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.