Journal
FUTURE ONCOLOGY
Volume 17, Issue 27, Pages 3595-3606Publisher
FUTURE MEDICINE LTD
DOI: 10.2217/fon-2021-0132
Keywords
gastric cancer; indels; microsatellite instability; MLH1 methylation and expression; molecular targets of MSI; MSI indices; next-generation sequencing; PCR; variant call format files; whole exome sequencing
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This study demonstrates that MSI-WES is an accurate and sensitive method for testing MSI in cancer, showing strong correlations with PCR-based MSI status and molecular targets.
Aim: To demonstrate that MSI-WES is an accurate testing method for microsatellite instability (MSI). Materials & methods: 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. Results: 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, MLH1 expression and MLH1 methylation status, at a level comparable to the strengths of correlation between PCR-based MSI status and molecular targets of MSI index/MLH1 expression and methylation. Conclusion: MSI-WES is a valid, adequate and sensitive approach for testing MSI in cancer.
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