server not working. Section 2.12 for
• The Infinity server is instructions.
not running. Report error to Cepheid
Technical Support.
6002 Infinity Server Incorrect version of Infinity Software defect. Report error to Cepheid
Server. Technical Support.
Required version <m>.
Version found <n>.
(<m> is the expected
version number and <n> is
the version number found.)

302-1288, April 2019
Table 9-9. Automation Subsystem Error Codes (Continued)
Error
6003 Infinity Server Undefined action has been Improper or tampered Report error to Cepheid
requested. installation. Technical Support.
6004 Infinity Server Infinity Server configuration Improper or tampered Report error to Cepheid
error: <test from server>. installation. Technical Support.
6005 Infinity Server The system has attempted Software problem that Report error to Cepheid
to transfer a cartridge from issued a “put” or “get” Technical Support.
a non-existent location. command to a location that
does not exist.
6006 Infinity Server Unable to move Gantry or 1. Emergency stop is Check that the Emergency
Conveyor while Emergency detected while gantry Stop button is released.
Stop is activated. is moving. If the problem persists after
OR checking that the
2. A gantry command or emergency stop is
start conveyor released, restart the
command has been system.
issued while the If the problem still persists
system is in or recurs, report error to
emergency stop Cepheid Technical Support.
mode.
6011 Infinity Server Automation failed to Infinity server failed to Report error to Cepheid
respond to command. respond to command. Technical Support.
6101 Digital Infinity Device Network Device Network operation Restart the system. See
Controller failure. Automation is not interrupted. Section 2.12 for
available. instructions.
Report error to Cepheid
Technical Support.
6102 Digital Infinity Device Network Device Network operation Restart the system. See
Controller failed to initialize with the interrupted. Section 2.12 for
initialization state of <n>. instructions.
(Where <n> is the state of Report error to Cepheid
the controller) Technical Support.
6103 Digital Incorrect version of Device Improper or tampered Report error to Cepheid
Controller Network driver. installation. Technical Support.
Required version <m>.
Version found <n>.
(Where <m> is the
expected version number
and <n> is the version
number found.)
6104 DeviceNet Infinity DeviceNet fails to Device Network operation Restart the system. See
Controller operate. has failed to operate. Section 2.12 for
Node <x> has an error instructions.
code of <y> and a status Report error to Cepheid
value of <z>. Technical Support.
(Where <x> is the node
number, <y> is the error
code and <z> is the status.)

302-1288, Rev. A April 2019
Error
6151 Gantry Gantry control failed to Gantry controller failure Restart the system. See
Controller initialize. found during Infinity server Section 2.12 for
initialization. instructions.
Technical Support.
6153 Gantry Gantry controller Communication failure to Restart the system. See
Controller communication failure. the gantry controller. Section 2.12 for
instructions.
Technical Support.
6221 Glass Door Attempt to perform motion Software defect. Report error to Cepheid
related command while the Technical Support.
Glass Door is opened.
6263 Gantry Gantry <a> axis stalled. Gantry position has 1. Inspect the cartridge
(Where <a> is one axis with exceeded the limit during for the presence of
w, x, y, z, or a combination move or end of the move in additional labels. If the
of these axes.) the axis or axes shown in label is on the side of
the message. the cartridge, it must
• A label has been be removed and
placed incorrectly on placed on the front of
the side of the the cartridge.
cartridge and is 2. Visually check if the
interfering with the module door is
gripper. opened.
• Physical obstruction 3. Visually check if there
such as the module is a physical
door may be opened obstruction (cartridge
when it should not be. in gripper dragging
• Gantry hardware against bottom lip of
failure. module door, cable
loose or snagging)
that would prevent the
gantry from placing
the cartridge.
If the error persists, report
error to Cepheid Technical
Support.
6269 Gantry W/Z recovery failed. Both Z and W axes are Customer manually retracts
extended. W and Z.
W axis is trapped inside of Report the error to Cepheid
a door-hook. Technical Support.

302-1288, April 2019
Error
6281 Gripper Gripper failed to pick up • A label has been 1. Inspect the cartridge
cartridge at <a>. placed incorrectly on for the presence of
(Where <a> is a location> the side of the additional labels. If the
cartridge and is label is on the side of
interfering with the the cartridge, it must
gripper. be removed and
• After a Get command, placed on the front of
there is no cartridge in the cartridge.
the gripper. 2. Check to see where
• Possibly a gantry the cartridge is located
motor problem. (i.e. in gripper, on the
instrument floor or not
present (user has
manually removed the
cartridge)).
6282 Gripper Gripper sensor failure. • A label has been 1. Inspect the cartridge
placed incorrectly on for the presence of
the side of the additional labels. If the
• Possible sensor or placed on the front of
gripper failure. the cartridge.
2. Follow prompt
message in the failure
handling.
Report the error to Cepheid
Technical Support.
6283 Gripper Invalid gripper command. Software defect. Check to see where the
Cannot pick up a cartridge cartridge is located (i.e. in
while already holding one gripper, on the instrument
or cannot release one when floor or not present (user
no cartridge is in gripper. has manually removed the
cartridge)).
6284 Gripper Gripper failure. • A label has been 1. Inspect the cartridge
placed incorrectly on for the presence of
the side of the additional labels. If the
• Gripper failed status placed on the front of
check. the cartridge.
2. Visually inspect the
gripper.
3. Restart the system.
See Section 2.12 for
instructions.

302-1288, Rev. A April 2019
Error
6341 Gantry Gantry scanner unable to • Cartridge barcode 1. User visually checks if
Scanner scan barcode. unreadable or missing. the cartridge is in the
• Scanner has failed. expected location.
• Lobby mapping error. 2. User visually checks if
the cartridge barcode
print is damaged.
3. User visually checks
to see if the gantry
scanner is emitting a
red light.
Technical Support.
6342 Gantry Gantry scanner unable to Internal scanner, control Report the error to Cepheid
Scanner scan barcode. line to the scanner, or Technical Support.
communication for the
scanner failed.
6343 Gantry Gantry scanner server Gantry barcode scanner Restart the system. See
Scanner failure. server failure. Section 2.12 for
instructions.
Technical Support.
6344 Gantry Gantry scanner initialization Barcode mismatch during 1. Check if the barcode
Scanner failed. gantry scanner self-test. on the back wall near
the conveyor is
damaged.
instructions.
3. Check if the barcode
on the back wall near
the conveyor has any
spilled material and
clean barcode.
If the error persists, call
6345 Gantry Gantry scanner returned Invalid barcode on cartridge Repeat the test with
Scanner invalid cartridge serial (serial number has a non- another cartridge.
number. digit character). If the error persists, call

302-1288, April 2019
Error
6381 Shuttle Shuttle if busy. • Software detects that 1. Close shuttle door and
GET/PUT command is retry (if shuttle door is
issued for shuttle not closed, this error
location while shuttle is can be induced).
open, 2. If closing shuttle door
• Software detects that does not resolve the
“SHLatch Off” problem, contact
command is issued Cepheid Technical
while GET/PUT with Support.
shuttle location is in
progress.
6441 Kiosk Scanner Kiosk scanner server failed The kiosk scanner barcode Restart the system. See
to start. server didn’t start during the Section 2.12 for
software initialization. instructions.
6442 Kiosk Scanner Unable to connect to kiosk Connection to kiosk Restart the system. See
scanner server. barcode scanner server Section 2.12 for
failed. instructions.
6443 Kiosk Scanner Invalid response [<x>] to a Scanner server defect. 1. Rescan the cartridge.
scanner command.Where 2. Restart the system.
<x> is the response. See Section 2.12 for
instructions.
6444 Kiosk Scanner Scanner command [<x>] • Scanner is off-line. Restart the system. See
failed due to reason [<y>] • Scanner is not plugged Section 2.12 for
in. instructions.
• Scanner is not in If the error persists, call
SNAPI mode. Cepheid Technical Support.
6481 System Cartridge SN [<x>] A cartridge was manually Retrieve this Cartridge SN
encountered where removed from a location [<x>] using the Retrieve
cartridge SN [<y>] was within the instrument while Cartridge workspace. See
expected the glass doors were open. Section 10.14.
(where <x> and <y> are
cartridge serial numbers
6482 System Expected to find Cartridge A cartridge was manually • Retrieve this cartridge
SN [<x>] in removed from a location from the shuttle.
<location_name>. Location within the instrument while • Check for any cartridge
empty the glass doors were open. inside the instrument
(where <x> is the cartridge on the floor.
serial number)

302-1288, Rev. A April 2019
Error
6483 System Remove service pendant, Service pendant is still 1. Remove the pendant
or close Xpertise software inserted after servicing. and close the glass
doors.
instructions.
6484 System Unexpected cartridge found A cartridge was manually Follow the instructions in
in <location_name> placed at the location while the on-screen prompt.
the glass doors were open.
6485 System Error Latching module door, Module door cannot be Pause system, remove
Module: [X] and [Y]. latched after cartridge was cartridge and rescan for
The following test Cartridge put in when the system is new test run.
SN: [xxxxxxxxx] cannot run under automation/door
load. Sample ID: [xxxxxxxx] latch mode.
Patient ID [xxxxxxxxx].

302-1288, April 2019
9.18 Troubleshooting Host Connectivity

9.18.1 Host Connectivity Indication
When the Xpertise software starts, host connectivity is automatically established if it is
enabled. If, during the operation the host connectivity is interrupted, a Host is
disconnected at ... message is displayed in the Message Log workspace. See
Figure 9-73).
Contact your host administrator to re-establish the connection.
Figure 9-73. Message Log Workspace Showing Host Interface Disconnected
Figure 9-73. Message Log Workspace Showing Host Interface Disconnected
9.18.2 Host Communication Buffer

If the communication between the GeneXpert Infinity system and the host is slow, the
data may be filling up in the communication buffer. When the communication buffer is
at and above 75%, the system will stop uploading results and provide a warning to the
user in the Message Log.
A message will be displayed in the Upload Result workspace if the host connection has
not been established or if the communication buffer is full when the UPLOAD RESULT
button as been selected. See Figure 9-74.
Select the OK button to acknowledge the error message.

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Figure 9-74. Upload Result Workspace Showing Host Disconnected or Buffer Almost Full Error
Figure 9-74. Upload Result Workspace Showing Host Disconnected or Buffer Almost Full Error
9.19 Export Log Files

The Export Log File workspace allows you to export log files of the following types for
troubleshooting purposes:
• Application Log (default to be selected)
• Infinity Server Log (default to be selected)
To export log files:
2. Select the EXPORT LOG FILE button (see Figure 9-76). The Export Log File

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Figure 9-77. Export Log File Workspace

3. Enter the From and To dates under the date range in the Export Log File workspace
as shown in Figure 9-77.
4. In the Log File Types to Export area, select the log(s) you want to export
(Application Log and/or Infinity Server Log).
5. Select the EXPORT button (see Figure 9-77). An Export Log File screen, displaying a
progress bar, indicates the progress of the exporting of log files. See Figure 9-78.
When the exporting process of all log files for the selected time period is completed,
a confirmation screen appears. See Figure 9-79.
Select the CLOSE button if you do not want to export the data files.
The exported log files are stored at C:\GeneXpert\Support. This data allows customers to
send log files for further troubleshooting to Cepheid Technical Support. The files are
stored as zip folders which makes it easier for customers to send the data to Cepheid
Technical Support.

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Figure 9-78. Export Log File Workspace – Progress Bar
Figure 9-78. Export Log File Workspace – Progress Bar


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9.20 Export Host Settings

Use the Export Host Settings workspace to export the host settings as a .csv file and save
it to be restored at a later time, if needed. The .csv file can also be sent to Cepheid
Technical Support for troubleshooting, if needed.
To export host settings:
1. Log into the system as an administrator. See Figure 9-80.
3. Select the EXPORT HOST SETTINGS button (see Figure 9-81). The Export Host
Settings workspace is displayed. See Figure 9-82.
Figure 9-80. Xpertise Software Home Workspace – Administrative Level Login

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Figure 9-81. Maintenance Menu – Administrative Level Login
Figure 9-81. Maintenance Menu – Administrative Level Login


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4. In the Host Settings to Export area, select the setting(s) to be exported (Host
Communication Settings, Host Test Codes or both).
5. Select the EXPORT button (see Figure 9-82). An Export Host Settings workspace
will be displayed to select the location of the host settings file. See Figure 9-83. The
default location of the host settings file will be the export folder.
When the host settings file has been saved, the Export Host Settings workspace will
6. Select the CLOSE button. See Figure 9-82.
The exported host settings file is stored at C:\GeneXpert\export. This file can be opened
using either Apache OpenOffice or Microsoft Excel. For information about how to open
.csv files, see Appendix C, Viewing Export (.csv) Files,
Figure 9-83. Export Host Settings Workspace
Figure 9-83. Export Host Settings Workspace

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9.21 Clearing Failed Automation Locations

When there is an automation problem at a location, that location is no longer available
for new tests. Once the automation problem has been resolved for that location, use the
Automation Failed Location workspace to let the system know that the problem has been
cleared and the location may now be used again.
If there are failed locations, an Information workspace will be displayed indicating that
there are failed locations and that they are not available for use. See Figure 9-84. Select
the OK button to close the Information workspace. Use the Automation Failed workspace
to clear the problem. Only an administrator level user can access the Automation Failed
workspace.
Figure 9-84. Information Workspace Indicating Failed Automation Locations
Figure 9-84. Information Workspace Indicating Failed Automation Locations
Note The Automation Failed Location Workspace is only accessible to administrators.
9.21.1 Accessing the Automation Failed Workspace

To access the Automation Failed workspace:
1. Log into the system at an administrator level. See Figure 9-85. A module showing an
Automation Failed Location is also shown.
3. Select the AUTOMATION FAILED LOCATION button (see Figure 9-86). The
Automation Failed Location workspace is displayed. See Figure 9-87.

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Automation Failed Location

Figure 9-86. Maintenance Menu – – Administrative Level Login
Figure 9-86. Maintenance Menu – – Administrative Level Login

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Figure 9-87. Automation Failed Location Workspace Showing Panels
Clear Site Panel Failed Site Panel
Figure 9-87. Automation Failed Location Workspace Showing Panels

There are four tabs in the Automation Failed Location workspace. The four tabs are:
• Module tab: Displays the clear and failed GeneXpert modules in the system.
• Accumulator tab: Displays the clear and failed accumulator locations in the system.
• Shuttle tab: Displays the clear and failed shuttle locations in the system.
• Other Locations tab: Displays the clear and failed lobby location in the system.
Each tab displays two panels, with arrow buttons to move a selected item from one panel
to the other. See Figure 9-87. Each panel allows the user to select single items or
multiple items.
There are two panels in each tab:
• Clear Site: Displays a list of locations that are clear (available to use).
• Failed Site: Displays a list of locations that have failed (not available to use).

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9.21.2 Clear Failed Location – Accumulator, Shuttle and Lobby

This section describes how to clear a failed accumulator, shuttle or lobby location. The
procedure is the same for all three location failures.
In the case of a lobby failed location, exiting and restarting the Xpertise software will clear the lobby
Note
failed location.
1. Select the tab (Shuttle, Accumulator or Other) in the Automation Failed Location
workspace corresponding to the failed location (see Figure 9-88). The selected tab
displays a Clear Site panel and a Failed Site panel with left and right direction arrows
between them. For this example, select the Accumulator tab.
2. In the Automation Failed Location workspace (see Figure 9-88), select the EDIT
button to make changes in the workspace.
Select the CLOSE button to exit the workspace without making any changes.
3. In the Automation Failed Location workspace, select the failed site(s) in the Failed
Site panel and move them to the Clear Site panel by selecting the left direction arrow
If desired, more than one failed location can be selected to move to the Clear Site panel by
Note selecting the Ctrl or Shift key while selecting the sites to be moved. All selected sites will be moved
to the Clear Site panel when the left direction arrow is selected.
In the example shown in Figure 9-88, the failed accumulator location is site 12.
4. Select the SAVE button.
5. The system will display the selected sites one at a time for you to indicate if there is
a cartridge in the failed site.
If the site is empty, select the EMPTY button. See Figure 9-90. If EMPTY is selected,
the system will continue on to the next selected location.
or
If there is a cartridge in the failed location, select the HAS CARTRIDGE button. The
system will prompt you that the site will need to be cleared later and then continues
on to the next selected location. See Figure 9-91.

