OncoMate® MSI Dx Analysis System

MD1340 OncoMate MSI Dx Analysis System

IVD for Microsatellite Instability Characterization

  • PCR-based fragment-sizing test used to determine microsatellite instability (MSI) status
  • MSI determination with strong agreement to IHC
  • CE-Marked and available in select European countries; FDA-cleared in the United States


Catalog number selected: MD2140

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OncoMate® MSI Dx Analysis System
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Accurately Determine the MSI Status of Colorectal Cancers Using the Gold Standard Method

The OncoMate® MSI Dx Analysis System is a fluorescent, multiplex PCR-based test to detect microsatellite instability (MSI) in colorectal cancer tumor samples. MSI is a form of genomic instability caused by the deletion of repeating bases within microsatellites during DNA replication due to the failure of the mismatch repair system (MMR) to correct these errors. The OncoMate® MSI Dx Analysis System is designed to provide physicians with a functional, molecular measurement of the level of DNA mismatch repair deficiency demonstrated within their patient’s tumor.

The FDA-cleared OncoMate® MSI Dx Analysis System (Cat.# MD2140) is available in the United States only. For information about availability in other regions, including the CE-marked system available in select European countries, please contact us.
microsatellite instability and cancer illustration

Patients with MSI-H Colorectal Cancer Tumors Should Be Tested for Lynch Syndrome

MSI-H status is used as a biomarker for Lynch syndrome, an inherited predisposition to certain cancers. This condition is caused by autosomal-dominant mutations to the major mismatch repair genes MLH1, MSH2, MSH6 or PMS2 as well as the EPCAM gene that inactivates MSH2. Testing for MSI using PCR provides valuable information about whether the DNA mismatch repair mechanisms controlled by these genes are functioning correctly within the cells of the tested sample.

Better Information to Inform Patient Decisions

The MSI gold standard research tool is now an IVD, enabling better access for clinical diagnostics laboratories. The OncoMate® MSI Dx Analysis System is an IVD medical device, leveraging the same informative MSI markers relied on by global clinical researchers for almost two decades. The improved system is designed for use as a diagnostic with colorectal cancer (CRC) patients to make more informed decisions.

In a retrospective study of colorectal cancers, the OncoMate® MSI Dx Analysis System showed concordance with immunohistochemistry and is intended to identify patients that may benefit from further diagnostic testing1.

Only Two Sections Required
Illustration of tumor and normal FFPE sections

FFPE sections with a tissue volume of 0.1mm3 to 2.0mm3. Tumor sample should have ≥30% viable tumor cells.

Minimal DNA Required
1 ng DNA is needed for MSI analysis with Oncomate

Uses only 1ng of amplification-quality DNA per reaction.

Assay Time Under 3 Hours 
OncoMate MSI analysis workflow takes 2.5 hours

Quick, multiplexed reaction, balanced for accuracy and efficiency, goes from DNA to answer in as little as 2.5 hours.

Sensitive and Specific Results
MSI results with OncoMate show strong agreement with IHC

Reliable MSI determination with strong agreement with IHC.

Sensitive Panel of Mononucleotide Repeat Markers

The OncoMate® MSI Dx Analysis System targets five mononucleotide repeat markers (BAT-25, BAT-26, NR-21, NR-24 and MONO-27) that were selected for high sensitivity and specificity to alterations in repeat lengths in samples containing mismatch repair defects2,3. For quality control and sample authentication of matched tumor and normal samples, the system uses two pentanucleotide repeat markers (Penta C and Penta D) that were selected for their high level of polymorphism and lower degree of MSI. In a study of colorectal cancers, the OncoMate® MSI Dx Analysis System showed concordance with immunohistochemistry (97.8% PPA)1.

Test Design and Marker Information

Target Markers

OncoMate DX MSI System target markers

NCI recommended, Revised Bethesda Panel and two pentanucleotide markers4.

Example Data

Representative microsatellite instability data.

Instability is determined by fragment size analysis on a capillary electrophoresis instrument following PCR amplification of DNA from a patient's normal and tumor tissue samples. Unstable loci in the tumor tissue are indicated by red arrows.

Tumor to Answer Overnight

The OncoMate® MSI Dx Analysis System is part of a broader workflow that includes DNA extraction from FFPE tissue samples, quantitation of DNA, amplification of specific microsatellite markers using multiplex PCR, fragment separation by capillary electrophoresis, and data analysis and interpretation.

