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Updated: Jan 30, 2026
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Published on: July 3, 2025
Molecular and Computational Methods for the Detection of Microsatellite Instability in Cancer
Laura G Baudrin1,2, Jean-François Deleuze1,3, Alexandre How-Kit1
1Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Paris, France.
Abstract:
Microsatellite instability (MSI) is a genomic alteration in which microsatellites, usually of one to four nucleotide repeats, accumulate mutations corresponding to deletions/insertions of a few nucleotides. The MSI phenotype has been extensively characterized in colorectal cancer and is due to a deficiency of the DNA mismatch repair system. MSI has recently been shown to be present in most types of cancer with variable frequencies (from <1 to 30%). It correlates positively to survival outcome and predicts the response to immune checkpoint blockade therapy. The different methods developed for MSI detection in cancer require taking into consideration two critical parameters which influence method performance. First, the microsatellite markers used should be chosen carefully to ensure they are highly sensitive and specific for MSI detection. Second, the analytical method used should be highly resolute to allow clear identification of MSI and of the mutant allele genotype, and should present the lowest limit of detection possible for application in samples with low mutant allele frequency. In this review, we describe all the different molecular and computational methods developed to date for the detection of MSI in cancer, how they have evolved and improved over the years, and their advantages and drawbacks.
Insights
Microsatellite instability (MSI) is a key genomic alteration found in many cancers. Detecting MSI accurately is crucial for predicting patient survival and response to immunotherapy.
Area of Science:
- Genomics
- Molecular Biology
- Cancer Research
Background:
- Microsatellite instability (MSI) is a genomic alteration resulting from DNA mismatch repair deficiencies.
- MSI is observed in various cancers, with frequencies ranging from less than 1% to 30%.
- MSI status impacts patient survival and predicts response to immune checkpoint blockade therapy.
Purpose of the Study:
- To review molecular and computational methods for detecting MSI in cancer.
- To discuss the evolution, advantages, and drawbacks of different MSI detection techniques.
- To highlight critical parameters for accurate MSI detection: marker selection and analytical method resolution.
Main Methods:
- Review of existing literature on MSI detection methods.
- Analysis of molecular techniques (e.g., PCR-based assays).
- Evaluation of computational approaches for MSI analysis.
Main Results:
- MSI detection methods have evolved significantly over time.
- Method performance is influenced by microsatellite marker choice and analytical resolution.
- Sensitive detection of MSI is vital for samples with low mutant allele frequencies.
Conclusions:
- Accurate MSI detection is essential for personalized cancer therapy.
- Careful selection of microsatellite markers and high-resolution analytical methods improve detection accuracy.
- Continued development of MSI detection techniques is important for advancing cancer treatment.
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