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Figure 9-88. Automation Failed Location Workspace Showing Accumulator Failed Site 12
Figure 9-88. Automation Failed Location Workspace Showing Accumulator Failed Site 12
Figure 9-89. Automation Failed Location Workspace
Figure 9-89. Automation Failed Location Workspace

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Figure 9-90. Clear Failed Location Workspace

Figure 9-91. Clear Failed Location Workspace with Instructions to Pause
Figure 9-91. Clear Failed Location Workspace with Instructions to Pause

6. Select the CONTINUE button (see Figure 9-91). The following workspace directs you
to select CONTINUE and then pause the system to remove the cartridge. See
Figure 9-92.

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Figure 9-92. Clear Failed Location Workspace with Continue Instructions
Figure 9-92. Clear Failed Location Workspace with Continue Instructions

7. Select the CONTINUE button in the Clear Failed Location workspace shown in
Figure 9-92.
8. Pause the system (see Section 10.9.12.2, Using Pause to Remove a Cartridge and
then Resume) and remove the cartridge(s) from the failed locations. Follow the
instructions in the workspace.
9. After cartridge(s) have been removed, return to the Automation Failed Location
workspace (see Figure 9-87), and repeat Step 1 through Step 5, selecting EMPTY.

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9.21.3 Clear Failed Location – Module

Caution
Failed module locations should only be cleared if the root cause of the failure has been identified
and corrected. Failure to identify and correct the root cause may result in recurrence of the failure,
equipment damage or loss of sample.
The system must be in Manual mode to clear a failed module location. See Section 5.6.2, Changing
Note
from Automation Mode to Manual Mode.
This section describes how to clear a failed module location.

1. Switch to Manual mode to clear the module. If you attempt to clear the failed
module while the system is in Automation mode, a message instructing you to
switch to Manual mode will be displayed. See Figure 9-93.
2. While the system is in Manual mode, navigate to the Clear Failed Location
workspace. See Section 9.21.1, Accessing the Automation Failed Workspace.
3. Select the Module tab in the Automation Failed Location workspace (see
Figure 9-94). The Module tab displays a Clear Site panel and a Failed Site panel with
left and right direction arrows between them.
4. In the Automation Failed Location workspace (see Figure 9-94), select the EDIT
button to make changes in the workspace.
Select the CLOSE button to exit the workspace without making any changes.
Figure 9-93. Clear Failed Location Workspace with Prompt to Switch to Manual Mode
Figure 9-93. Clear Failed Location Workspace with Prompt to Switch to Manual Mode

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Figure 9-94. Automation Failed Location Workspace Showing Module Failed Site D1

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5. In the Automation Failed Location workspace, select the failed module(s) in the
Failed Site panel and move them to the Clear Site panel by selecting the left direction
arrow button. See Figure 9-95.
If desired, more than one failed location can be selected to move to the Clear Site panel by
Note selecting the Ctrl or Shift key while selecting the sites to be moved. All selected sites will be moved
to the Clear Site panel when the left direction arrow is selected.
In the example shown in Figure 9-95, the failed module location is site D1.
6. Select the SAVE button.
7. The system will display the selected sites one at a time for you to indicate if there is
a cartridge in the failed site.
If the site is empty, select the EMPTY button. See Figure 9-96. If EMPTY is selected,
the system will continue on to the next selected location.
or
If there is a cartridge in the failed location, select the HAS CARTRIDGE button. The
system will prompt you that the site will need to remove the cartridge and then
continues on to the next selected location. See Figure 9-97.
8. Manually remove the cartridge from the module and select the CONTINUE button to
clear the failed location (see Figure 9-97). The system will continue to the next
selected location.
Caution
If cartridges are not removed, the system may encounter a collision when switched back to
Automation mode. Always remove the cartridges from the modules when prompted to do so.

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9. When all locations have been cleared, the Failed Site panel will be empty. See
Figure 9-98. Select the CLOSE button to close the Automation Failed Location
workspace.
Figure 9-97. Clear Failed Location Workspace – Remove Cartridge in Failed Module
Figure 9-97. Clear Failed Location Workspace – Remove Cartridge in Failed Module
10. Switch the system to Automation Mode. See Section 5.6.4, Changing from Manual
Mode to Automation Mode.
Figure 9-98. Automation Failed Location Workspace Showing No Failed Module Locations
Figure 9-98. Automation Failed Location Workspace Showing No Failed Module Locations

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9.22 Failure Handling

When the system encounters certain failures, the software will activate failure handling
procedures to maintain the system integrity. The audible alarm will be turned on if it is
enabled. Prompt messages will be shown to provide the failure information and guide
you with appropriate actions.
Depending on where the failure occurs, you may not be able to place new orders. See the
prompt message for details; however, tests that are already running in the GeneXpert
modules will continue and test results will be available.
9.22.1 Failure Locations

A location may be excluded from future operation until the failed condition has been
cleared and the system has been serviced. The affected location could be an accumulator
site, a GeneXpert module, the shuttle site or the lobby. See Section 9.21.2, Clear Failed
Location – Accumulator, Shuttle and Lobby, or Section 9.21.3, Clear Failed Location –
Module.
A warning message will be provided to notify the user that these locations are not
available due to a failed condition.
9.22.2 Return an Affected Cartridge

An affected cartridge may be rejected and returned to the accumulator or waste
container, depending on availability.
9.22.3 Disable New Test Orders

The software will stop accepting new test orders. The system is still fully functional.
9.22.4 Prompt User for Non-Accessible Module

If a cartridge cannot be removed from or put into a GeneXpert module, a message will
be displayed.
9.22.5 Prompts to Fix a Specific Failure

Follow the system prompts:
• Pause and then remove all cartridges from the conveyor
• Pause the system to remove a cartridge from the location indicated in the message

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9.22.6 Prompt User to Switch to Manual Mode or Reboot the

Instrument
You may need to switch to Manual mode operation to continue processing tests or to
reboot the instrument when tests are completed.
9.22.7 Prompt User to Contact Technical Support due to

Repetitive Failures
The system monitors for recurring failures and prompts you to contact Cepheid
Technical Support regarding the recurring failure condition.
9.22.8 Prompt for Technical Support

If there is no specific instruction, please contact Cepheid Technical Support regarding
the encountered failure conditions with details from the Message Log.
9.23 Decontamination for Shipping

Prior to shipping instrument components, ensure that they have been cleaned for the
removal of biohazards. Contact Cepheid Technical Support before shipping any system
components. Follow shipping regulations.
Follow the cleaning instructions described in the following sections, if possible.
• Section 9.4.1, Cleaning the Kiosk Table Top, Monitor, Mouse and Keyboard
• Section 9.5, Cleaning the Conveyor Belt
• Section 9.6, Vacuuming the Rear Fan Filters
• Section 9.8, Cleaning the Cartridge Bays and Plunger Rods

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10 Features and Functions
This chapter is organized to make it easy to look up all details about a particular feature
of the GeneXpert Infinity systems.
This chapter is organized as follows:
• Section 10.1, AC Power
• Section 10.2, Uninterruptible Power Source (UPS)
• Section 10.3, USB and Ethernet Ports
• Section 10.4, Computer Systems
• Section 10.5, Infinity Hardware Components
• Section 10.5.1, Conveyor
• Section 10.5.2, Kiosk Barcode Scanner
• Section 10.5.3, Lobby
• Section 10.5.4, GeneXpert Modules
• Section 10.5.5, Accumulator Shelves
• Section 10.5.6, Shuttle
• Section 10.5.7, Waste Disposal Shelf
• Section 10.5.8, Waste Container
• Section 10.5.9, Front Glass Doors
• Section 10.5.10, Robotic Gantry
• Section 10.5.11, EMERGENCY STOP Button
• Section 10.6, Software Modules
• Section 10.6.1, Cartridge Life Cycle
• Section 10.6.2, Assay Shelf Life
• Section 10.6.3, Infinity Scheduler
• Section 10.7, User Interface Conventions
• Section 10.7.1, Touchscreen User Interface Conventions
• Section 10.7.2, Access Windows Desktop
• Section 10.8, Overview of the Graphical User Interface

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Features and Functions
• Section 10.9, Dashboard Panel

• Section 10.9.1, Home Icon
• Section 10.9.2, Manage Host Orders Icon
• Section 10.9.3, Cartridge I/O Icon
• Section 10.9.4, View Outstanding Orders Icon
• Section 10.9.5, View Another Test Icon
• Section 10.9.6, Glass Doors Icons
• Section 10.9.7, Shuttle Open Icon
• Section 10.9.8, Database Alert Icon
• Section 10.9.9, Module Status Icon
• Section 10.9.10, Waste Container Capacity and Contents Icon
• Section 10.9.11, Silence Alarm Icon
• Section 10.9.12, Pause Icon
• Section 10.9.13, Manual Mode Icon
• Section 10.9.14, System Error Icon
• Section 10.10, Status Bar
• Section 10.11, Message Log
• Section 10.12, Menu Panel
• Section 10.12.1, ORDERS Menu Button
• Section 10.12.2, RESULTS Menu Button
• Section 10.12.3, DATA MANAGEMENT Menu Button
• Section 10.12.4, SETUP Menu Button
• Section 10.12.5, MAINTENANCE Menu Button
• Section 10.13, Workspace Panel
• Section 10.14, Retrieving Cartridges from the Accumulator
• Section 10.15, Removing a Cartridge That Has Not Been Ordered

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10.1 AC Power
The AC power switch is located on the lower right side of the GeneXpert Infinity system
(viewing from the front of the system). See Figure 10-1.
AC Power Switch

See Chapter 4, Performance Characteristics and Specifications for power specifications.
Cepheid supplies a 20 Amp power supply cord. To connect to AC power, follow the
instructions in Section 10.2, Uninterruptible Power Source (UPS).

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10.2 Uninterruptible Power Source (UPS)

The UPS provides brownout protection, transient suppression, and maintains power to
the system for a brief period of time (approximately 5 minutes) in case of AC power
loss. Specifications for UPS unit are shown in Section 4.2 and Section 4.3.
To use a UPS in different countries:
For North America Only

1. Plug the GeneXpert Infinity system into the UPS output as shown in Figure 10-2.
2. Using the supplied Cepheid P/N 100-4049 cable, plug the UPS input into a properly-
grounded 20 Amp wall outlet as shown in Figure 10-2.
For Other Countries

1. Plug the GeneXpert Infinity system into the UPS output as shown in Figure 10-2.
2. Using the supplied Cepheid P/N 100-4048 cable, plug the UPS input into a properly
grounded 20 Amp wall outlet as shown in Figure 10-2.
Figure 10-2. UPS Connection using Cepheid’s Supplied UPS Cables
UPS
AC Wall Receptacle
Cepheid P/N 100-4049
(for North America) Input
or

(for Europe/International)
GeneXpert Infinity Output
AC Power Cord
from Infinity
Figure 10-2. UPS Connection using Cepheid’s Supplied UPS Cables

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10.3 USB and Ethernet Ports

The Universal Serial Bus (USB) ports allow you to attach a printer and other accessories
to the kiosk computer. There are two ports located on the USB and Network Access
Panel, which is located on the rear, left side of the system. One of the USB ports
contains the wireless keyboard and mouse receiver and is not available for other devices.
See Figure 10-3. Two more USB ports are located on the left side of the kiosk computer
monitor. See Figure 10-4.
The LIS LAN Port is an Ethernet port that allows the GeneXpert Infinity system to be
connected to a host computer (LIS system). See Figure 10-3.
The Remote Diagnostic LAN port allows remote diagnostic connections to the Internet.
See Figure 10-3.
Figure 10-3. USB and Ethernet Ports
USB Port 1
USB Port 2 with Wireless

Keyboard and Mouse Receiver
LIS/LAN Port (Ethernet 1)
User Mode Dongle

(Cepheid P/N 700-3572)
Remote Diagnostics LAN

Port (Ethernet 2)
Figure 10-3. USB and Ethernet Ports
Caution
Do not unplug the wireless keyboard and mouse receiver from USB port 2. If the receiver is
unplugged, you will not be able to use the keyboard and mouse.

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Caution
Do not plug an external mouse connector into a USB port while the system is running.
Do not remove the user dongle shown in Figure 10-3. It must be inserted to operate the
Important
instrument.
Figure 10-4. USB Port Locations on Left Side of Monitor
USB Ports
Figure 10-4. USB Port Locations on Left Side of Monitor
10.4 Computer Systems

The GeneXpert Infinity systems have two built-in computers. The kiosk computer (or
PC) is the main user interface computer. See Figure 10-5. It runs the Xpertise software
that the operator uses. This computer has a touchscreen interface and is supplied with a
wireless mouse and keyboard. The second computer is an embedded computer that
controls the conveyor, gripper and gantry. See Figure 10-5. The two computers
communicate with each other through an Ethernet connection.
In addition to the two computers, there is also a separate controller for gantry operation.

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Figure 10-5. Kiosk Computer and Embedded Computer
Kiosk Computer
Embedded Computer
Figure 10-5. Kiosk Computer and Embedded Computer
Warning The computers shown in Figure 10-5 are inside the Infinity system and are not user-
accessible. Hazardous voltages are present behind the panels on the back of the Infinity
system and they must not be removed. Removal of the panels exposes the user to hazardous
voltages that can cause severe injury or death.
The monitor has a touchscreen display. See Figure 10-6. You may make selections either
via the touchscreen or by using the supplied mouse. The English-character keyboard is
used for data entry.
The wireless keyboard and mouse both require AA batteries. The batteries should be
replaced either periodically or when poor performance is observed. See Section 9.10 for
a procedure for testing and replacing the batteries. To save battery life, turn off the
wireless keyboard and mouse when not in use for long periods of time.

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Figure 10-6. Monitor, Mouse and Keyboard
Touchscreen Monitor
Wireless Mouse
Wireless Keyboard
Figure 10-6. Monitor, Mouse and Keyboard
10.5 Infinity Hardware Components

10.5.1 Conveyor
The conveyor stand houses the conveyor belt with an auto-sensor. The auto-sensor
detects when a cartridge has been placed into the load zone. See Figure 10-7.
After you order a test, the prepared cartridge is placed on the conveyor. The conveyor
belt moves the cartridge from the kiosk to the lobby. See Figure 10-8.
The conveyor belt moves whenever the beam is interrupted, such as when a cartridge is
placed on the conveyor belt.

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Figure 10-7. Conveyor and Other Components
Kiosk Barcode
Scanner
Conveyor Belt
Kiosk Table Top
Load Zone
Figure 10-7. Conveyor and Other Components
10.5.2 Kiosk Barcode Scanner

The kiosk barcode scanner, shown in Figure 10-7, is used to scan the Patient ID barcode
(optional), the specimen’s Sample ID barcode (optional) and the cartridge’s barcode data
into the system. All data is automatically entered into the appropriate fields during the
data entry process.

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10.5.3 Lobby
The lobby position, shown in Figure 10-8, is the transition location between the
conveyor and the gantry.
Figure 10-8. Lobby Position and Other Components
Shuttle Door
Shuttle
Conveyor Belt
Lobby Position
Waste Disposal
Shelf
Figure 10-8. Lobby Position and Other Components
10.5.4 GeneXpert Modules

Each panel contains eight GeneXpert modules. A sample-prepared cartridge is inserted
by the gantry into a GeneXpert module, where the sample is processed for detection of a
specific genetic sequence or organism.
Each GeneXpert module is a location where a test can be performed. The Infinity-48s
system can configured with up to 48 GeneXpert modules and the Infinity-80 system can
be configured with up to 80 GeneXpert modules.