Illustration of a Maxwell CSC Instrument for DNA Isolation
Isolate DNA

from FFPE samples using the Maxwell® CSC DNA FFPE Kit and the Maxwell® CSC Instrument

Illustration of a Quantus Fluorometer
Quantitate DNA

using fluorescent DNA quantitation reagents (e.g., QuantiFluor® Dx dsDNA System) and instruments

Illustration of a PCR amplification tube and pipette tip
Amplify DNA

using the OncoMate® MSI Dx Analysis System

Illustration of an electropharogram for CE calibration
Calibrate the Dye Spectrum

using the OncoMate® 5C Matrix Standards

Illustration of a capillary electrophoresis instrument
Separate and Detect Fragments

using the Applied Biosystems® 3500 Dx Genetic Analyzer

Illustration of an electropherogram the OncoMate MSI Dx Analysis System
Data Analysis and Reporting

using the OncoMate® MSI Dx Interpretive Software


Turnaround Time:
In as little as 10 hours or overnight


Overview of the OncoMate® MSI Dx Analysis System Workflow

Compatibility Specifications


Normal and tumor FFPE tissue samples with a volume of 0.1–2.0mm3. Tumor samples must contain at least 30% viable tumor cells.

DNA Quantity and Quality

A target of 1ng per reaction, as estimated by a dsDNA binding dye (e.g., QuantiFluor® Dx dsDNA System). This method provides a reliable estimate of DNA concentration with highly fragmented DNA like that purified from FFPE

Thermal Cycling

Use a thermal cycler that allows block ramp rates from 3.9°C to 5.0°C per second.

Data Analysis Software

Amplification products are analyzed using the OncoMate® MSI Dx Interpretive Software.

Spectral Calibration

Prior to first use, perform a spectral calibration of the capillary electrophoresis instrument using the OncoMate® 5C Matrix Standard.

Capillary Electrophoresis

Amplification products are analyzed by capillary electrophoresis using the Applied Biosystems® 3500 Dx Genetic Analyzer in “Diagnostic Mode”.

Automated Software for Easy MSI Analysis

Capillary electrophoresis data requires further analysis to assign marker and size information. We have developed an automated MSI interpretation software that summarizes critical data features and provides an automated MSI status determination.

View Software

Seamless Support for Adopting OncoMate® MSI Dx in Your Lab

Our team is dedicated to partnering with you to ensure success and has broad experience training laboratories. We offer an online user training course as well as virtual and in-person training to get your lab up and running with the OncoMate® MSI Dx Analysis System more efficiently.

Important MSI Publications and Guidelines

Microsatellite instability resulting from deficiencies in DNA mismatch repair (MMR) can occur due to mutations (sporadic or germline) or hypermethylation of MMR genes. These changes disrupt expression of functional MMR proteins, allowing replication 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. Instability, or mutations, of mononucleotide repeat microsatellite sequences are particularly sensitive to replication errors and can be the first evidence of MMR deficiency. Individuals with Lynch syndrome, the primary hereditary tumor syndrome associated with MSI-H, have an inherited defect which disrupts normal MMR function, making these individuals predisposed for the development of certain cancers, including colorectal cancers. MSI status has a long history of aiding in the identification of patients who may benefit from additional genetic testing to identify whether or not they are a Lynch syndrome carrier.

NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines®)5.

Stjepanovic, N. et al. (2019) Hereditary gastrointestinal cancers: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Annals of oncology: official journal of the European Society for Medical Oncology 30, 1558-1571, doi:10.1093/annonc/mdz233 (2019). 

Bacher, J. W. et al. (2004) Development of a fluorescent multiplex assay for detection of MSI-High tumors. Dis Markers 20, 237-250, doi:10.1155/2004/136734. 

Boland, C. R. and Goel, A. (2010) Microsatellite instability in colorectal cancer. Gastroenterology 138, 2073-2087.e2073, doi:10.1053/j.gastro.2009.12.064. 

Umar, A. et al. (2004) Revised Bethesda Guidelines for hereditary nonpolyposis colorectal cancer (Lynch syndrome) and microsatellite instability. Journal of the National Cancer Institute 96, 261-268, doi:10.1093/jnci/djh034. 

