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Related Experiment Video

Updated: Oct 27, 2025

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

Henry O Ebili1,2, Adedeji Oj Agboola2, Emad Rakha1

  • 1Division of Cancer & Stem Cell, University of Nottingham, Nottingham, NG7 2UH, UK.

Future Oncology (London, England)
|July 22, 2021
PubMed
Summary

Whole exome sequencing (WES) accurately measures microsatellite instability (MSI) in cancer. This next-generation sequencing method aligns well with traditional PCR-based tests, offering a sensitive approach for MSI detection.

Keywords:
MLH1 methylation and expressionMSI indicesPCRgastric cancerindelsmicrosatellite instabilitymolecular targets of MSInext-generation sequencingvariant call format fileswhole exome sequencing

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Area of Science:

  • Oncology
  • Genomics
  • Molecular Diagnostics

Background:

  • Microsatellite instability (MSI) is a key biomarker in cancer diagnostics and treatment selection.
  • Accurate and efficient methods for MSI detection are crucial for clinical applications.
  • Whole exome sequencing (WES) offers a comprehensive genomic profiling approach.

Purpose of the Study:

  • To validate microsatellite instability Whole Exome Sequencing (MSI-WES) as a precise diagnostic tool for MSI.
  • To assess the concordance of MSI-WES with established MSI testing methods.
  • To evaluate the correlation of MSI-WES with molecular indicators of MSI.

Main Methods:

  • Analysis of microsatellite-based indels in whole exome sequencing (WES) data from 441 gastric cancer cases.
  • Utilized Unix-based algorithms to quantify indel frequencies and derive next-generation sequencing-based MSI indices.
  • Compared MSI-WES results with PCR-based MSI status and molecular targets (MLH1 expression and methylation).

Main Results:

  • MSI-WES demonstrated near-perfect concordance with PCR-based MSI status.
  • MSI-WES showed moderate to good correlations with MLH1 expression and methylation.
  • The performance of MSI-WES in correlating with molecular targets was comparable to PCR-based MSI status.

Conclusions:

  • MSI-WES is a valid, adequate, and sensitive method for assessing microsatellite instability in cancer.
  • This next-generation sequencing approach provides a reliable alternative for MSI testing.
  • MSI-WES can be effectively integrated into cancer diagnostics.