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10.5.4.1 Eight-Pack Panel

An eight-pack panel consists of eight GeneXpert modules. Each eight-pack panel
provides communication interface between GeneXpert modules and the Xpertise
software. Figure 10-9 shows the eight-pack panel.
Figure 10-9. Eight-Pack Panel
Figure 10-9. Eight-Pack Panel
10.5.4.2 Module Names

Each GeneXpert module is identified with a letter followed by a number to indicate its
position within the system.
The arrangement of the lettering of the eight-pack panels is shown in Figure 10-10 for
the Infinity-48s and Figure 10-11 for the Infinity-80.
In Figure 10-10 (Infinity-48s) and in Figure 10-11 (Infinity-80), each block (A, B, C, etc.) represents
Note
four GeneXpert modules. Within each block, modules are labeled 1 through 4.

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Figure 10-10. Infinity-48s Module Locations
I1 I2 I3 I4 J1 J2 J3 J4 K1 K2 K3 K4 L1 L2 L3 L4
Bank #5 Bank #6
Modules 33 to 40 Modules 41 to 48
E1 E2 E3 E4 F1 F2 F3 F4 G1 G2 G3 G4 H1 H2 H3 H4
Bank #3 Bank #4
C1 C2 C3 C4 D1 D2 D3 D4
Bank #2
Modules 9 to 16
A1 A2 A3 A4 B1 B2 B3 B4
Bank #1
Modules 1 to 8
GeneXpert Infinity-48s Module Locations
Figure 10-10. Infinity-48s Module Locations

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Figure 10-11. Infinity-80 Module Locations
O1 O2 O3 O4 P1 P2 P3 P4 Q1 Q2 Q3 Q4 R1 R2 R3 R4 S1 S2 S3 S4 T1 T2 T3 T4
Bank #8 Bank #9 Bank #10

Modules 57 to 64 Modules 65 to 72 Modules 73 to 80
I1 I2 I3 I4 J1 J2 J3 J4 K1 K2 K3 K4 L1 L2 L3 L4 M1 M2 M3 M4 N1 N2 N3 N4

Bank #3 Bank #4
A1 A2 A3 A4 B1 B2 B3 B4 C1 C2 C3 C4 D1 D2 D3 D4
Bank #1 Bank #2
GeneXpert Infinity-80 Module Locations

Figure 10-11. Infinity-80 Module Locations
10.5.5 Accumulator Shelves

The accumulator shelves are waiting areas where:
• A cartridge waits to be loaded into a module when no module is available to run the
cartridge.
• A cartridge is retained after the test is completed, if the system is configured to retain
cartridges.
• A cartridge is temporarily held because it cannot be processed due to an unreadable
barcode or unrecognized cartridge serial number.
The accumulator site is a physical location located above each module. Each site can
store one cartridge.

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10.5.5.1 Infinity-48s Accumulator Shelves/Sites

The accumulator sites are numbered the same as the modules. On the Infinity-48s, site 1
is in the bottom left accumulator shelf and site 48 is in the top right accumulator shelf.
See Figure 10-12.
Figure 10-12. Infinity-48s Accumulator Shelf/Site Locations
Accumulator Slots 33 to 40 Accumulator Slots 41 to 48
I1 I2 I3 I4 J1 J2 J3 J4 K1 K2 K3 K4 L1 L2 L3 L4
Bank #5 Bank #6
Accumulator Slots 17 to 24 Accumulator Slots 25 to 32 Accumulator Shelf

and Site Locations
Bank #3 Bank #4
Accumulator Slots 9 to 16
C1 C2 C3 C4 D1 D2 D3 D4
Bank #2
Modules 9 to 16
Accumulator Slots 1 to 8
A1 A2 A3 A4 B1 B2 B3 B4
Bank #1
Modules 1 to 8
GeneXpert Infinity-48s Accumulator Locations
Figure 10-12. Infinity-48s Accumulator Shelf/Site Locations

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10.5.5.2 Infinity-80 Accumulator Shelves/Sites

The accumulator sites are numbered the same as the modules. On the Infinity-80, site 1
is in the bottom left accumulator shelf and site 80 is in the top right accumulator shelf.
See Figure 10-13.
Figure 10-13. Infinity-80 Accumulator Shelf/Site Locations
Accumulator Slots 57 to 64 Accumulator Slots 65 to 72 Accumulator Slots 73 to 80
O1 O2 O3 O4 P1 P2 P3 P4 Q1 Q2 Q3 Q4 R1 R2 R3 R4 S1 S2 S3 S4 T1 T2 T3 T4

Accumulator Slots 33 to 40 Accumulator Slots 41 to 48 Accumulator Slots 49 to 56 Accumulator
I1 I2 I3 I4 J1 J2 J3 J4 K1 K2 K3 K4 L1 L2 L3 L4 M1 M2 M3 M4 N1 N2 N3 N4
Shelf and Site
Locations
Bank #3 Bank #4
A1 A2 A3 A4 B1 B2 B3 B4 C1 C2 C3 C4 D1 D2 D3 D4
Bank #1 Bank #2
GeneXpert Infinity-80 Accumulator Locations
Figure 10-13. Infinity-80 Accumulator Shelf/Site Locations
10.5.6 Shuttle
The shuttle is the area where the system can dispense a used or rejected cartridge
through the Cartridge I/O workspace. See Figure 10-14. The shuttle can also be used to
submit STAT orders. See Figure 10-8 for a picture of the shuttle inside the system. This
area can be accessed by the operator. A sensor is present in the shuttle to detect and
indicate if any cartridges are present.
A user command at the user interface is required to unlatch the shuttle door so that the
cartridges can be inserted or removed.
Shuttle sites are physical locations within the shuttle. See Figure 10-15. Each shuttle site
can hold one cartridge. For each site, the cartridge is tracked via the cartridge serial
number.

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Figure 10-14. Shuttle Loading Drawer in Open Position
Shuttle Loading
Drawer (Open)
Figure 10-14. Shuttle Loading Drawer in Open Position

Figure 10-15. Shuttle Sites in the Loading Drawer
Site 1 Site 2 Site 3 Site 4
Shuttle Loading
Drawer (Closed)
Figure 10-15. Shuttle Sites in the Loading Drawer

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10.5.7 Waste Disposal Shelf

A cartridge is moved into the waste disposal shelf after a test is completed (if the
cartridge is not retained). See Figure 10-16. When this shelf is full, the next used
cartridge placed on the self pushes an older used cartridge into the waste container.
Figure 10-16. Waste Disposal Shelf
Used Cartridges
Waste Disposal Shelf
Figure 10-16. Waste Disposal Shelf
10.5.8 Waste Container

The waste container holds up to 400 cartridges. See Figure 10-17. A sensor detects the
presence or absence of the waste container and the system software counts the number of
cartridges before emptying.
The system will provide a warning when the Waste Container Almost Full Cartridge Count
reaches the specified number of cartridges. The default value for the Waste Container
Almost Full Cartridge Count is 350 cartridges. This value is set in the Automation
workspace. See Section 2.8. The system will not allow new tests to be ordered when the
cartridge count is 400 cartridges.

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Figure 10-17. Waste Container Location
Waste Container
(10-Pack Kit)
Waste Access Door
Figure 10-17. Waste Container Location
The Infinity ships with one package of 50 plastic bags and a kit of 10 waste containers. See
Note Section 9.9, Replacing the Waste Container Bag for details on plastic bag use. Additional waste
containers and bags can be purchased from Cepheid.
10.5.8.1 Disposal Counter

A waste counter is maintained to track each cartridge set for disposal. You can see the
Disposed Cartridge count by selecting the waste container icon on the dashboard.
When the system is initialized, the system continues with the previous Disposed
Cartridge count before the shutdown. This is set to zero when the waste container is
confirmed to be emptied.
When you confirm the waste container is emptied, please remove all used cartridges in the
Important
waste container. This allows the system to maintain an accurate waste counter.

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10.5.8.2 Waste Container Sensor

The GeneXpert Infinity system’s automated system uses a beam waste container sensor
to monitor the presence and absence of the waste container. See Figure 10-18.
Section 10.9.10 describes the possible waste container states.
Figure 10-18. Waste Container Sensor
Waste Container Sensor
Figure 10-18. Waste Container Sensor
10.5.8.3 Waste Management Alert Mode

While the system is in Waste Management Alert mode:
• No new test can be ordered
• Completed cartridges will not be removed from the modules
10.5.8.4 Waste Management Recovery Mode

Once the user empties the waste container, the recovery tasks for Waste Management
Alert mode is to:
• Remove completed cartridges from the modules
• Resume new test ordering process

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10.5.9 Front Glass Doors

Two sets of interlocks, one per glass door, are provided to pause all movement of the
gantry and conveyor if any of the glass doors are opened.
The glass doors can either be latched or closed. The difference between the two states
are as follows:
• Latched indicates that the glass doors are slid to the closed position and the
mechanical latch has engaged, preventing the user from opening the doors.
• Closed indicates the glass doors are slid to the closed position, but the mechanical
latches are not yet engaged (the user could still slide the door back open).
10.5.10 Robotic Gantry

The robotic gantry automatically picks up sample-prepared cartridges from the lobby
location and places the cartridges into the GeneXpert modules or to accumulator shelves
for processing. See Figure 10-19.
After test completion, the robotic arm moves tested cartridges from the GeneXpert
module to be off-loaded to the shuttle, waste container or the accumulator. If instructed,
the cartridge(s) in the accumulator can be retrieved through the shuttle.
10.5.10.1 Gripper
The gripper grips, holds and/or releases the cartridge. See Figure 10-20.
10.5.10.2 Gantry Barcode Scanner

An internal 2D matrix barcode reader is located on the gantry arm to scan the cartridge
barcode when the cartridge is about to be moved from the conveyor. See Figure 10-20.
Whenever a cartridge is being picked up from the lobby, the cartridge barcode is read to
obtain the cartridge serial number to confirm which cartridge is being moved.
The gantry scanner may scan the cartridge barcode at other times. When the glass doors
have been opened, such as during a pause, then all sites must be validated and the
scanner scans cartridges before picking them up to verify it is the correct cartridge.

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10.5.10.3 Module Door Mechanism

The module doors are individually opened and closed by a mechanism on the gantry. See
Figure 10-20.
Figure 10-19. Gantry shown on Infinity-48s System
Gantry
EMERGENCY
STOP Button
Figure 10-19. Gantry shown on Infinity-48s System
10.5.11 EMERGENCY STOP Button

The EMERGENCY STOP button is located on the front of the monitor. See Figure 10-19.
When this hardware EMERGENCY STOP button is pressed, it shuts down power to stop
the transport system immediately. The Xpertise software will indicate that the system is
in emergency stop mode. See Section 8.2, EMERGENCY STOP Button for details.

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Figure 10-20. Gantry Components
Gripper
Gantry Barcode
Scanner
Module Door
Mechanism
Figure 10-20. Gantry Components
10.6 Software Modules

10.6.1 Cartridge Life Cycle
Each test is uniquely identified by a cartridge-unique identification (or Unique Device
Identifier [UDI]). The cartridge unique identification is a combination of assay, cartridge
serial number and lot identification. Table 10-1 shows the possible automation states for
a cartridge.
Table 10-1. Possible Cartridge Automation States
Cartridge State During Description

Ordered From placement of order until seen Test ordered but cartridge has not been scanned by the
in the lobby. gantry or picked up.
Rejected • When the scan fails at the lobby No matching order according to the cartridge serial
or shuttle. number and order cancelled by the user.
or
Unreadable cartridge barcode.

A Sample ID of “Failed Scan” and a unique SN number
will be created to track this cartridge order.

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Table 10-1. Possible Cartridge Automation States (Continued)

• When a pending cartridge Pending order that was cancelled by the user or the user
already is in the system. cancels a DECTECTED cartridge.
• When test is stopped after The user stops a test while it is in one of the following
waiting for an available module states:
and before running in a • Preparing Site
GeneXpert module.
• Preloading
• Module Ready
• Loading
Removed From submission of an order until • User cancels an order before placing the cartridge on
the order is cancelled by the user the conveyor or shuttle.
before the cartridge is seen in the
lobby or shuttle.
Cartridge was removed to the
outside of the system via the shuttle
or scanned out when the system was
paused.
Pending From time seen in lobby to time • Cartridge, with a known serial number matching an
picked up for transfer to a GeneXpert existing order, has been picked up and moved to or is
module, accumulator or shuttle. in the accumulator or the shuttle.
• In module while being scheduled due to preloading or
load failure.
Expired After order, the cartridge is in the • Ordered test but the cartridge was never seen in the
lobby, shuttle, accumulator or lobby or shuttle and its prepared cartridge shelf life
outside of the system. has expired.
• A pending test that is unable to start the test before
the prepared cartridge shelf life expires.
• A detected cartridge has passed the maximum
prepared cartridge shelf life after it has been
detected.
Detected Detected in the lobby. No matching order, according to the cartridge serial
number.
Preparing Site A GeneXpert module has been • Automation mode: Cartridge is being moved.
scheduled to run this cartridge and • Manual mode: Preparing the GeneXpert module to
the system is preparing the module. run a test.
Preloading The GeneXpert module has been • Automation mode: The cartridge is in the GeneXpert
prepared and the cartridge is being module. The module is performing preload self-test.
moved into the module. • Manual mode: The module is performing pre-load
self-test.
Module Ready After the GeneXpert module has • Automation mode: Not applicable.
completed the preloaded self-test • Manual mode: Waiting for the user to insert the
and is waiting for door latch. cartridge and close the module door.
Loading The loading and pre-run self-test The cartridge is inside a GeneXpert module.
Unloadable From cartridge that has been Cartridge has failed to be loaded twice.
transferred to the shuttle after failing
to load into modules or into the
accumulator if the shuttle is not
available.

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Table 10-1. Possible Cartridge Automation States (Continued)

Running After the cartridge has been Running a test.
successfully loaded into a
GeneXpert module.
Finished After the test is finished and the Order that has a finished test.
cartridge is still in the GeneXpert
module.
Retained From test is completed and moved to Retained.
the accumulator.
Discarded • From test is completed and Finished and disposed.
moved to the waste shelf by the
gantry in Automation mode.
• From test is completed in
Manual mode.
10.6.2 Assay Shelf Life

As soon as a cartridge barcode has been scanned in the Order Test workspace, the test
order time is initialized. Remaining shelf-life is tracked by the system so that cartridges
that have expired will not be processed.
On-board stability is the amount of time that the cartridge can have the sample in it
before the test must be started.
A prepared cartridge is considered to be near the end of shelf-life if its remaining shelf-
life is 10 minutes or less. A notification via the user interface is given when a cartridge
is near its end of shelf-life.
10.6.3 Infinity Scheduler

The Infinity scheduler determines the order in which the queue of outstanding cartridge
orders will be run on the available GeneXpert modules.
Cartridges that have STAT priority are moved to the head of the queue. Within the STAT
priority cartridges, they are further ordered by:
• Closest Order Expiration Time
• If there are two cartridges that have the same Closest Order Expiration Time, the
assay with highest priority will go first.
Similarly, for the normal priority cartridges, they are further ordered by the same criteria.
However, a normal priority cartridge will be prioritized over a STAT cartridge if it is
necessary to prevent the order from expiring before the test is started.
If the cartridge is unable to reserve a module within the remaining shelf-life, the
cartridge order is marked with Expired Order status.

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The user can reserve modules for STAT cartridges or normal cartridges that will expire
before a module becomes available. See STAT Modules Reserved in Section 2.8,
Configuring the System Automation.
See Figure 5-31 for an example of an Order Test workspace with STAT selected.
Expired Orders
Expired cartridge orders are removed from the queue and placed on available
accumulator slots. If all accumulator slots are full, the user should move a few cartridges
from the accumulator using the Cartridge IO workspace. After this transfer is completed,
the gantry will automatically move expired cartridges from the conveyor to the
accumulator.
They will remain in the Outstanding Order List with Expired Order status. If the user has
manually removed a cartridge with Expired Order status, the system will remove the
order from the Outstanding Order List after 48 hours.
10.7 User Interface Conventions

10.7.1 Touchscreen User Interface Conventions
The Xpertise software’s user interface is a touchscreen-based graphical user interface.
Table 10-2 describes the navigation conventions for the Xpertise software. In this
manual, the term “select” will be used to indicate the selection of an item using the
touchscreen interface. The same action can be accomplished by “clicking” the mouse. In
some cases, “click” is specified because it may be easier to use the mouse instead of the
touchscreen due to the size of the icon or other reasons.
Table 10-2. User Interface Conventions
Touchscreen
Action Touchscreen Description Mouse Action Mouse Description
Single Tap Select a single item. Single Click Position the mouse pointer on the item
Position the pointer on the item that is to that is to be selected. Click the left
be selected. Tap the item once to select mouse button once to select the item.
the item.
Shift-Tap Select adjacent items. Shift-Click Click the first entry with the left-mouse
Tap the first entry while holding down the button, press and hold down the Shift
Shift key, and tap the final entry to key, and click the final entry to highlight
highlight selected items. selected items.
Ctrl-Tap Select non-adjacent items. Ctrl-Click Click the first entry with the left-mouse
Tap the first entry while holding down the button, press and hold down the Ctrl
Ctrl key, and tap each additional entry to key, and click each additional entry to be
be selected. selected.