Rubenstein, J. H. et al. (2015) American Gastroenterological Association Institute Guideline on the Diagnosis and Management of Lynch Syndrome. Gastroenterology 149, 777-782; quiz e716-777, doi:10.1053/j.gastro.2015.07.036. 

Herzig, D. O. et al. (2017) Clinical Practice Guidelines for the Surgical Treatment of Patients With Lynch Syndrome. Dis Colon Rectum 60, 137-143, doi:10.1097/DCR.0000000000000785. 

Stoffel, E. M. et al. (2015) Hereditary colorectal cancer syndromes: American Society of Clinical Oncology Clinical Practice Guideline endorsement of the familial risk-colorectal cancer: European Society for Medical Oncology Clinical Practice Guidelines. Journal of Clinical Oncology : official journal of the American Society of Clinical Oncology 33, 209-217, doi:10.1200/JCO.2014.58.1322. 

Sepulveda, A. R. et al. (2017) Molecular Biomarkers for the Evaluation of Colorectal Cancer: Guideline From the American Society for Clinical Pathology, College of American Pathologists, Association for Molecular Pathology, and American Society of Clinical Oncology. Archives of Pathology & Laboratory Medicine 141, 625-657, doi:10.5858/arpa.2016-0554-CP. 

Hampel, H. et al. (2015) A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. Genet Med 17, 70-87, doi:10.1038/gim.2014.147. 

Boardman, L. A. et al. (2020) AGA Clinical Practice Update on Young Adult-Onset Colorectal Cancer Diagnosis and Management: Expert Review. Clin Gastroenterol Hepatol 18, 2415-2424, doi:10.1016/j.cgh.2020.05.058. 

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Medical Information

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  1. OncoMate® MSI Dx Analysis System Technical Manual #TM543 (2021) Promega Corporation.
  2. Bacher, J. et al. (2004) Dis. Markers 20, 237.
  3. Luchini, C. et al. (2019) Annals of Oncology. 30, 1232.
  4. Umar, A. et al. (2004) J. Natl. Cancer Inst. 96, 261–8. 
  5. Referenced with permission from NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines®) for Genetic/Familial High-Risk Assessment: Colorectal V. 2.2023 © National Comprehensive Cancer Network, Inc, 2023. All rights reserved. Accessed March 28, 2024. To view most recent and complete version of the guideline, go online to nccn.org.

    NCCN makes no warranties of any kind whatsoever regarding the content, use or application and disclaims any responsibility for their application or use in any way.

Intended Use Statement:

The OncoMate® MSI Dx Analysis System is a qualitative multiplex polymerase chain reaction (PCR) test intended to detect the deletion of mononucleotides in 5 microsatellite loci (BAT-25, BAT-26, NR-21, NR-24 and MONO-27) using matched tumor and normal DNA obtained from formalin fixed paraffin-embedded (FFPE) colorectal tissue sections. The OncoMate® MSI Dx Analysis System is for use with the Applied Biosystems® 3500Dx Genetic Analyzer and OncoMate® MSI Dx Interpretive Software.  

The OncoMate® MSI Dx Analysis System is indicated in patients diagnosed with colorectal cancer (CRC) to detect microsatellite instability (MSI) as an aid in the identification of probable Lynch syndrome to help identify patients that would benefit from additional genetic testing to diagnose Lynch syndrome.

Results from the OncoMate® MSI Dx Analysis System should be interpreted by healthcare professionals in conjunction with other clinical findings, family history, and other laboratory data.

The clinical performance of this device to guide treatment decision for MSI high patients has not been established.


What's in the box?

Item Part # Size Concentration

Water, Amplification Grade

MD193A 1 × 1,250μl

OncoMate® MSI 5X Master Mix

MD280A 1 × 200μl

Size Standard 500

MD500A 1 × 100μl

OncoMate® MSI 5X Primer Mix

MD705A 1 × 200μl

2800M Control DNA

MD810A 1 × 25μl 10ng/μl

Certificate of Analysis

Search by lot number

Use Restrictions

For In Vitro Diagnostic Use. This product is only available in certain countries.

Storage Conditions


Patents and Disclaimers

U.S. Pat. No. 9,139,868, European Pat. No. 2972229, Japanese Pat. No. 6367307 and other patents pending.

TMR-ET, CXR-ET and WEN dyes are proprietary.


Other Resources

From questions to in-person trainings, our team of experts is here to help your clinical lab run smoothly.

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