Detection of Microsatellite Instability Biomarkers via Next-Generation Sequencing. Methods Mol Biol 2020;2055:119-132
Date
09/11/2019Pubmed ID
31502149Pubmed Central ID
PMC7010320DOI
10.1007/978-1-4939-9773-2_5Scopus ID
2-s2.0-85071994590 (requires institutional sign-in at Scopus site) 37 CitationsAbstract
A high level of microsatellite instability (MSI-H+) is an emerging predictive and prognostic biomarker for immunotherapy response in cancer. Recently, MSI-H+ has been detected in a variety of cancer types, in addition to the classical cancers associated with Lynch Syndrome. Clinical testing for MSI-H+ is currently performed primarily through traditional polymerase chain reaction (PCR) or immunohistochemistry (IHC) assays. However, next-generation sequencing (NGS)-based approaches have been developed which have multiple advantages over traditional assays. For instance, NGS has the ability to interrogate thousands of microsatellite loci compared with just 5-7 loci that are detected by PCR. In this chapter, we detail the biochemical and computational steps to detect MSI-H+ from analysis of paired tumor and normal samples through NGS. We begin with DNA extraction, describe sequencing library preparation and quality control (QC), and outline the bioinformatics steps necessary for sequence alignment, preprocessing, and MSI-H+ detection using the software tool MANTIS. This workflow is intended to facilitate more widespread usage and adaptation of NGS-powered MSI detection, which can be eventually standardized for routine clinical testing.
Author List
Bonneville R, Krook MA, Chen HZ, Smith A, Samorodnitsky E, Wing MR, Reeser JW, Roychowdhury SAuthor
Hui-Zi Chen MD, PhD Assistant Professor in the Medicine department at Medical College of WisconsinMESH terms used to index this publication - Major topics in bold
Biomarkers, TumorGene Library
High-Throughput Nucleotide Sequencing
Humans
Microsatellite Instability
Neoplasms
Prognosis
Sequence Analysis, DNA
