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

ABSTRACT Aim: To demonstrate that microsatellite instability (MSI) whole exome sequencing (WES) is an accurate next-generation sequencing (NGS)-based MSI-testing method. Materials & Methods: Microsatellite-based indels were counted in the variant call-formatted WES data of 441 gastric cancer cases using Unix-based algorithms, and the counts expressed as a fraction of the genome sequenced to obtain the NGS-based MSI indices. Results: The NGS-based MSI indices showed a near-perfect concordance with polymerase chain reaction (PCR)-based MSI status; and moderate to good correlations with the molecular targets of MSI (MTM) index, MLH1 expression and MLH1 methylation status, at a level comparable to the strengths of correlation between PCR-based MSI status and MTM index/MLH1 expression and methylation. Conclusion: MSI-WES is a valid, adequate, and sensitive approach for testing MSI in cancer.