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Microsatellite Instability Analysis (MSI)

Characterize MSI Status of Your Research Samples

  • Greater accuracy than immunohistochemistry (IHC) for identifying MSI-high samples
  • Fluorescent Multiplex PCR-based method using DNA extracted from precious samples
  • Easier to use, less expensive and faster turnaround than NGS


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Microsatellite Instability Analysis (MSI)
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Focus Your Research on DNA Mismatch Repair Dysfunction Using the Proven Gold Standard Method

The MSI Analysis System, Version 1.2, is a fluorescent multiplex PCR-based method for detecting microsatellite instability (MSI). MSI is a form of genomic instability caused by the insertion or deletion of repeating bases called microsatellites during DNA replication and the failure of the mismatch repair system (MMR) to correct these errors. 

Illustration of MSI analysis in cancer research

MSI Analysis Workflow

In a routine research laboratory, the time from sample input to MSI status determination can range from overnight to two days. With the MSI Analysis System, you can have data ready for analysis overnight.

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DNA Isolation

5 hours including incubation

msi workflow maxwell purification

Maxwell® RSC Instrument and Maxwell® RSC FFPE DNA Kit.

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~3 hours

msi workflow amplification

MSI Analysis System, v1.2

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Capillary Electrophoresis

45 minutes

msi workflow ab3500 instrument
Applied Biosystems® 3500, 3130 or 310 Genetic Analyzer
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Data Analysis

<1 hour

msi workflow analysis

Customer CE Analysis Software

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Characterizing MSI Status

MSI analysis typically involves comparing allelic profiles of microsatellite markers generated by amplification from matching pairs of test samples. The presence of alleles in the abnormal sample that are not found in the corresponding normal sample are indicative of MSI. The Promega MSI Analysis System includes seven multiplexed  markers for analysis of the MSI-high (MSI-H) phenotype; five nearly monomorphic mononucleotide repeat markers (BAT-25, BAT-26, MONO-27, NR-21 and NR-24) and two highly polymorphic pentanucleotide repeat markers (Penta C and Penta D) , which are a quality control for sample authentication of matched normal and tumor. 

Tumor Research Samples

MSI electropharogram for tumor research tissue
Panels A, B, and C were generated with research consented colorectal cancer using an Applied Biosystems® 3500 xL Genetic Analyzer. After comparison to its source-matched normal reference sample (Panels D, E and F, right), microsatellite instability is noted at markers BAT-26, NR-21, BAT-25, MONO-27, and NR-24 and is considered MSI high (MSI-H).

Source-Matched Normal Reference Sample

MSI electropharogram for normal tissue
Panels D, E, and F were generated with normal reference tissue from the same source individual as the research consented colorectal cancer using an Applied Biosystems® 3500 xL Genetic Analyzer.

MSI as a Research Marker for Immunotherapeutic Response

Presented at the 2017 Annual Meeting of the Association of Molecular Pathology by Dr. James R. Eshleman.

Important MSI Publications

Microsatellite instability has become an increasingly relevant tool in genetic and immuno-oncology research. Deficiencies in DNA mismatch repair (MMR) can be caused by hereditary, germline mutations or hypermethylation. Either mechanism disrupts expression of functional MMR proteins, allowing transcription errors to accumulate across the genome. Global genomic mutations disrupt normal cellular function, which leads to unchecked growth and cancers but also produces novel proteins. These “foreign” proteins can be immunogenic, recruiting immune effector cells to that tissue. Instability, or mutations, of mononucleotide repeat microsatellite sequences are particularly sensitive to transcription errors and can be the first evidence of an MMR deficiency.

Bacher, J.W. et al. (2004) Development of a Fluorescent Multiplex Assay for Detection of MSI-High Tumors. Disease markers 20, 237–250.
Le, D.T. et al. (2017) Mismatch-repair deficiency predicts response of solid tumors to PD-1 blockade. Science 10.1126/science.aan6733.
Le, D.T. et al. (2015) PD-1 Blockade in Tumors with Mismatch-Repair DeficiencyNew Engl. J. Med. 372, 2509–20.
Boland, C.R. et al. (2010) Microsatellite Instability in Colorectal Cancer. Gastroenterology 138, 2073–87.
Murphy, K.M. et al. (2006) Comparison of the Microsatellite Instability Analysis System and the Bethesda Panel for the Determination of Microsatellite Instability in Colorectal Cancers. J. Mol. Diagn. 8, 305–11.
MSI panels and bins for GeneMapper® software can be downloaded for consistent data analysis. Panels and bins text files simplify and standardize data analysis by providing automated assignment of genotypes using GeneMapper® 4.0, 4.1, and 5.0 software.


What's in the box?

Item Part # SizeConcentrationAvailable Separately

K562 DNA High Molecular Weight

DD208A 1 × 3μg10ng/μl

Internal Lane Standard 600

DG107A 1 × 150μl View Product

Gold ST★R 10X Buffer

DM241C 1 × 300μl

MSI 10X Primer Pair Mix

MD174A 1 × 100μl

Nuclease-Free Water

P119A 1 × 1,250μl View Product


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Download SDSPDF (261 KB) – English (United States)

Certificate of Analysis

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Use Restrictions

For Research Use Only. Not for Use in Diagnostic Procedures.

Storage Conditions


Patents and Disclaimers

U.S. Pat. Nos. 7,749,706 and 7,902,343.



  • Acquired RAS or EGFR mutations and duration of response to EGFR blockade in colorectal cancer.
    2016 Nat. Commun.
  • See all citations

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