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10.7.2 Access Windows Desktop

To access the Windows desktop, press the Windows key and the M key on the keyboard
at the same time. All windows are minimized to allow the user to interact with the
Windows desktop.
10.8 Overview of the Graphical User Interface

This section provides an overview of the graphical user interface. See Figure 10-21.
Figure 10-21. Xpertise Software Graphical User Interface
Dashboard Panel Workspace Panel Status Bar Menu Panel
Message Log
Figure 10-21. Xpertise Software Graphical User Interface

The graphical user interface (GUI) consists of five main sections or panels. See
Figure 10-21:
• Section 10.9, Dashboard Panel
• Section 10.10, Status Bar
• Section 10.11, Message Log
• Section 10.12, Menu Panel
• Section 10.13, Workspace Panel

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10.9 Dashboard Panel

This section provides an overview of the dashboard panel. The dashboard panel is
located at the top left side of the user interface. See Figure 10-21. It consists of the
following basic touchscreen icons:
Home icon. See Section 10.9.1 for details.
Manage Host Orders icon. See Section 10.9.2 for details.
Cartridge I/O icon. See Section 10.9.3 for details.
View Outstanding Orders icon. See Section 10.9.4 for details.
View Another Test icon. See Section 10.9.5 for details.
Glass Doors icon. See Section 10.9.6 for details.
Shuttle Open icon. See Section 10.9.7 for details.
Database Alert icon. See Section 10.9.8 for details.
Module Status icon. See Section 10.9.9 for details.
Waste Container icon. See Section 10.9.10 for details.
Silence Alarm icon. See Section 10.9.11 for details.
Pause icon. See Section 10.9.12 for details.

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Manual Mode icon (shown only with the Infinity is in Manual mode). See Section 10.9.13 for
details.
System Error icon (shown only when there is a system error). See Section 10.9.14 for details.
Note Some icons shown above will only be displayed if certain conditions occur.
See Appendix B, Icons and Display Symbology for a complete list of icons displayed in the Xpertise
Note
software.
10.9.1 Home Icon

When the Home icon is pressed, it returns to the Xpertise Software Home workspace.
10.9.2 Manage Host Orders Icon

The Manage Host Orders icon is used to manage orders from a host computer.
When the Manage Host Orders icon is green, it indicates that there are outstanding host
orders available for the GeneXpert Infinity system user to order on the system.
The Manage Host Orders icon can be used as a shortcut to view all host-ordered tests that
have not yet been processed or submitted to GeneXpert Infinity system. See
Figure 10-22 for a menu map of the Manage Host Orders icon.
Figure 10-22. Manage Host Orders Icon Menu Map
Manage Host
Orders Icon
Manage Host Orders
Order Test
Figure 10-22. Manage Host Orders Icon Menu Map

The graphical icon shows two statuses:
• The green icon indicates host orders exist that have not been assigned to a test.
• The white icon indicates no host orders exist or all host orders have been assigned to
a test.

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Pressing the Manage Host Orders icon displays the Manage Host Orders workspace. See
Figure 10-23.
See Section 5.8.1, Ordering a Test with Host Connectivity for a description of the
content and menu buttons in the Manage Host Orders workspace.
Section 5.6, Ordering a Test in Manual Mode provides complete information on
connectivity between the GeneXpert Infinity system and the host.
Figure 10-23. Manage Host Orders Workspace Example
Figure 10-23. Manage Host Orders Workspace Example
10.9.3 Cartridge I/O Icon

Select the Cartridge I/O icon to display the Cartridge I/O workspace. See Figure 10-24
and Figure 10-25. Use the Cartridge I/O workspace to remove cartridges from the
system.
For additional information about how to remove cartridges from the system using the
Cartridge I/O workspace, see Section 10.14, Retrieving Cartridges from the Accumulator
and Section 10.15, Removing a Cartridge That Has Not Been Ordered.

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Figure 10-24. Cartridge I/O Workspace – Shuttle Tab
Figure 10-24. Cartridge I/O Workspace – Shuttle Tab

Figure 10-25. Cartridge I/O Workspace – Accumulator Tab
Figure 10-25. Cartridge I/O Workspace – Accumulator Tab

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10.9.4 View Outstanding Orders Icon

The View Outstanding Orders icon is used to view orders that have been submitted to the
GeneXpert Infinity system and are waiting for automated processing.
An Outstanding Order table contains test orders that have not been started. Once a
cartridge has been successfully started or returned to the user, the order is removed from
this list. See Figure 10-26 for a menu map of the View Outstanding Orders icon.
Figure 10-26. View Outstanding Orders Icon Menu Map
View Outstanding
Orders Icon
View Outstanding
Orders
View Order
Figure 10-26. View Outstanding Orders Icon Menu Map

The graphical icon shows three statuses:
• The white icon indicates there are no outstanding orders.
• The green icon indicates there are outstanding orders that are waiting to be
processed. No user intervention is required.
• The red icon indicates there are outstanding test orders that are waiting to be
processed and are near the expiring prepared cartridge shelf-life. User attention is
required or the cartridge will expire. These may be cartridges that are near the end of
shelf-life or in one of the following states: rejected, expired, detected or unloadable.
Pressing the View Outstanding Orders icon displays the View Outstanding Orders
workspace. See Figure 10-27. The View Outstanding Orders icon can be pressed from
any Xpertise workspace.
The following buttons are available in the View Order workspace panel:
• VIEW ORDER – Allows you to view the selected order. The View Order workspace
displays the details about an order that has not yet been completed.
To view the outstanding order(s), highlight the row of the order to view and select
the VIEW ORDER button. See Figure 10-27. The View Order workspace will be
displayed.

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Figure 10-27. View Outstanding Orders Workspace Example
Figure 10-27. View Outstanding Orders Workspace Example
• CANCEL ORDER – Allows you to cancel the selected order.

A. To cancel an order, select CANCEL ORDER button, located on right side of the
B. The system asks (or queries) for confirmation. If you confirm with NO, the
system returns to View Order workspace panel. If you confirm with YES, the
system changes the cartridge status to Rejected and the cartridge is moved to the
accumulator.
• REMOVE OLD ORDERS – Removes orders that are two days old or more and deletes
them from the system. The order must meet the following criteria:
• The cartridge must be in the DISCARDED status
or
• The cartridge must be in the EXPIRED status and KIOSK location
• CLOSE – Closes this workspace and returns to the View Outstanding Orders
workspace.
To view the outstanding order(s), highlight the row of the order you desire to view and
select the VIEW ORDER button. See Figure 10-28. The View Order workspace will be
The View Order workspace allows you to view the details about an order.

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Figure 10-28. View Outstanding Orders Workspace

Figure 10-29. View Order Workspace Example
Figure 10-29. View Order Workspace Example
Note The five fields indicated in the Figure 10-29 will appear with an asterisk (*) if the data was scanned.

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10.9.5 View Another Test Icon

The View Another Test feature allows you to find tests (in-progress or completed)
associated with the optional Patient ID and/or the Sample ID. The feature is also useful
to find test results. The View Another Test icon can be pressed from any Xpertise
workspace.
In the Xpertise software workspace dashboard, select the View Another Test icon. The
View another Test workspace is displayed. See Figure 10-30. You can now view the
results of the tests.
To view a test, highlight the test in the list that you wish to view and select the VIEW
RESULTS button.
A Patient ID column shown in the View Another Test workspace will contain patient IDs only if it has
been enabled in the system configuration. If it is not enabled, the column will not be displayed.
Note
Patient ID data will only be displayed if it was entered into the database. If no data was entered, the
Patient ID entry will be blank.
Figure 10-30. View Another Test Workspace Example
Figure 10-30. View Another Test Workspace Example

See Section 5.5.3, Viewing Test Results for details of viewing tests for basic and detail
users.

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10.9.6 Glass Doors Icons

The Glass Door icons display the status of the glass doors. There are two glass door
indicators used to indicate the status:
• Glass Doors Open – indicates that the glass doors are open. Doors must be
completely closed for automation operation.
• Glass Doors Unlocked – indicates that the glass doors are unlocked and it is possible
to access the automation area.
10.9.7 Shuttle Open Icon

The Shuttle Open icon is displayed on the dashboard panel whenever the shuttle is open.
10.9.8 Database Alert Icon

The Database Alert icon is located on the dashboard and indicates database capacity. The
icon will change depending upon how much capacity is left in the database.
• The green icon indicates that the database capacity is OK. The database size is below
80% utilization. No user intervention is required.
• The green and yellow icon indicates that the database capacity is almost full. The
database size is between 80% and 90% utilization. No user intervention is required
but intervention will be required soon.
• The green, yellow and red icon indicates that the database capacity is full. The
database size is above 90% utilization. User intervention is required very soon.
10.9.9 Module Status Icon

The Module Status icon is located on the dashboard and indicates status of the Infinity
module usage for non-STAT and for STAT module. The icon will change depending
upon how high the module usage is for each type of module. When the Module Status
icon on the dashboard is pressed, the Module Status workspace is displayed.
Automation Mode
In Automation mode, reserved STAT modules are shown in the Module Status icon as
orange circles and the non-STAT modules are shown as green squares.See Figure 10-31.
See Section 2.8 for information on setting up the STAT modules and utilization
parameters.

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Figure 10-31. Module Status Icon
Non-STAT Module
Status
Reserved STAT
Module Status
Figure 10-31. Module Status Icon
Reserved STAT Module Status Icons

• Low Usage –The icon with the single orange circle indicates the utilization is
between 0 and not more than the Upper Limit for Low Usage as low usage of reserved
STAT modules.
• Medium Usage –The icon with two orange circles indicates the utilization is greater
than the Upper Limit for Low Usage and not more than Upper Limit for Medium Usage
as medium usage of reserved STAT modules.
• Full Usage –The icon with three orange circles indicates the utilization is greater than
Upper Limit for Medium Usage as full usage of reserved STAT modules.
Non-STAT Module Status Icons

• Low Usage –The icon with the single row of green squares indicates the utilization is
between 0 and not more than the Upper Limit for Low Usage as low usage of non-
STAT modules.
• Medium Usage –The icon with two rows of green squares indicates the utilization is
greater than the Upper Limit for Low Usage and not more than Upper Limit for Medium
Usage as medium usage of non-STAT modules.
• Full Usage –The icon with three rows of green squares indicates the utilization is
greater than Upper Limit for Medium Usage as full usage of non-STAT modules.
When you select the Module Status icon on the dashboard, the Module Status workspace

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Figure 10-32. Module Status Workspace
Figure 10-32. Module Status Workspace

The Module Status workspace shows all of the modules, their status, whether any tests
are currently running in each module and information about tests currently running.
Select CLOSE to exit the Module Status workspace.
Manual Mode
In Manual mode, only non-STAT modules are shown as green rectangles.
• Low Usage –The icon with the single row of green rectangles indicates the utilization
is between 0 and not more than the Upper Limit for Low Usage as low usage of non-
STAT modules.
• Medium Usage –The icon with two rows of green rectangles indicates the utilization
is greater than the Upper Limit for Low Usage and not more than Upper Limit for
Medium Usage as medium usage of non-STAT modules.
• Full Usage –The icon with three rows of green rectangles indicates the utilization is
greater than Upper Limit for Medium Usage as full usage of non-STAT modules.

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10.9.10 Waste Container Capacity and Contents Icon

The Waste Container icon is located on the dashboard and indicates status of the Infinity
waste container. The icon will change depending upon how many cartridges have been
placed in the waste container or if the waste container is not present in the system.
• Waste Access Door Unlocked –When the waste container door is unlocked, an icon
with a lock will be displayed beside the waste container icon to indicate the waste
access door is unlocked. You must complete the waste container replacement
procedure to lock the access door.
• Waste Container Absent –When the waste container is removed from the system to
empty the used cartridges, the waste container icon will change to the Waste
Container Absent icon to indicate that the waste container is not detected by the
sensor.
• Waste Container Normal –The icon with two rows of green squares indicates that the
cartridge count is less than the Almost Full Level. This is the normal operating mode
icon.
• Waste Container Almost Full –The icon will add two rows of orange squares above
the green squares when the cartridge count is greater than the Almost Full Level. The
operator should plan to empty the waste container soon.
• Waste Container Full –The icon will add a row of red squares when the cartridge
count reaches 100% of the Full Level. In addition, the system will operate in Waste
Management Alert mode. The operator must empty the waste container immediately.
See Section 2.8 for information on setting up the parameters for the waste container.
Each cartridge disposed onto the waste disposal shelf is moved into the waste container.
When the system is initialized during startup, the system continues with the previous
cartridge count in the waste container before the system was shut down.
When the user empties the waste container, the counter will be reset to zero after the
user confirms that the waste container has been emptied.
When you select the Waste Container icon on the dashboard, the Waste Container
workspace is displayed showing the disposed cartridge count of the waste container. See
Figure 10-33.
See Section 9.9, Replacing the Waste Container Bag for details on how to remove and
replace the waste container bag.

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Waste Management Alert Mode

While the system is in Waste Management Alert mode:
• No new test can be ordered
• Completed cartridges will not be removed from the modules
Once the user empties the Waste Container, the Infinity system will:
• Remove completed cartridges from the modules
• Resume new test order process
10.9.11 Silence Alarm Icon

The Silence Alarm icon is located on the dashboard and allows you to silence the audible
alarm when the alarm is triggered by one of the alarm messages.
The audible alarm feature of the Infinity system is enabled when shipped from the
factory, but, it can be disabled by the administrator users in the system configuration
settings. When the audible alarm feature is enabled and the system detects an alarm
error, the system turns on the alarm. The alarm will last for 5 minutes starting from the
time of detection of the alarm or until you select the Silence Alarm icon.
If multiple alarm errors have been detected and you do not select the Silence Alarm icon
to silence the alarm, then the alarm will last 5 minutes from the most recent alarm error.

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10.9.12 Pause Icon

The Pause icon is located on the dashboard and allows the user to pause the system. The
user is allowed to pause the automated system after the currently edited workspace is
saved if it is in Edit mode.
Note The Pause icon is only available when the system has completed initialization.
When the Pause icon is pressed, it pauses the automation operation and causes the
Infinity system to perform the following:
• pauses cartridge order processing
• pauses the gantry at its home position at the end of its current move
• stops the conveyor
• unlatches the glass doors
The Pause feature can be used:
• to adjust a cartridge and then resume
• to remove a cartridge with scan then resume
The above scenarios are described below:
10.9.12.1 Using Pause to Adjust a Cartridge and then Resume

1. Select the Pause icon located on the dashboard (see Figure 10-34). The Pause -
2. Read and perform the instructions provided in the Pause - Confirmation workspace
(see Figure 10-35) and select the CONFIRM PAUSE button. The Pause - Cartridge
Adjustment workspace is displayed. See Figure 10-36.
Select the CANCEL button if you do not want to pause the system.
Note The glass doors will unlatch and can be opened after confirming that you want the system to pause.
3. Read and perform the instructions provided in the Pause - Cartridge Adjustment
workspace. See Figure 10-36. Adjust any cartridges that need to be reseated.
Note Do not add or remove any cartridges from the system during this procedure.
4. After you have finished adjusting any cartridges, select the RESUME button. The
Pause - Resume workspace is displayed. See Figure 10-37.
5. In the Pause - Resume workspace, close the glass doors and then select the RESUME
Note The system will not resume if the glass doors have not been closed.

