title: Microsatellite instability detection by next generation sequencing.
abstract: BACKGROUND
  Microsatellite instability (MSI) is a useful phenotype in cancer diagnosis and prognosis. Nevertheless, methods to detect MSI status from next generation DNA sequencing (NGS) data are underdeveloped.
  
  
  METHODS
  We developed an approach to detect the MSI phenotype using NGS (mSINGS). The method was used to evaluate mononucleotide microsatellite loci that were incidentally sequenced after targeted gene enrichment and could be applied to gene or exome capture panels designed for other purposes. For each microsatellite locus, the number of differently sized repeats in experimental samples were quantified and compared to a population of normal controls. Loci were considered unstable if the experimental number of repeats was statistically greater than in the control population. MSI status was determined by the fraction of unstable microsatellite loci.
  
  
  RESULTS
  We examined data from 324 samples generated using targeted gene capture assays of 3 different sizes, ranging from a 0.85-Mb to a 44-Mb exome design and incorporating from 15 to 2957 microsatellite markers. When we compared mSING results to MSI-PCR as a gold standard for 108 cases, we found the approach to be both diagnostically sensitive (range of 96.4% to 100% across 3 panels) and specific (range of 97.2% to 100%) for determining MSI status. The fraction of unstable microsatellite markers calculated from sequencing data correlated with the number of unstable loci detected by conventional MSI-PCR testing.
  
  
  CONCLUSIONS
  NGS data can enable highly accurate detection of MSI, even from limited capture designs. This novel approach offers several advantages over existing PCR-based methods.
authors.affiliation: Department of Laboratory Medicine, University of Washington, Seattle WA;
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Salipante
authors.affiliation: Department of Laboratory Medicine, University of Washington, Seattle WA;
authors.forename: Sheena M
authors.initials: SM
authors.lastname: Scroggins
authors.affiliation: Department of Internal Medicine, Division of Human Genetics, The Ohio State University, Columbus, OH.
authors.forename: Heather L
authors.initials: HL
authors.lastname: Hampel
authors.affiliation: Department of Laboratory Medicine, University of Washington, Seattle WA;
authors.forename: Emily H
authors.initials: EH
authors.lastname: Turner
authors.affiliation: Department of Laboratory Medicine, University of Washington, Seattle WA; cpritch@uw.edu.
authors.forename: Colin C
authors.initials: CC
authors.lastname: Pritchard
mesh_terms: D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D053842:Microsatellite Instability; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D009369:Neoplasms / Q000175:diagnosis; D010641:Phenotype