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    Fast Facts: Comprehensive Genomic Profiling: Making precision medicine possible
    Fast Facts: Comprehensive Genomic Profiling: Making precision medicine possible
    Fast Facts: Comprehensive Genomic Profiling: Making precision medicine possible
    Ebook177 pages1 hour

    Fast Facts: Comprehensive Genomic Profiling: Making precision medicine possible

    By B.L. Rapoport, G. Troncone, F. Schmitt and S. Nayler

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    About this ebook

    Cancer is a multifaceted disease in which genetic changes induce uncontrolled tumor growth. Genomic characterization of cancer is now leading to better diagnostic, prognostic and predictive biomarkers, and effective individualized management. 'Fast Facts: Comprehensive Genomic Profiling' provides a crash course in the science, methods and application of genomic profiling. Assuming only the most basic knowledge – or memory – of cell biology, the authors provide an overview of DNA and RNA biology and next-generation sequencing. This sets in context the descriptions of prognostic and predictive biomarkers for different cancer types and genomic-based treatments. Finally, but importantly, some of the practicalities of gaining and interpreting genomic information are described. Whether you need a primer or a refresher, this short colorful book demystifies this complex subject. Contents: • Genetic mutations and biomarkers • Understanding next-generation sequencing • Elements of comprehensive genomic profiles • Role in precision oncology • Predictive and prognostic biomarkers • Overcoming barriers to genotype-directed therapy
    LanguageEnglish
    PublisherS. Karger
    Release dateNov 3, 2020
    ISBN9783318068191
    Fast Facts: Comprehensive Genomic Profiling: Making precision medicine possible

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      Book preview

      Fast Facts - B.L. Rapoport

      Introduction

      The ability to decode DNA sequences is providing scientists with powerful insights into cancer biology. From a molecular perspective, cancer is a multifaceted disease involving multiple genetic variations and subsequent changes in gene expression patterns that induce uncontrolled tumor growth. The genomic characterization of cancer is leading to the identification and use of better diagnostic, prognostic and predictive biomarkers and more effective management.

      The introduction of rapid DNA-sequencing procedures has significantly accelerated biological and medical research and discoveries. Academic researchers obtained the first DNA sequences in the early 1970s, using arduous procedures based on two-dimensional chromatography. Frederick Sanger was awarded two Nobel prizes, one for the sequencing of proteins and the other for the sequencing of DNA.

      The next step from Sanger sequencing, next-generation sequencing (NGS), enables genome sequencing at high speed and low cost. By increasing the affordability, accessibility and reliability of DNA and RNA high-throughput sequencing platforms, NGS has revolutionized the practice of oncology, enabling clinicians to deliver personalized care to their patients. It is important to emphasize that while NGS provides molecular information, the treating clinician should interpret this in light of the clinical picture of the patient. The NGS platform does not recommend how to treat a patient.

      Personalized medicine – an innovative concept – tailors therapeutic approaches to patients based on their genomic, epigenomic and proteomic profiles. The assessment of mutations associated with sensitivity or resistance to various forms of treatments provides oncologists with strong evidence to support treatment strategies for specific cancers.

      Fast Facts: Comprehensive Genomic Profiling reminds healthcare professionals of basic DNA and RNA biology and provides an accessible overview of NGS, prognostic and predictive biomarkers for different cancer types and molecular-guided treatment options.

      Basic principles in cell biology

      The human body is constituted of trillions of cells, the fundamental building blocks of all living organisms. Cells provide structure for the body, take in nutrients from food, convert those nutrients into energy and carry out specific functions. The nucleus functions as the cell’s control center, sending instructions to the cell to grow, mature, divide or die (apoptosis).

      DNA is the body’s hereditary material – it can be duplicated during the process of cell division. Most of the cellular DNA is packaged into thread-like structures called chromosomes, which are found in the nucleus. Humans have 23 pairs of chromosomes, giving a total of 46 chromosomes. Each chromosome is made up of DNA tightly coiled many times around proteins called histones that support its structure (Figure 1.1). At each end of a chromosome there is a telomere, a region of repetitive nucleotide sequences. Telomeres protect the end of the chromosome from deterioration or fusion with neighboring chromosomes.

      Figure 1.1 The DNA molecules are wrapped around complexes of histone proteins and ‘packed’ into the chromosomes. Telomeres at the ends of the chromosome comprise long stretches of repeated TTAGGG sequences, which help stabilize the chromosomes.

      A small amount of DNA can be found in the mitochondria – this is referred to as mitochondrial DNA (mtDNA) (see later).

      DNA bases. The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C) and thymine (T). Human DNA comprises about 3 billion bases. It is essential to appreciate that more than 99% of those bases are the same in all people. The sequence of these bases controls the information available for building, developing and preserving the body.

      Nucleotides and DNA structure. DNA bases pair up with each other, A with T and C with G, to form a unit called a base pair (bp). Each base is also attached to a sugar molecule and a phosphate molecule. Together, a base, sugar and phosphate are called a nucleotide. Nucleotides are arranged in two long strands that form a double helix (Figure 1.2). Although the circumstances of the discovery of DNA structure in the 1950s are fairly well known, they are usefully summarized in a 2019 article on Watson and Crick’s original paper in Nature.¹

      Figure 1.2 (a) Double-stranded DNA forms a double helix. The two strands are joined by hydrogen bonds between the bases. The sugar–phosphate backbones run in opposite directions, so a 3' end on one strand aligns with a 5' end on the other strand. (b) A ball-and-stick model of a single base (adenine in this figure) with part of the helix backbone. Gray, carbon; white, hydrogen; blue, nitrogen; red, oxygen; and orange,

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