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Figure 10-35. Pause - Confirmation Workspace

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Figure 10-36. Pause - Cartridge Adjustment Workspace

Figure 10-37. Pause - Resume Workspace

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10.9.12.2 Using Pause to Remove a Cartridge and then Resume

If you remove cartridges from the instrument during pause, you must scan the cartridge
Important
barcode in the Pause - Scan Cartridge Barcode workspace. See Figure 10-41.
Caution Do not attempt to remove a cartridge from a GeneXpert module if the module door is not fully
opened. Do not force the GeneXpert module door open. Forcing the module door open will
cause damage to the GeneXpert module. Call Cepheid Technical Support if the module door
will not open.
1. Select the Pause icon located on the dashboard (see Figure 10-38). The Pause -
2. Read and perform the instructions provided in the Pause - Confirmation workspace
(see Figure 10-39) and select the CONFIRM PAUSE button. The Pause - Cartridge
Adjustment workspace is displayed. See Figure 10-40.
Select the CANCEL button if you do not want to pause the system.
Note The glass doors will unlatch and can be opened after confirming that you want the system to pause.
3. Read and perform the instructions provided in the Pause - Cartridge Adjustment
workspace. See Figure 10-40. Remove and scan any cartridges that are stuck or have
been dropped by the gantry.

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Figure 10-41. Pause - Scan Cartridge Barcode Workspace
Figure 10-41. Pause - Scan Cartridge Barcode Workspace

4. Read and perform the instructions provided in the Pause - Scan Cartridge Barcode
workspace. See Figure 10-41. Scan the barcode of the cartridge that was removed
from the system.
The cartridge barcode is successfully scanned when you hear the beep. The Pause -
Removed Cartridge workspace will be displayed automatically after the cartridge is
scanned displaying the cartridge order information. See Figure 10-42.
If there are no other cartridges to remove, select the RESUME button. The Pause -
Resume workspace is displayed. See Figure 10-44.
If there are additional cartridges to remove, select the REMOVE ANOTHER
CARTRIDGE button. The Pause Cartridge Adjustment workspace is displayed.
If the system cannot find the cartridge order information, a warning is displayed. See
Figure 10-43. Select the OK button. The Pause - Resume workspace is displayed.
See Figure 10-44.
5. In the Pause - Resume workspace, close the glass doors and then select the RESUME
Note The system will not resume if the glass doors have not been closed.

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Figure 10-42. Pause - Removed Cartridge Workspace
Figure 10-42. Pause - Removed Cartridge Workspace

Figure 10-43. Pause - Scan Cartridge Barcode Workspace – Cannot Find Cartridge Scanned
Figure 10-43. Pause - Scan Cartridge Barcode Workspace – Cannot Find Cartridge Scanned

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10.9.13 Manual Mode Icon

The Manual Mode icon is located on the dashboard and is displayed when the system is in
manual operation mode.
Manual mode can be used when the automated system is not fully functional. The user
can load the cartridge in the GeneXpert module following the manual operation
directions displayed in the Manual Load - Load Cartridge workspace.
See the following sections for instructions about how change operation modes:
• Section 5.6.2, Changing from Automation Mode to Manual Mode
• Section 5.6.4, Changing from Manual Mode to Automation Mode

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10.9.14 System Error Icon

The System Error icon will be displayed on the dashboard whenever an error occurs on
the system. Select the System Error icon to display the error message.
System errors can be generated by:
• Gantry (Automation Down)
• Gripper
• Gantry Scanner
• Kiosk Scanner
The dashboard displays one error status icon for each subsystem that currently has error
conditions. Errors and other system messages are displayed in the Message Log
In addition to the System Error icon, there is also a separate Host Communication Error
icon to indicate host communication is down.

For this example, the kiosk scanner is non-functional. The error will be indicated by the
error icon being displayed in the dashboard (see Figure 10-46). To confirm the source of
the error, select the Error icon to display more information about the error. See
Figure 10-47. Hover over the icon to see more information.

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Select Error Icon to Display Source of Error

Hover Over Icon to Display More Information

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See Chapter 9, Service and Maintenance for a complete list of error messages. Chapter 9
provides detailed explanations of:
• Infinity-specific automation error messages (starting at Section 9.17.6).
• GeneXpert module-specific error messages (starting at Section 9.17.1).
10.10 Status Bar

This section provides an overview of the status bar. The status bar is located at the top
right corner of the user interface. See Figure 10-48. It consists of five touchscreen icons.
Figure 10-48. Status Bar
Exit Xpertise Software

Change Password
Logout
Login
Current User Name
Figure 10-48. Status Bar
Current User Name. The full name of the currently logged in user is displayed.
Login icon. Users can log in by selecting the Login icon.
When there is at least one defined user, a user name and password prompt is provided during
the startup process.
If the user logs in correctly, the user is allowed to operate the system as described in
Section 2.6.2, Specifying User Permissions.
If the user enters an incorrect user name and password combination, a warning prompt is
displayed and the system will continue showing the login dialog.
User re-login: When the system is already operational, another user may login. After a valid entry
of the user name and password, the previous user is logged out and the new user is logged in.
User Tracking: The user name is tracked for tests started and is stored in the message log.

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Logout icon. Users can log out by selecting the Logout icon.
The software will be running with limited access. When the user exits the system, they are
automatically logged out and the software is terminated.
No-User Mode: When a user logs out without exiting the software, the system is in a no-user
mode. When the user logs out of the system, any current editing should be saved or cancelled.
However, tests-in-progress will continue. In no-user mode, the system is limited to viewing only
(no modifications are allowed) with only the following features available:
• Login
• Exit
• Maintenance– GX Maintenance-Module Report
• Reminders (on dashboard)
• Module Status (on dashboard)
• Waste Capacity (on dashboard)
• Message Log (on dashboard)
• About workspace
Change Password icon. Users can change their own password by selecting the Change
Password icon or using the menu option Change Password to display the Change Password
workspace. After a valid entry of the current password and duplicate entries of the new password,
the new password is effective. The duplicate entries of the new password must match.
Passwords are not displayed in clear text. Passwords must be at least six alphanumeric
characters and up to ten characters long.
Exit Xpertise Software icon. The system displays the confirmation prompt followed by database
backup and archive reminders. After confirming the reminders, the system will continue with the
shutdown process and the Xpertise software will close. The computer desktop will be displayed.
See Appendix B, Icons and Display Symbology for a complete list of icons displayed in the Xpertise
Note
software.

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10.11 Message Log

When the Message Log icon is pressed, the Message Log workspace opens and displays
the most recent messages in the Message Log workspace. See Figure 10-49.
The message log contains all of the system messages (error messages, reminder
messages and information messages). The application launch time and software version
are shown immediately after the software is launched followed by a module self-test of
each module.
Figure 10-49. Message Log Workspace showing System Errors and Messages
Message Type
Figure 10-49. Message Log Workspace showing System Errors and Messages
When the Message Log icon is pressed, the PREVIEW PDF button appears in the
workspace (see Figure 10-49). Select the PREVIEW PDF button to display a Message Log
Report in the Adobe Reader window. See Figure 10-50. From Adobe Reader, the file can
be saved or printed, if needed.

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Figure 10-50. Message Log Workspace in Adobe Reader showing System Errors and Messages
Figure 10-50. Message Log Workspace in Adobe Reader showing System Errors and Messages
Reminder Messages
Reminder messages provide status of various Infinity automation subsystems. These are
not error messages. Table 10-3 lists the reminder messages.
Table 10-3. Automation Subsystem Reminder Messages
Message
Code Subsystem User Interface Message Reminder Dashboard
6201 Emergency Stop Emergency Stop activated. Emergency Stop Activated

7202 Emergency Stop Emergency Stop de-activated. Emergency Stop De-Activated
7221 Glass Doors Glass doors are latched. Glass Door Latched
7222* Glass Doors Glass doors are unlatched. Glass Door Unlatched
7223 Glass Doors Glass doors are closed. Glass Door Closed
7224 Glass Doors Glass doors are open. Glass Door Open
* Not in Xpertise 6.6.

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Informational Messages
Informational messages provide status of various Infinity automation subsystems. These
are not error messages. Table 10-4 contains a partial list of the informational messages.
Table 10-4. Automation Subsystem Informational Messages
Subsystem User Interface Message

Waste Container Waste Container available.
Module Modules not detected.
Module Modules <X> loses communication.
System Full Automation Operating Mode.
System Analysis Operating Mode.
System Manual Operating Mode.
10.12 Menu Panel

The Menu panel consists of the buttons on the right side of the screen. The Main menu
consists of five touchscreen buttons. See Figure 10-51.
Figure 10-51. Xpertise Software Home Page Showing Main Menu Buttons
Figure 10-51. Xpertise Software Home Page Showing Main Menu Buttons
The Menu panel buttons allow navigation to other workspaces (screens). When you
select these main command buttons, the subcommand buttons are displayed (according
to your user privilege) as shown in the menu map shown in Figure 10-52.

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The Main Menu Options are:

• Orders
• Results
• Data Management
• Setup
• Maintenance
The menu map shown in Figure 10-52 will vary, depending on which user type is logged in and
which options have been made available to each user type by the system administrator. The menu
Note map in Figure 10-52 is for users with administrative privileges. The MANAGE HOST ORDERS
button under the ORDERS menu will be active only when the Infinity system is connected to a host
computer.
Figure 10-52. Menu Panel Menu Map
Figure 10-52. Menu Panel Menu Map

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10.12.1 ORDERS Menu Button

Pressing the ORDERS menu button (see Figure 10-53) displays the Order Test menu. See
Figure 10-54.
Figure 10-53. Xpertise Software Home Page

Figure 10-54. Xpertise Software Home Page – Orders Menu Shown
Figure 10-54. Xpertise Software Home Page – Orders Menu Shown

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Below is a list of where the functionality of the buttons in the Orders menu workspace
(see Figure 10-54) are described in this manual:
• ORDER TEST button
• See Section 5.5.2, Ordering a Test in Automation Mode
• See Section 5.6.3, Ordering a Test in Manual Mode
• VIEW OUTSTANDING ORDERS button
• See Section 10.9.4, View Outstanding Orders Icon
• FIND ORDER button
• The FIND ORDER button displays the Find Order workspace. The Find Order
workspace is described below.
• MANAGE HOST ORDERS button
• See Section 5.8.1, Ordering a Test with Host Connectivity
• STOP TEST button
• See Section 5.5.7, Stopping a Test in Progress
• BACK button
• The BACK button returns you to the previous menu (Main menu).
Find Order Workspace

The Find Order workspace allows you to find an ordered test (outstanding, in-progress or
finished) associated with the Patient ID (if Use Patient ID is selected in the System
Configuration General workspace), Sample ID and assay. See Figure 10-56.
The Find Order workspace is useful if you are not sure where an order is in the system,
but know the Patient ID, Sample ID or assay.
To navigate to the Find Order workspace:
1. In the Xpertise Software Home workspace (see Figure 10-53), select the ORDERS
button. The Orders menu will be displayed. See Figure 10-55.
2. Select the FIND ORDER button (see Figure 10-55). The Find Order workspace is

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Figure 10-56. Find Order Workspace
Figure 10-56. Find Order Workspace

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3. Enter the Patient ID (if Use Patient ID is selected in the System Configuration
General workspace), the Sample ID and/or assay information for the order you want
to find:
• Patient ID – You can enter the exact Patient ID, a single-character wildcard
(_ [underscore]) combined with exact characters or a multiple-character
wildcard (%) with or without exact characters.
The Patient ID field limitations will apply except that the wildcard characters
(_ [underscore] and %) are allowed.
• Sample ID – You can enter the exact Sample ID, a single-character wildcard
(_ [underscore]) combined with exact characters or a multiple-character
wildcard (%) with or without exact characters.
The Sample ID field limitations will apply except that the wildcard characters
• Assay – Select an assay from the drop down menu. The menu is a list of active
and non-research assays with unique assay names.
4. After entering the Patient ID, Sample ID and/or assay, select the FIND button. See
Figure 10-56. The system searches the orders in the database.
• If the order has been found and it has not started yet or completed, the View
Order workspace (see Figure 10-57) is displayed with the found order.
• If the order is not found, the message Order is not found in the system. is
displayed.
The Find Order workspace displays the orders (see Figure 10-58). The Find Order
workspace lists the orders associated with the Patient ID, Sample ID and/or assay
that you requested.
5. Select or highlight the order you would like to view, then select the VIEW button. See
Figure 10-58.
If the selected order is an outstanding order, the View Order workspace is displayed,
showing the selected order. See Figure 10-57. Select the CANCEL ORDER button to
cancel the outstanding order, if desired.
If the selected order is running (in-progress) or finished, the View Results
workspace is displayed, showing the selected order. See Figure 10-59. Select the
REPORT button to print the test report for the selected test or VIEW ANOTHER TEST
button to return to the Find Order workspace and view another test.
6. Select the CLOSE button. The Find Order workspace, View Order workspace or
View Results workspace is closed and the Order menu is displayed. See
Figure 10-55.

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Figure 10-57. View Order Workspace Showing Found Order
Figure 10-57. View Order Workspace Showing Found Order

Figure 10-58. Find Order Workspace Example Showing the Status of Orders
Figure 10-58. Find Order Workspace Example Showing the Status of Orders

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Figure 10-59. View Results Workspace Example Showing Completed Found Order
Figure 10-59. View Results Workspace Example Showing Completed Found Order
10.12.2 RESULTS Menu Button

Pressing the RESULTS menu button (see Figure 10-60) displays the Results menu. See
Figure 10-61. The Results menu is used for viewing test results and generating various
reports.
Below is a list of where the functionality of the buttons in the Results menu workspace
• VIEW RESULTS button
• See Section 5.5.3.1, Basic User View Results
• See Section 5.5.3.2, Detail User and Administrative View Results
• SPECIMEN REPORT button
• See Section 10.12.2.1, Specimen Report
• PATIENT REPORT button
• See Section 10.12.2.2, Patient Report (If Use Patient ID is Enabled)
• PATIENT TREND REPORT button
• See Section 10.12.2.3, Patient Trend Report (If Use Patient ID is Enabled)

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• TEST SUMMARY button

• See Section 10.12.2.4, Test Summary
• CONTROL TREND REPORT button
• See Section 10.12.2.5, Control Trend Report
• ASSAY STATISTICS REPORT button
• See Section 10.12.2.6, Assay Statistics Report
• BACK button

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Figure 10-61. Xpertise Software Home Page showing Results Menu
10.12.2.1 Specimen Report

The Specimen Report provides you with an overview of the test results for the selected
specimen in the database.
To view the Specimen Report:
2. In the Results menu, select the SPECIMEN REPORT button (see Figure 10-62). The
Specimen Report workspace is displayed. See Figure 10-63.
3. Specify the following criteria to print a specimen report that includes the desired
data range and assay(s):
• Date Range – Select All to view all dates or Select to view report(s) for a specific
date range. For Select, enter the desired date range.
(_ [underscore]) combined with exact characters, a multiple-character wildcard
(%) with or without exact characters or leave the field blank to include all
Sample IDs.

