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MSI was examined using over 7000 target microsatellite loci and compared to the reference genome hg19 from the University of California, Santa Cruz (UCSC) Genome Browser database. The number of microsatellite loci that were altered by insertion or deletions (indels) was counted for each sample. Only indels that increased or decreased the number of repeats were considered. Genomic variants in the microsatellite loci were detected using the same depth and frequency criteria as we used for mutation detection. MSI-NGS results were compared to results from over 2000 matching clinical cases analyzed with traditional PCR-based methods. The threshold to determine MSI-High by NGS was determined to be 46 or more loci with indels to generate a sensitivity of >95% and specificity of >99%.3
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