MSI-WES: a simple approach for microsatellite instability testing using whole exome sequencing.

To demonstrate that MSI-WES is an accurate testing method for microsatellite instability (MSI). Microsatellite-based indels were counted in the variant call-formatted whole exome sequencing (WES) data of 441 gastric cancer cases using Unix-based algorithms, and the counts expressed as a fraction of the genome sequenced to obtain next-generation sequencing-based MSI indices. The next-generation sequencing-based MSI indices showed a near-perfect concordance with PCR-based MSI status, and moderate to good correlations with the molecular targets of MSI index, expression and methylation status, at a level comparable to the strengths of correlation between PCR-based MSI status and molecular targets of MSI index/ expression and methylation.