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Figure 10-63. Specimen Report Workspace
Figure 10-63. Specimen Report Workspace

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• Assay – The following assay selection options are available:

• All – This option enables you to include all non-research assays (both active
and inactive) in the database. This option is the default selection.
When this option is selected, check boxes in the Select column in the assay
table will be selected for the listed assays. See Figure 10-63.
• Select – When this option is selected, the assay table will be enabled and
check boxes will be de-selected for the listed assays.
About the Assay Table – The software displays a list of assays (both
active and inactive) with all active assays first, then alphabetically ordered
by assay name, and then ordered by assay version.
You can mark the check box in the Select column to select one or more
assays in the database.
4. When the Specimen Report parameters have been selected, select one or both of the
following buttons:
specify. Select the GENERATE REPORT FILE button on Specimen Report
workspace (see Figure 10-63) to create the PDF file of the test report. The
Specimen Report workspace will display the number of sample IDs matching
the selection criteria (see Figure 10-64). Select the OK button.
The Generate Report File dialog box will appear (see Figure 10-65), which
enables you to save the file to a specified location. Select the SAVE button once
you have navigated to the specific location. To view the Specimen Report, go to
the location you saved the report, open the Specimen Report and print it.
Note The default location for saving the Specimen Report is C:\genexpert\report.
Information may vary depending upon the options selected in the system. For example, the report
Note may contain the Patient ID and Patient ID 2 if these options are enabled in the System
Configuration General workspace.
• PREVIEW PDF – Select the PREVIEW PDF button on the Specimen Report
workspace (see Figure 10-63). The Specimen Report workspace will display
the number of sample IDs matching the selection criteria (see Figure 10-64).
Select the OK button.A PDF file will be created and displayed in the Adobe
Reader window. See Figure 10-66. You can save and print the PDF file from the
Adobe Reader software.
• Select the CLOSE button to close this workspace.
An example page from a printed Specimen Report is shown in Figure 10-67.

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Figure 10-64. Specimen Report Workspace – Confirmation Screen
Figure 10-64. Specimen Report Workspace – Confirmation Screen


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Figure 10-66. Specimen Report Example Shown in Adobe Reader
Figure 10-66. Specimen Report Example Shown in Adobe Reader

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Figure 10-67. Specimen Report Example Page
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10.12.2.2 Patient Report (If Use Patient ID is Enabled)

The Patient Report provides test results for one patient according to the Patient ID in the
database.
To view the Patient Report:
2. In the Results menu, select the PATIENT REPORT button (see Figure 10-68). The
Patient Report workspace is displayed. See Figure 10-69.
3. Specify the following criteria to print a patient report that includes the desired data
range and assay(s):
• Date Range – Select All to view all dates or Select to view report(s) for a specific
Patient IDs.

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Figure 10-69. Patient Report Workspace
Figure 10-69. Patient Report Workspace

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Figure 10-70. Patient Report Workspace – Confirmation Screen
Figure 10-70. Patient Report Workspace – Confirmation Screen


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4. When the Patient Report parameters have been selected, select one or more of the
following buttons:
specify. Select the GENERATE REPORT FILE button on Patient Report
workspace (see Figure 10-69) to create the PDF file of the test report. The
Patient Report workspace will display the number of patient IDs matching the
selection criteria (see Figure 10-70). Select the OK button.
The Generate Report File dialog box will appear (see Figure 10-71), which
enables you to save the file to a specified location. Select the SAVE button once
you have navigated to the specific location. To view the Patient Report, go to
location you saved the report, open the Patient Report and print it.
Note The default location for saving the Patient Report is C:\genexpert\report.
• PREVIEW PDF – Select the PREVIEW PDF button on the Patient Report
workspace (see Figure 10-69). The Patient Report workspace will display the
number of patient IDs matching the selection criteria (see Figure 10-70). Select
the OK button. A PDF file will be created and displayed in the Adobe Reader
window. See Figure 10-72. You can save and print the PDF file from the Adobe
Reader software.
An example page from a printed Patient Report is shown in Figure 10-73.

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Figure 10-72. Patient Report Example Shown in Adobe Reader
Figure 10-72. Patient Report Example Shown in Adobe Reader

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Figure 10-73. Patient Report Example Page
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10.12.2.3 Patient Trend Report (If Use Patient ID is Enabled)

The Patient Trend Report provides an overview of the quantitative test results of a
specific quantitative assay for a patient.
The Patient Trend Report can only be used for quantitative assays. It is not used for qualitative
Note
assays.
To view the Patient Trend Report:

2. In the Results menu, select the PATIENT TREND REPORT button (see Figure 10-74).
The Patient Trend Report workspace is displayed. See Figure 10-75.
3. Specify the following criteria to print a Patient Trend Report that includes the
desired data range and assay:
• Date Range – Select All to view all dates or Select to view results for a specific
• Criteria – Select the criteria for the report:
• Patient ID – Enter the exact Patient ID. If the exact Patient ID is not known,
use the FIND PATIENT ID button to search for the Patient ID. For use of the
FIND PATIENT ID button, see Find Patient ID Workspace on page 10-82.
• Select Assay – Select the desired assay from the drop down box. Assays are
shown in alphabetical order. Only quantitative assays are shown.
• Show target reference line at – Enter the value for the desired target
reference line. The value must be larger than the Lower Quantitative Level
(LQL) value and less than the Upper Quantitative Level (UQL) value.
• Specify y-axis maximum value – Check the check box and enter this
optional value for the Y-axis of the graph. Entering or changing this value
allows the user to zoom in or out on the graph.
• Plot quantitative value in log format – If this option is checked, the graph
will be plotted using the log-10 value of the quantitative value. The default
for this option is checked.

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Figure 10-75. Patient Trend Report Workspace
Figure 10-75. Patient Trend Report Workspace

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4. After selecting the Patient Trend Report parameters, select one or more of the
following buttons:
specify. Select the GENERATE REPORT FILE button on Patient Trend Report
workspace (see Figure 10-75) to create a PDF file of the Patient Trend Report.
The Generate Report File workspace will be displayed (see Figure 10-76),
which enables you to save the file to a specified location.
Select the SAVE button once you have navigated to the specific location. To
view the Patient Trend Report, go to location you saved the report, open the
Patient Trend Report and print it.
Note The default location for saving the Patient Trend Report is C:\genexpert\report.

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Figure 10-77. Patient Trend Report Example Shown in Adobe Reader
Figure 10-77. Patient Trend Report Example Shown in Adobe Reader

window. See Figure 10-77. You can save and print the PDF file from the Adobe
Reader software.
• VIEW GRAPH – Opens the Patient Trend Graph workspace and displays a graph
of the of all results that meet the selection criteria for a specific patient. Test
results of ERROR, INVALID and NO RESULT are excluded from the graph. See
Figure 10-78. Select the OK button after viewing the graph to return to the
Patient Trend Report workspace.
An example of a printed Patient Trend Report is shown in Figure 10-79 and
Figure 10-80.

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Figure 10-78. Patient Trend Graph Workspace
Figure 10-78. Patient Trend Graph Workspace

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Figure 10-79. Patient Trend Report Example – Page 1
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Find Patient ID Workspace

The Find Order workspace allows users to find a Patient ID using a partial Patient ID
and wildcard characters.
To navigate to the Find Patient ID workspace:
1. In the Patient Trend Report workspace (see Figure 10-75), select the FIND PATIENT
ID button. The Find Patient ID workspace will be displayed. See Figure 10-81.
In the Patient ID field, (see Figure 10-81), enter the search criteria.You can enter a
partial Patient ID, a single-character wildcard (_ [underscore]) combined with exact
characters or a multiple-character wildcard (%) with or without exact characters.
2. After entering the Patient ID search criteria, select the FIND button (see
Figure 10-81). The database will be searched and a list of Patient IDs will be
displayed matching the search criteria. See Figure 10-82.
Figure 10-81. Find Patient ID Workspace
Figure 10-81. Find Patient ID Workspace

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Figure 10-82. Find Patient ID Workspace showing Matching Search Criteria
Figure 10-82. Find Patient ID Workspace showing Matching Search Criteria

3. If the desired Patient ID is found, select the row with the Patient ID. The OK button
will become active. See Figure 10-82.
If no Patient ID is found that matches the search criteria, the message No Patient ID
was found. is displayed.
4. Select the OK button to transfer the selected Patient ID to the Patient ID field in the
Patient Trend Report workspace.
5. Continue entering criteria for the Patient Trend Report. See Step 3 in
Section 10.12.2.3, Patient Trend Report (If Use Patient ID is Enabled).

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10.12.2.4 Test Summary

The Test Summary provides the user with a comma-separated value (.csv) file of
completed tests matching the selection criteria.
To view the Test Summary:
2. In the Results menu, select the TEST SUMMARY button (see Figure 10-83). The Test
Summary workspace is displayed. See Figure 10-84.
3. Specify the following criteria to create a .csv file that includes the desired data range
and assay(s):
• Date Range – Select All to view all dates or Select to create a .csv file for a
specific date range. For Select, enter the desired date range.
Patient IDs.
Patient ID is only available if Use Patient ID is enabled in the System Configuration General
Note
workspace.

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Figure 10-84. Test Summary Workspace
Figure 10-84. Test Summary Workspace

Sample IDs.

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Figure 10-85. Export Test Summary Workspace
Figure 10-85. Export Test Summary Workspace

Figure 10-86. Test Summary Report Example
Figure 10-86. Test Summary Report Example

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4. Select the EXPORT button (see Figure 10-84). The Export Test Summary workspace
will be displayed. See Figure 10-85.
Note The default location for saving the Test Summary Report is C:\genexpert\export.
5. In the Export Test Summary workspace (see Figure 10-85), verify the location to
save the report and select the SAVE button. The file will be saved as a .csv file in the
selected location.
6. Select the CLOSE button to close this workspace.
If you choose, you can now print or view this report. The report may be opened using
Apache OpenOffice, Microsoft Excel or another software program that will allow
opening a .csv file. See Appendix C, Viewing Export (.csv) Files for instructions to open
and view the .csv file.
10.12.2.5 Control Trend Report

You can use the Control Trend report to verify the quality of the system or the reagents.
For example, you can generate a negative control trend report to check for
cross-contamination. You can also generate other external control trend reports to check
the new lots of reagents that come to your facility.
The Control Trend Report only reports on tests using external controls. External controls are test
Note
types that are not “specimens”.
For specific instructions on creating a Control Trend report, see Section 6.4, Control
Trend Reports.
10.12.2.6 Assay Statistics Report

The Assay Statistics Report is a report showing the number of tests performed for each
assay over a period of time with monthly breakdown values.
To view the Assay Statistics Report:
2. In the Results menu, select the ASSAY STATISTICS REPORT button (see
Figure 10-87). The Assay Statistics Report workspace is displayed. See
Figure 10-88.

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Figure 10-88. Assay Statistics Report Workspace
Figure 10-88. Assay Statistics Report Workspace

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3. Specify the following criteria to print an Assay Statistics Report that includes the
desired data range and assay(s):
• Date Range – Select Last 12 Months to view assays run during the last year or
Select to view assays run during a specific date range. For Select, enter the
desired date range.
4. After selecting the Assay Statistics Report parameters, select one or more of the
following buttons:
specify. Select the GENERATE REPORT FILE button on the Assay Statistics
Report workspace (see Figure 10-88) to create the PDF file of the report. The
Generate Report File dialog box will appear (see Figure 10-89), which enables
you to save the file to a specified location. Select the SAVE button once you
have navigated to the specific location. To view the Assay Statistics Report, go
to the location you saved the report, open the report and print it.
Note The default location for saving the Assay Statistics Report is C:\genexpert\report.
window. You can save and print the PDF file from the Adobe Reader software.
An example page from a printed Assay Statistics Report is shown in Figure 10-91.

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Figure 10-90. Assay Statistics Report in Adobe Reader
Figure 10-90. Assay Statistics Report in Adobe Reader

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Figure 10-91. Assay Statistics Report Example Page
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10.12.3 DATA MANAGEMENT Menu Button

Pressing the DATA MANAGEMENT menu button (see Figure 10-92) displays the Data
Management menu. See Figure 10-93. The Data Management menu is used for archiving
tests and retrieving tests that were previously archived.

Figure 10-93. Xpertise Software Home Page showing Data Management Menu
Figure 10-93. Xpertise Software Home Page showing Data Management Menu

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The functions available in the database management menu will vary depending upon the login level
Note and options set up by the system administrator. The screen shown in Figure 10-93 shows a detail
user level login accessed during system startup.
Below is a list of where the functionality of the buttons in the Data Management menu
workspace (see Figure 10-93) are described in this manual:
• ARCHIVE TEST button
• See Section 5.7.1, Archiving the Tests
• RETRIEVE TEST button
• See Section 5.7.2, Retrieving Tests from an Archive File
• BACK button
Additional data management functions are described in Section 5.7, Managing Test
Results Data.
10.12.4 SETUP Menu Button

Pressing the SETUP menu button (see Figure 10-94) displays the Setup menu. See
Figure 10-95. The Setup menu is used to set up system parameters, system user access,
manage assays, set up system automation parameters and change system operation mode.
Administration users will see the menu shown in Figure 10-95. Detail users will see
fewer menu options.

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Figure 10-95. Xpertise Software Home Page – Setup Menu Shown (Administration User)
Figure 10-95. Xpertise Software Home Page – Setup Menu Shown (Administration User)
Below is a list of where the functionality of the buttons in the Setup menu workspace
• USER ADMINISTRATION button
• See Section 2.6.3, Managing Users.
• USER TYPE CONFIGURATION button
• See Section 2.6.2, Specifying User Permissions.
• SYSTEM CONFIGURATION button
• See Section 2.7, Configuring the System.
• AUTOMATION CONFIGURATION button
• See Section 2.8, Configuring the System Automation and Section 2.8.2,
Cartridge Retention Workspace.
• MANAGE ASSAYS button
• See Section 2.10, Managing Assay Definitions and Lot Specific Parameters.
• INSTALLATION QUALIFICATION button
• See Section 2.9, Verifying Proper Installation and Setup.

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• CHANGE OPERATION MODE button

• See Section 5.6.2, Changing from Automation Mode to Manual Mode
• See Section 5.6.4, Changing from Manual Mode to Automation Mode
• BACK button
10.12.5 MAINTENANCE Menu Button

Pressing the MAINTENANCE menu button (see Figure 10-96) displays the Maintenance
menu. See Figure 10-97 or Figure 10-98 (if logged in with administrative privileges).
The Maintenance menu allows you to perform various instrument maintenance tasks
such as cleaning instrument parts and exporting software log files for troubleshooting.

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Figure 10-97. Xpertise Software Home Page – Maintenance Menu Shown with Detail User Login
Figure 10-97. Xpertise Software Home Page – Maintenance Menu Shown with Detail User Login
Figure 10-98. Xpertise Software Home Page – Maintenance Menu Shown with Administrator User Login
Figure 10-98. Xpertise Software Home Page – Maintenance Menu Shown with Administrator User Login

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Below is a list of where the functionality of the buttons in the Maintenance menu
workspace (see Figure 10-97 and Figure 10-98) are described in this manual:
• GX MAINTENANCE button
See Section 9.8, Cleaning the Cartridge Bays and Plunger Rods.
• SYSTEM LOG button
See Section 9.12.2, System Log Report.
• EXPORT LOG FILE button
See Section 9.19, Export Log Files.
• AUTOMATION FAILED LOCATION button
See Section 9.21, Clearing Failed Automation Locations.
The AUTOMATION FAILED LOCATION button is only available if the user is logged in with
Note
administrator privileges. See Figure 10-98.
• CLEAN CONVEYOR button

See Section 9.5, Cleaning the Conveyor Belt.
• ABOUT button
The ABOUT button displays information about the Xpertise software and software
license agreement. This information is described on page 10-97.
• BACK button
The BACK button returns you to the previous menu (Main menu).
ABOUT Button
The ABOUT button (see Figure 10-97) opens the About Xpertise Software workspace.
See Figure 10-99.

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Figure 10-99. About Xpertise Software Workspace
Figure 10-99. About Xpertise Software Workspace

To view the Xpertise software license agreement, select the LICENSE button (see
Figure 10-99). The software license agreement will open in Adobe Reader. See
Figure 10-100. Read the complete software license agreement by scrolling through the
document in Adobe Reader. After reading the software license agreement, close Adobe
Reader.
Select the CLOSE button to close the About Xpertise Software workspace. See
Figure 10-99.

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Figure 10-100. Xpertise Software License Agreement Shown in Adobe Reader
Figure 10-100. Xpertise Software License Agreement Shown in Adobe Reader
10.13 Workspace Panel

The workspace panel displays the workspace corresponding to selected dashboard icons
or menu options. The currently selected Menu panel buttons or Menu options are also

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Figure 10-101. Xpertise Software Graphical User Interface Workspace Sections
Module Status Section Workspace Title
Message Log Workspace
Figure 10-101. Xpertise Software Graphical User Interface Workspace Sections

The graphical user interface (GUI) consists of four main sections or panels. See
Figure 10-101.
• Module Status Section – The Module Status section shows the status of each module
in the system. This section indicates modules are at available for test, disabled,
running a test and other module status conditions.
• Workspace Title – The Workspace Title identifies the workspace that is currently
displayed.
• Workspace – The workspace displays fields for data entry or information for the
selected option.
• Message Log – Pressing the Message Log icon populates the workspace panel with
the message log. See Section 10.11, Message Log.

