We are thrilled to share the presentation of Stephanie Chrysanthou, PhD, our R&D Manager at Integrated Genomics Operation Memorial Sloan Kettering Cancer Center, on detection of germline alterations in solid #cancer patient samples by adaptive sampling 🙌 presented at the Nanopore Community Meeting conference in Boston! Our core has closely partnered with the Molecular Pathology & Diagnostics lab to benchmark Adaptive Sampling long read #sequencing for detecting germline #mutations against prior MSK-IMPACT profiles generated by hybridization capture short-read sequencing. Adaptive Sampling is a promising approach due to reduced technical complexity and TAT, there is no need for sample batching and it facilitates the resolution of large complex structural #variants. Due to the live #basecalling capacity of the #nanopore technology, the sequencing can be stopped if a fragment does not match the uploaded target .bed file, thus enriching on-target fragment #sequencing. Briefly, our on-instrument data workflow includes: 1) filtering of the raw .pod5 files based on the on-target decision, 2) SUP basecalling, 3) GRCh38 alignment, 4) SNV/SV calling using #EPI2ME and #SEVERUS pipelines. On a routine basis, this workflow, from #hmwDNA extraction to data analysis, takes 3.5 days. Feel free to watch the full presentation here 👇 (it's free to register and you'll get access to all ONT conference presentations!) Oxford Nanopore Technologies https://lnkd.in/ezE_vsYT
Integrated Genomics Operation
Research Services
New York, New York 291 followers
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About us
The Integrated Genomics Operation (IGO) core enables basic, clinical, and translational science by providing a broad range of services and expertise to investigators interested in evaluating gene expression, chromosome structure, and nucleotide sequence. Our services are comprehensive, rapid, and user-friendly. Through the centralized management of all sequencing activities at MSK, the core empowers scientists with an array of technological options and the most efficient and cost-effective means of performing high-throughput genomics.
- Website
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https://www.mskcc.org/research/ski/core-facilities/integrated-genomics-operation-igo
External link for Integrated Genomics Operation
- Industry
- Research Services
- Company size
- 11-50 employees
- Headquarters
- New York, New York
- Type
- Educational
- Specialties
- Genomics, Transcriptomics, Sequencing, Spatial Transcriptomics, Whole Exome Sequencing, Whole Genome Sequencing, ATAC-Seq, ChIP-Seq, Single Cell RNA-Seq, DNA Extraction, RNA Extraction, and Long-read sequencing
Locations
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Primary
Get directions
1250 First Avenue
New York, New York 10065, US