• Test Code:
  • Department:
  • Test Synonyms:
    Hereditary Nonpolyposis Colorectal CancerMismatch repair genes and proteinsColorectal cancerMLH1, MSH2, MSH6, PMS2Lynch Syndrome
  • CPT Code(s):

Microsatellites are short, tandemly repeated DNA sequences from 1-6 base pairs in length.  Microsatellite markers can be used to detect a form of genetic instability called Microsatellite Instability (MSI)1,2.  MSI is a consequence of germline or somatic inactivation of mismatch repair genes (including MSH2, MSH6, MLH1 and PMS2).  Loss or downregulation of the expression of the protein products of these genes results in failure of the DNA mismatch repair system.  Due to their repetitive sequence composition, microsatellite sequences are especially vulnerable to this type of mutation, resulting in increase in length of the microsatellite segment. Such changes are detectable by comparing microsatellite allele size variations between matching normal and tumor samples.

This test can be performed in conjunction with our immunohistochemistry staining for the following MMR proteins: MLH1, MSH2, MSH6, and PMS2.  (Please contact Client Services at (855) 535-1522 to add IHC testing)
*All samples which are MSI high and MLH1 unstained by IHC can be reflexed to BRAF testing to aid in the determination of the genetic basis of the individual’s colorectal cancer, i.e., hereditary vs. sporadic, for additional charge. (Please contact Client Services at (855) 535-1522 to add BRAF testing.)

Reasons for Referral:
MSI is a tumor screening test for all all newly diagnosed colorectal cancer patients to identify patients who may have an inherited form of colorectal cancer (Hereditary Nonpolyposis Colon Cancer or Lynch Syndrome). About 15% of patients having MSI tumors have Lynch Syndrome, while the remaining have a sporadic form of CRC; 95% of patients with Lynch Syndrome have MSI. Patients with MSI tumors and the absence of a specific mismatch repair gene can be tested by mutation analysis to identify the gene defect. Family members at risk for having inherited the familial mutation can be tested to determine whether they are at risk for developing CRC due to Lynch Syndrome and if so, undergo frequent surveillance screening.


PCR:  Fluorescently labeled primers for coamplification of five mononucleotide repeat markers (BAT-25, BAT-26, NR-21, NR-24 and MONO-27).

Samples with instability in two or more of these mononucleotide markers are designated MSI-High (MSI-H), whereas those with one unstable marker are designated MSI-Low (MSI-L).  Samples with no detectable alterations are MSI-stable (MSS).  These designations are in accordance with the National Cancer Institute’s Bethesda guidelines.

Specimen Requirements:


-1 paraffin tissue block of tumor with minimal normal tissue

If tissue blocks cannot be sent:

Tumor: 5 unstained slides of Tumor at 5 micron + 1 H&E

DNA: 200ng at 50-100ng/µL (DNA must be extracted in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or CMS)

A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES.  Please include detailed clinical information, including ethnicity, clinical history, and family history.

Test Performed (Days):


Turn Around Time:

7 - 14 days

Shipment Sensitivity Requirements:

  • Package and ship specimen to remain cold, but not frozen. 
  • Ship via overnight express, using the FedEx priority overnight label provided. 
  • Contact Client Services for shipping kits and instructions at (855) 535-1522.


  1. Umar, A et al. (2004).  J. Natl. Cancer Inst. 96:261-8.
  2. Strate, LL and Syngal S (2005) Cancer Causes and Control 16:201-203

Additional Info:

The Knight Cancer Institute at Oregon Health & Science University is a pioneer in the field of precision cancer medicine. The institute's director, Brian Druker, M.D., helped prove it was possible to shut down just the cells that enable cancer to grow. This breakthrough has made once-fatal forms of the disease manageable and transformed how cancer is treated. The OHSU Knight Cancer Institute is the only National Cancer Institute-designated Cancer Center between Sacramento and Seattle – an honor earned only by the nation's top cancer centers. It is headquarters for one of the National Cancer Institute's largest research collaboratives, SWOG, in addition to offering the latest treatments and technologies as well as hundreds of research studies and clinical trials.

Learn More