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Tests Since Launch Workspace

After system initialization has been completed, the workspace panel displays the Tests
Since Launch workspace and the top level Menu buttons. The Tests Since Launch
workspace provides a table with the most recent 400 tests started since the software was
launched. See Figure 10-101.
To view the test results for a test that was recently performed (i.e. since the system was
last shut down or 400 tests), the results may be viewed by double-selecting any test
listed in the Tests Since Launch workspace. The View Results workspace will be
displayed for the selected test.
10.14 Retrieving Cartridges from the Accumulator

This section describes how to use the Cartridge I/O workspace (see
Figure 10-105) to transfer cartridges from the accumulator to the shuttle for manual
removal. Cartridges can be moved individually using the MOVE TO SHUTTLE button in
the Cartridge I/O workspace, or, alternatively, all cartridges available for transfer can be
moved by selecting the FILL SHUTTLE button in the Cartridge I/O workspace.
To retrieve a cartridge from the accumulator and move it to the shuttle:
1. On the dashboard, select the red View Outstanding Orders icon to see the cartridge(s)
that need attention. See Section 10.9.4, View Outstanding Orders Icon for more
information about this icon. The View Outstanding Orders workspace is displayed.
See Figure 10-102.
2. To cancel the test order at Accumulator Site 1 (ACC1), select the first row indicating
Detected for ACC1. See Figure 10-102.
3. Select the CANCEL ORDER button (see Figure 10-102). The View Outstanding
Orders workspace confirmation screen is displayed. See Figure 10-103.
4. Select the YES button (see Figure 10-103). The Detected row indicates Rejected. See
Figure 10-104.

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Figure 10-103. View Outstanding Orders Workspace Confirmation Screen
Figure 10-103. View Outstanding Orders Workspace Confirmation Screen

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Figure 10-104. View Outstanding Orders Workspace After Canceling Order
Figure 10-104. View Outstanding Orders Workspace After Canceling Order

Figure 10-105. Cartridge I/O Workspace
Figure 10-105. Cartridge I/O Workspace

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5. Select the Cartridge I/O icon (see Figure 10-104). The Cartridge I/O workspace is
6. There are two ways to move the cartridge(s) from the accumulator to the shuttle:
A. If you want to move an individual cartridge from the accumulator to the shuttle,
in the Accumulator tab, select the check box(es) adjacent to the cartridge row(s)
representing the cartridge(s) you want to remove and select the MOVE TO
SHUTTLE button. See Figure 10-105. The gantry will move four cartridges at a
time to the shuttle until all selected cartridges have been moved.
The Cartridge I/O workspace Shuttle tab then appears as shown in
Figure 10-106.
or
B. To move all eligible cartridges from the accumulator to the shuttle, in the
Accumulator tab, select the FILL SHUTTLE button. See Figure 10-105.
The Cartridge I/O workspace Shuttle tab then appears as shown in
Figure 10-107.
The gantry retrieves the cartridge(s) from the accumulator and moves the
cartridge(s) to the shuttle.
Figure 10-106. Cartridge I/O Workspace showing Shuttle Tab

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Figure 10-108. Cartridge I/O Workspace showing Remove Cartridges
Figure 10-108. Cartridge I/O Workspace showing Remove Cartridges

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7. Select the OPEN SHUTTLE button (see Figure 10-106 or Figure 10-107). The shuttle
will unlatch and the Cartridge I/O workspace instructing you to unload the cartridges
from the shuttle is displayed. See Figure 10-108.
8. Slowly pull the shuttle door open and remove all the cartridges. See Figure 10-109.
Important You must remove all cartridges from the shuttle.
9. As instructed in the Cartridge I/O workspace (see Figure 10-108), close the shuttle
door and select the OK button. The Cartridge I/O workspace Accumulator tab will
show that all cartridges have been removed from the accumulator. See
Figure 10-110.
Figure 10-109. Open the Shuttle Door and Remove the Cartridges
1 2
Figure 10-109. Open the Shuttle Door and Remove the Cartridges
10. Select the CLOSE button to close the Cartridge I/O workspace. See Figure 10-110.

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Figure 10-110. Cartridge I/O Workspace showing Accumulator Tab
Figure 10-110. Cartridge I/O Workspace showing Accumulator Tab
10.15 Removing a Cartridge That Has Not Been Ordered

If a cartridge is placed on the conveyor belt but an order has not been entered for the
cartridge, it will be placed on the accumulator. When it has been placed on the
accumulator, the Reminder icon will indicate that action is required and the View
Outstanding Orders icon will be red. See Figure 10-111.
To retrieve the cartridge for processing or removal from the system:
1. On the dashboard (see Figure 10-111), select the red View Outstanding Orders icon to
see the cartridge that needs attention. The View Outstanding Orders workspace will
2. In the Outstanding Orders workspace (see Figure 10-112), the cartridge that needs
attention will display a Cartridge Status of Detected. Note the time before the
cartridge is to expire under the Minutes to Expire column.
3. Select the cartridge to be removed from the system and select the CANCEL ORDER
button (see Figure 10-112). The confirmation will be displayed confirming that the
order should be cancelled. See Figure 10-113. Select the YES button. The Cartridge
Status will change to Rejected.

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Figure 10-111. Xpertise Software Screen showing Red View Outstanding Orders Icon
Figure 10-111. Xpertise Software Screen showing Red View Outstanding Orders Icon
Figure 10-112. View Outstanding Orders Workspace showing Cartridge Detected
Figure 10-112. View Outstanding Orders Workspace showing Cartridge Detected

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Figure 10-113. View Outstanding Orders Workspace Confirmation to Cancel Order
Figure 10-113. View Outstanding Orders Workspace Confirmation to Cancel Order

4. In the dashboard panel (see Figure 10-114), select on the CARTRIDGE I/O icon. The
Cartridge I/O workspace will be displayed showing the shuttle tab. See
Figure 10-115.
5. In the Cartridge I/O workspace (see Figure 10-115), select on the Accumulator tab.
The Accumulator tab will be displayed showing the rejected cartridge. See
Figure 10-116.
6. Remove the cartridges from the shuttle. See Section 10.14, Retrieving Cartridges
from the Accumulator. Follow the procedure to move cartridges from the
accumulator to the shuttle and to remove the cartridges from the shuttle starting with
Step 6.
If there is time to process the cartridge before it expires, enter the order for the cartridge
and place it back into the system.

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Figure 10-114. View Outstanding Orders Workspace showing Cartridge Rejected
Figure 10-114. View Outstanding Orders Workspace showing Cartridge Rejected

Figure 10-115. Cartridge I/O Workspace Shuttle Tab
Figure 10-115. Cartridge I/O Workspace Shuttle Tab

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Figure 10-116. Cartridge I/O Workspace Accumulator Tab Showing Rejected Cartridge
Figure 10-116. Cartridge I/O Workspace Accumulator Tab Showing Rejected Cartridge

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A Glossary
.gxa file – an assay definition file.

.gxr file – a lot-specific parameter file.
.gxx file – an archive file that contains multiple tests.
assay definition – a series of programmed steps to perform sample preparation,
amplification, and detection procedures.
accumulator – a shelf above the modules that hold cartridges that are not ready for
testing, are awaiting for a GeneXpert module to become available or holds cartridges
that have completed testing and have been marked for retention.
amplification curve – a graph with fluorescence detected plotted against the number
of PCR cycles. It is a graphical representation of the proportional relationship of
fluorescence detected and amplicon generated. A real-time amplification curve has three
distinct phases: baseline, log-linear and plateau. The increase in fluorescence is
proportional to the amount of amplicon generated and can be used to define the cycle
threshold.
conveyor – transports the cartridge from the kiosk into the instrument.
curve fit – the creation of a curve that best fits a specified set of data points on a
graph.
cycle threshold (Ct) – the first cycle in which the fluorescence reaches a specified
threshold. The Ct can be determined by analyzing the amplification curve (primary
curve).
data reduction – the process in which the system analyzes the raw data based on the
settings in the assay definition to determine the test result.
DMS (Data Management System – could be a stand-alone small scale information
system or compliment an LIS in the same facility. A DMS is a software application
which handles receiving, processing and storing information.
endogenous control (EC) – a control gene from the sample that normalizes targets
and/or helps ensure that sufficient sample is used in the test
endpoint – the fluorescence reading for the last cycle of a thermal cycling protocol.
I-CORE module – the component inside the GeneXpert module that performs PCR
amplification and detection (Intelligent Cooling/heating Optical REaction).
instrument module – an individual hardware component within which fluidic and
thermocycling protocols occur. Each module consists of a bay for holding a cartridge, a
plunger drive, a valve drive, an ultrasonic horn and an I-CORE module.
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Glossary
internal control (IC) – a control that helps verify the performance of the PCR
reagents and prevent a false negative result. The internal control PCR assay assesses if
there is any inhibition, possibly by components in the sample. The internal control is
provided in the cartridge and should be positive in a negative sample.
LIS (Laboratory Information System) – is a software application which handles
receiving, processing, and storing information generated by medical laboratory
processes. These systems often must interface with instruments and other information
systems, such as hospital information systems (HIS).
lobby – end of the conveyor at which the gantry (robotic arm) picks up a cartridge.
lot-specific parameters (LSP) – information about a reagent lot that is required by
some assay definitions to determine the test results. The lot-specific parameters are
included in the GeneXpert cartridge 2D barcodes and in the lot-specific parameter (.gxr)
files.
manual entry – entry of data into a field using the keyboard. Some fields provide a
choice between scanning the data or manually entering the data, such as Patient ID or
Sample ID.
module – see instrument module.
primary curve – a plot of fluorescence vs. cycle number. A real-time growth curve
should have three distinct phases: baseline, log-linear and plateau. The increase in
fluorescence is proportional to the amount of amplicon generated and can be used to
define the cycle threshold.
probe check – Before the start of the PCR reaction, the Infinity system measures the
fluorescence signal from the probes to monitor bead rehydration, reaction-tube filling,
probe integrity and dye stability. Probe Check passes if it meets the assigned acceptance
criteria.
reporter – a fluorescent dye or dye complex used to detect specific amplification
products.
sample processing control (SPC) – a control that helps ensure that a sample was
correctly processed. The SPC, which is included in the cartridge, is processed with the
sample and detected by PCR.
shuttle – holds used or rejected cartridges to be accessed by the operator. Transports
STAT priority cartridges into the instrument.
site – see instrument module.
system log – a report of incidents of instrument module self-tests and errors.
test – the laboratory process used to determine the presence of a substance and
measure the amount of that substance. In the Xpertise software, a test is a record of how
a specimen is processed. The record includes the instrument module ID, the assay
information, Sample ID, test type and notes about the test.
test type – the sample that is designated as a specimen, positive control or negative
control in the test.
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B Icons and Display Symbology
This chapter provides a list of all of the icons used in the Xpertise software for the
GeneXpert Infinity systems. For more information on each icon, see Chapter 10,
Features and Functions.
The topics are as follows:
• Section B.1, Status Bar Icons
• Section B.2, Dashboard Panel Icons
• Section B.3, Error Message Icons
• Section B.4, Menu Panel Command Buttons
• Section B.5, Access Windows Desktop
• Section B.6, Computer Desktop Icons
B.1 Status Bar Icons

The status bar icons are described in more detail in Section 10.10, Status Bar.
Table B-1. Status Bar Icons
Icon Description
Current User Name: Lists the current user name
Login: Allows users to log in to the Xpertise software
Logout: Allows users to log out of the Xpertise software
Change Password: Allows users to change their password
Exit: Exits the Xpertise software
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Icons and Display Symbology
B.2 Dashboard Panel Icons

The status bar icons are described in more detail in Section 10.9, Dashboard Panel.
Table B-2. Dashboard Panel Icons
Icon Description
Home: Returns to the top level of the menu panel buttons
Host (white): Indicates no host orders are pending
Host (green): Indicates a new test has been ordered by the host
Host (red): Indicates communication has been lost with the host
View Outstanding Orders (white): Indicates no outstanding orders
View Outstanding Orders (green): Indicates outstanding order(s) present
View Outstanding Orders (red/white): Indicates an outstanding order needs

attention
View Another Test: Command button to view another test
Glass Doors Unlocked: Indicates glass doors are unlocked
Glass Doors Open: Indicates one or more glass doors are open
Shuttle Open: Indicates that the shuttle is open
Database Status: Indicates that the database is empty or low
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Table B-2. Dashboard Panel Icons (Continued)
Icon Description
Database Status: Indicates that the database is almost full
Database Status: Indicates that the database is full
Non-STAT Module Status Icons for Automation Mode Only
System Utilization: Indicates that the system utilization is low for Non-STAT
modules
System Utilization: Indicates that the system utilization is medium for Non-STAT
modules
System Utilization: Indicates that the system utilization is high for Non-STAT
modules
STAT Module Status Icons for Automation Mode Only
System Utilization: Indicates that the system utilization is low for STAT modules
System Utilization: Indicates that the system utilization is medium for STAT
modules
System Utilization: Indicates that the system utilization is high for STAT modules
Waste Container: Indicates that the waste container door is unlocked
Waste Container: Indicates that the waste container is missing
Waste Container: Indicates that the waste container level is empty or low
Waste Container: Indicates that the waste container level is almost full
Waste Container: Indicates that the waste container level is full

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Table B-2. Dashboard Panel Icons (Continued)
Icon Description
Silence Alarm: Press button to silence the audible alarm
Pause: Press button to pause the automation system
Manual Mode: Indicates that the system is operating in Manual Mode
Error: Indicates that an error is present
Analysis Mode: Indicates that the system is operating in Analysis Mode
B.3 Error Message Icons

The error message icons are shown in Table B-3. Additional error message details are
described in Section 10.11, Message Log.
Table B-3. Error Message Icons and Buttons
Icon Description
Message Log: Button to display the Message Log
Information Message: Indicates an information message and no action is

required
Reminder Message: Indicates an automation reminder message that an action
has occurred with the automation subsystem
Host Communication Error: Indicates host communication is down
Automation Error: Indicates automation is down
Gantry Error: Indicates the gantry has an error

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Table B-3. Error Message Icons and Buttons (Continued)
Icon Description
Gripper Error: Indicates the gripper has an error
Gantry Scanner Error: Indicates the gantry scanner has an error
Kiosk Scanner Error: Indicates the kiosk scanner has an error
B.4 Menu Panel Command Buttons

The menu panel command buttons are shown in Table B-4 arranged alphabetically.
Additional menu panel command button details are described in Section 10.12, Menu
Panel.
Table B-4. Menu Panel Command Buttons
Button Description Located In Menu
ABOUT: Displays information about the Xpertise software MAINTENANCE
ASSAY STATISTICS REPORT: Generates the Assay Statistics Report RESULTS
AUTOMATION CONFIGURATION: Allows configuration of the system

SETUP
automation functions
AUTOMATION FAILED LOCATION: Allows clearing of failed locations after

MAINTENANCE
resolution of the error
Used in various
BACK: Returns to the previous menu or screen
menus
CHANGE OPERATION MODE: Used to change operation mode between

SETUP
Automation Mode and Manual Mode

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Table B-4. Menu Panel Command Buttons (Continued)
CLEAN CONVEYOR: Used to clean the conveyor belt MAINTENANCE
DATABASE
CLOSE: Closes the current workspace or menu MANAGEMENT
and various menus
DATABASE
COMPACT DATABASE: Used to compact the database
MANAGEMENT
CONTROL TREND REPORT: Generates the Control Trend Report RESULTS
DATA MANAGEMENT: Opens the Data Management menu to perform data

Top Level Menu
management activities
DATABASE
DATABASE BACKUP: Backs up the database MANAGEMENT
DATABASE
DATABASE INTEGRITY CHECK: Checks the integrity of the database
MANAGEMENT
DATABASE
DATABASE RESTORE: Restores a database backup
MANAGEMENT
EXPORT HOST SETTINGS: Exports the host settings to a .csv file in the
event they need to be restored in the future or if they are needed by Cepheid MAINTENANCE
Technical Support for troubleshooting.
EXPORT LOG FILE: Export the Application and Infinity Server log files for use
MAINTENANCE
by Cepheid Technical Support
FIND ORDER: Used to find a specific order in the system ORDERS
GX MAINTENANCE: Opens the GX Maintenance menu to allow maintenance

MAINTENANCE
on the modules
INSTALLATION QUALIFICATION: Creates the Installation Qualification

SETUP
Report

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MAINTENANCE: Opens the Maintenance menu to perform maintenance on Top Level Menu
the system
MANAGE ASSAYS: Allows importing and management of ADF files SETUP
MANAGE HOST ORDERS: Accesses the Manage Host Orders workspace ORDERS
ORDER TEST: Allows the user to order a test ORDERS
ORDERS: Opens the Order menu to allow the user to order tests and perform
Top Level Menu
other functions relating to tests
PATIENT REPORT: Creates a Patient Report RESULTS
RESULTS: Opens the Results menu to allow the user to view test results and
Top Level Menu
generate reports relating to tests
SETUP: Opens the Setup menu to allow the user to make changes to the Top Level Menu
system configuration and system user accounts
SPECIMEN REPORT: Creates a Specimen Report RESULTS
STOP TEST: Stops a running test ORDERS
SYSTEM CONFIGURATION: Allows a system administrator to change the

SETUP
system configuration
SYSTEM LOG: Creates a System Log Report MAINTENANCE
TEST SUMMARY: Creates a .csv file of completed tests matching the

RESULTS
selection criteria

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USER ADMINISTRATION: Allows a system administrator to add, delete or

SETUP
modify user accounts
USER TYPE CONFIGURATION: Allows a system administrator to change the SETUP

default privileges assigned to each user level
VIEW OUTSTANDING ORDERS: Allows the user to view all orders entered
ORDERS
into the system but not yet completed
VIEW RESULTS: Allows a user to view the results of a test RESULTS
B.5 Access Windows Desktop

When the Infinity system starts up, the user has access to the Windows desktop. After
starting the Xpertise software, the Windows desktop is no longer visible. To minimize all
windows and access the Windows desktop, press the Windows key and the M key at the
same time. See Figure B-1.
Figure B-1. Access to Windows Desktop
Windows Key M Key
Figure B-1. Access to Windows Desktop

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B.6 Computer Desktop Icons

The computer desktop icons commonly installed on the Infinity computer desktop are
shown in Table B-5.
The icons shown in Table B-5 are the icons normally found on the computer desktop. There may be
additional icons not listed that have been added by the customer or Cepheid. There may also be
Note
some icons that have been deleted by the customer and are no longer present on the computer
desktop.
Table B-5. Computer Desktop Icons
Icon Description
Xpertise Software: Shortcut icon to start up the Xpertise software
System Shutdown: Shortcut icon to shut down the Infinity system
Infinity Operator Manual: Shortcut icon to the GeneXpert Infinity System

Operator Manual
Adobe Reader: Shortcut icon to open the Adobe Reader software
GeneXpert Folder: Shortcut icon to the GeneXpert folder that contains the
database backup files, exported assays, archived tests, log files and
reports.

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Table B-5. Computer Desktop Icons (Continued)
Icon Description
Norton AntiVirus: Shortcut icon to the Norton AntiVirus utility
GeneXpert Support Database Backup: Shortcut icon to the GeneXpert

Support database backup utility to provide a database file to Cepheid
Technical Support. This utility is for troubleshooting purposes only by
Cepheid Remote Service Access: Shortcut icon to allow Cepheid

Technical Support to access the Infinity system for troubleshooting
purposes. This utility is for Cepheid Technical Support personnel use only.
ELO Touchscreen Calibration: Shortcut icon to allow Cepheid Technical

Support to perform touchscreen calibration on the monitor. This utility is for
Cepheid Service personnel use only.

302-1288, Rev. A April 2019
C Viewing Export (.csv) Files
This appendix explains how to view export files. The topics are as follows:
• Section C.1, Introduction
• Section C.2, Configuration
• Section C.2.1, Apache OpenOffice
• Section C.2.2, Microsoft Excel
• Section C.3, Opening and Viewing .csv Files
• Section C.3.1, Apache OpenOffice
• Section C.3.2, Microsoft Excel
• Section C.3.3, Setting the Default Program
C.1 Introduction
The Xpertise software exports some files as comma-separated value (.csv) files to
provide a backup of the information or for sending files to Cepheid Technical Support
for troubleshooting. The functions that create .csv files are the Export Host Settings and
Test Summary.
These files may be viewed using Microsoft Excel, Apache OpenOffice or another
software program that supports .csv files. Microsoft Excel will be installed on
GeneXpert Infinity systems shipped prior to Xpertise 6.8 software. Beginning with
Xpertise 6.8 software, Apache OpenOffice will be installed. For customers that have
upgraded their software from an version prior to Xpertise 6.8, it is possible to have both
Microsoft Excel and Apache OpenOffice installed.
This appendix provides instructions for the configuration of Apache OpenOffice on your
system. Apache OpenOffice is used for viewing, formatting and storing .csv files. On
initial startup, the program must be configured for proper display of the .csv files.
For GeneXpert Infinity systems using software versions prior to Xpertise 6.3, Microsoft Excel (part of
Microsoft Office software) is used for displaying .csv files, and no configuration is necessary for that
Note
software. If you need assistance, see the Technical Assistance section in the Preface for contact
information.
This appendix also provides instructions for viewing .csv files using Apache OpenOffice
and Microsoft Excel.
GeneXpert Infinity System Operator Manual C-1

302-1288, Rev. A April 2019
Viewing Export (.csv) Files
C.2 Configuration
C.2.1 Apache OpenOffice
This section describes the initial configuration of Apache OpenOffice. This procedure
will only need to be done when Apache OpenOffice in initially started. All settings will
be saved and used whenever Apache OpenOffice is used except as noted in the section
on using Apache OpenOffice.
1. If you are currently running Xpertise, either exit the Xpertise software or press the
Windows key and the M key to access the computer desktop.
2. From the GeneXpert Folder shortcut on the computer desktop, navigate to the export
folder.
3. In the export folder, right-click on the .csv file you want to open. When the drop-
down menu appears, click Open with and select OpenOffice Calc. See Figure C-1.
Figure C-1. Opening a .csv File to Configure Apache OpenOffice
Figure C-1. Opening a .csv File to Configure Apache OpenOffice
C-2 GeneXpert Infinity System Operator Manual

302-1288, Rev. A April 2019
Figure C-2. Registration Screen
Figure C-2. Registration Screen

4. On initial startup of Apache OpenOffice, a Welcome dialog box will be displayed
(see Figure C-2). Click Next to display the User Name dialog box. See Figure C-3.
Figure C-3. User Name Dialog Box
Figure C-3. User Name Dialog Box

5. Enter the requested information (name and initials) into the User Name dialog box
and click Finish. The Text Import dialog box will be displayed. See Figure C-4.

302-1288, April 2019
Figure C-4. Text Import Screen showing Default Settings
Figure C-4. Text Import Screen showing Default Settings

6. For the Import Character set drop-down menu:
• For single-byte languages, select Unicode (UTF-8).
• For multi-byte languages, select Unicode.
7. For the Separator options (see Figure C-5):
• Uncheck Semicolon.
• Uncheck Space.
• Check Comma.
• Check Quoted field as text.

302-1288, Rev. A April 2019
Figure C-5. Text Import Screen with New Settings Selected
Figure C-5. Text Import Screen with New Settings Selected

8. After making selections, click OK. The .csv file will be open. See Figure C-6.
9. In the .csv file, select all the active cells by clicking in the upper left corner of the
file display, as shown in Figure C-6. The active cells will turn blue.
10. Right-click in the blue area on column A. A drop-down menu will appear at the right
of the column (see Figure C-7).

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Figure C-6. All Cells Selected

Figure C-7. Drop-Down Menu to Select Column Width
Right-Click in Column A

302-1288, Rev. A April 2019
Figure C-8. Column Width Dialog Box
Figure C-8. Column Width Dialog Box

11. In this drop-down menu, click Column Width. The Column Width dialog box is
displayed. See Figure C-8.
12. Click the check box to the left of Default value and then click OK to close the dialog
box. The column widths will then adjust and the file will be formatted, as shown in
Figure C-9. Click anywhere in the blank columns to deselect the blue cells and turn
the cells white again.
13. Click Save under the File menu to save the document. The save format dialog box
shown in Figure C-10 may appear. If so, choose Keep Current Format, and the dialog
box will close.

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Figure C-9. Final View of File with Columns Adjusted

Figure C-10. Format Saving Dialog Box
Figure C-10. Format Saving Dialog Box

302-1288, Rev. A April 2019
14. This completes the configuration set-up for the initial .csv file. For all subsequent
.csv files no setup will be required, and it will only be necessary to acknowledge the
existing settings selected in this procedure.
15. Close Apache OpenOffice.
16. Continue running Xpertise, if desired, by selected the Xpertise icon from the task bar
or by restarting Xpertise from the shortcut icon on the desktop.
C.2.2 Microsoft Excel

If the GeneXpert Infinity system has Microsoft Excel installed, it will already be
configured. No configuration should be required.
C.3 Opening and Viewing .csv Files

C.3.1 Apache OpenOffice
This section describes how to open and view .csv files using Apache OpenOffice.
See Section C.2, Configuration for in-depth instructions for configuring Apache OpenOffice.
Note
Some earlier GeneXpert Infinity systems may have Microsoft Office installed, and .csv files can be
opened and viewed using the Excel program available in that software suite as well.
2. In the GeneXpert folder on the computer desktop, navigate to the Export folder.
3. In the Export folder, right-click on the .csv file you want to open. When the drop-
down menu is displayed, click Open with and select OpenOffice Calc (see
Figure C-11). The Text Import dialog box will be displayed. See Figure C-12.
4. In the Text Import dialog box, verify that the check boxes to the left of Comma and
Quoted field as text have been checked. See Figure C-12.

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Figure C-11. Opening a .csv File with Apache OpenOffice
Figure C-11. Opening a .csv File with Apache OpenOffice

Figure C-12. Text Import Screen with Correct Settings Selected

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Right-Click in Column A

302-1288, April 2019
5. After verifying that the correct options have been selected, click OK. The .csv file
will open. See Figure C-13.
6. In the .csv file, select all the active cells by clicking in the upper left corner of the
file display, as shown in Figure C-13. The active cells will turn blue.
7. Right-click in the blue area on column A. A drop-down menu will appear at the right
of the column (see Figure C-13).
8. In this drop-down menu, click Column Width.
9. The Column Width dialog box is displayed. See Figure C-14
10. Click the check box to the left of Default value and then click OK to close the dialog
box. The column widths will then adjust and the file will be formatted, as shown in
Figure C-15. Click anywhere in the blank columns to deselect the blue cells and turn
the cells white again.
11. Click Save under the File menu to save the document.
12. After viewing or changing the file, close Apache OpenOffice.
13. Continue running Xpertise, if desired, by selected the Xpertise icon from the task bar
or by restarting Xpertise using the shortcut icon on the desktop.

302-1288, Rev. A April 2019
C.3.2 Microsoft Excel

This section describes how to open and view .csv files using Microsoft Excel.
Microsoft Excel will only be installed on earlier GeneXpert Infinity systems that had Xpertise
Note
software earlier than version 6.3.
3. In the Export folder, double-click on the .csv file you want to open. The .csv file will
open.
4. After the file opens, view or modify the information, as required.
5. Click Save under the File menu to save the document.
6. After viewing or changing the file, close Apache OpenOffice.
7. Continue running Xpertise, if desired, by selecting the Xpertise icon from the task
bar or by restarting Xpertise using the shortcut icon on the desktop.
C.3.3 Setting the Default Program

This section describes how to set the default program to view .csv files. After setting the
default program, .csv files may be opened by double-clicking on the filename instead of
having to select the program to open and view the files.
This section is applicable only to systems that have both Microsoft Excel and Apache OpenOffice
Note
installed on their systems.
3. In the Export folder, right-click on the .csv file you want to open. When the drop-
down menu is displayed, click Choose default program... (see Figure C-16). The
Open with dialog box will be displayed. See Figure C-17.
4. Select the desired program to use (OpenOffice Calc or Microsoft Excel.
5. Click OK.
The default program has now been set for viewing .csv files in the future. This feature
can also be changed at any time if the desired program changes.

302-1288, April 2019
Figure C-16. Choosing the Default Program to Open .csv Files
Figure C-16. Choosing the Default Program to Open .csv Files


302-1288, Rev. A April 2019

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GeneXpert® Infinity System

GeneXpert Infinity-48s GeneXpert Infinity-80

Xpertise™ Software Version 6.8

302-1288, Rev. A April 2019

GeneXpert Infinity System Operator Manual 3

Table of Hazardous Substance’s Names and Concentrations

Product Name: GeneXpert® Infinity System

California Proposition 65 Warning

4 GeneXpert Infinity System Operator Manual

2 Setup / Installation Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

GeneXpert Infinity System Operator Manual TOC-1

2.7.4 Host Communication Settings Workspace . . . . . . . . . . . . . . . . . . . . . . . . . 2-32

3 Principles of Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1

TOC-2 GeneXpert Infinity System Operator Manual

4 Performance Characteristics and Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1

5 Operating Instructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1

GeneXpert Infinity System Operator Manual TOC-3

5.5.5 Generating Test Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-72

TOC-4 GeneXpert Infinity System Operator Manual

6 Calibration Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1

7 Operational Precautions and Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1

9 Service and Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1

GeneXpert Infinity System Operator Manual TOC-5

9.5 Cleaning the Conveyor Belt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-15

TOC-6 GeneXpert Infinity System Operator Manual

9.18 Troubleshooting Host Connectivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-102

10 Features and Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-1

GeneXpert Infinity System Operator Manual TOC-7

10.5.8 Waste Container . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-17

TOC-8 GeneXpert Infinity System Operator Manual

10.12 Menu Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-54

B Icons and Display Symbology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-1

C Viewing Export (.csv) Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-1

GeneXpert Infinity System Operator Manual TOC-9

TOC-10 GeneXpert Infinity System Operator Manual

GeneXpert Infinity System Operator Manual LOF-1

Figure 2-30 Automatic Archive Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-30

LOF-2 GeneXpert Infinity System Operator Manual

GeneXpert Infinity System Operator Manual LOF-3

Figure 5-18 Xpertise Software Exit Workspace Confirmation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-19

LOF-4 GeneXpert Infinity System Operator Manual

Figure 5-53 Order Test – Patient ID Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-47

GeneXpert Infinity System Operator Manual LOF-5

LOF-6 GeneXpert Infinity System Operator Manual

Figure 5-123 Xpertise Software Home Workspace Setup Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-107

GeneXpert Infinity System Operator Manual LOF-7

Figure 5-158 Compact Database Workspace – Compact Database Complete . . . . . . . . . . . . . . . .5-133

LOF-8 GeneXpert Infinity System Operator Manual

GeneXpert Infinity System Operator Manual LOF-9

LOF-10 GeneXpert Infinity System Operator Manual

Figure 9-32 Plunger Rod Maintenance Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-39

GeneXpert Infinity System Operator Manual LOF-11

Figure 9-67 Exclude Modules From Test Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-71

LOF-12 GeneXpert Infinity System Operator Manual

Figure 10-4 USB Port Locations on Left Side of Monitor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10-6

GeneXpert Infinity System Operator Manual LOF-13

Figure 10-39 Pause - Confirmation Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10-44

LOF-14 GeneXpert Infinity System Operator Manual

GeneXpert Infinity System Operator Manual LOF-15

Figure 10-108 Cartridge I/O Workspace showing Remove Cartridges . . . . . . . . . . . . . . . . . . . . . . .10-105