Test Code: 7610

Lynch Syndrome: Microsatellite Instability
Test Code: 7610
Turnaround time: 3 weeks


Lynch syndrome, caused by a germline mutation in a mismatch repair gene or associated with tumors exhibiting MSI, is characterized by an increased risk of colon cancer and other cancers (e.g., of the endometrium, ovary, stomach, small intestine, hepatobiliary tract, upper urinary tract, brain, skin). Individuals with Lynch syndrome have an approximately 80% lifetime risk for colon cancer. The average age of colorectal cancer diagnosis is 61 years. Women with Lynch syndrome have a 20%-60% lifetime risk of endometrial cancer. The average age of diagnosis of endometrial cancer is age 46-62 years. Among women with Lynch syndrome who develop both colon cancer and endometrial cancer, approximately 50% present first with endometrial cancer. In Lynch syndrome, the mean age of diagnosis of gastric cancer is age 56 years, with intestinal-type adenocarcinoma being the most commonly reported pathology. Lynch syndrome-associated ovarian cancers have a mean age of diagnosis of 42.5 years; approximately 30% are diagnosed before age 40 years.

The diagnosis of Lynch syndrome can be made on the basis of the Amsterdam Clinical Criteria or by molecular genetic testing for germline mutations in one of several mismatch repair (MMR) genes. The Amsterdam Criteria, first established in 1990 for research purposes, were later modified to include the other Lynch syndrome-related cancers for clinical diagnostic purposes. The Amsterdam Criteria are 1) Three or more family members, one of whom is a first-degree relative of the other two, with a confirmed diagnosis of colorectal cancer 2) Two successive affected generations 3) One or more colorectal cancers diagnosed before age 50 years. The modified Amsterdam Criteria replace “colorectal cancer” with “any Lynch syndrome- related cancers.” The sensitivity and specificity of the Amsterdam Criteria for identifying a mutation in the mismatch repair genes MSH2 and MLH1 have been reported to be 61% and 67%, respectively. The sensitivity is increased to 78% using the modified Amsterdam Criteria. However, broadening the criteria decreases the specificity.

Cancers arising in cells with defective mismatch repair gene function exhibit an inconsistent number of microsatellite nucleotide repeats when compared to normal tissue, a finding referred to as “microsatellite instability.” A panel of at least five markers is used to assess microsatellite instability (MSI) in tumor tissue and normal tissue. A tumor is classified as MSI-high if more than 30% of the markers show instability, MSI-low if fewer than 30% of the markers show instability, and MSI-stable if 0% of the markers show instability. Approximately 90% of colon cancers from families meeting Amsterdam Criteria are MSI-high. The likelihood of detecting a germline mutation in an individual with an MSI-stable tumor is extremely low.

The combination of MSI and immunohisotchemistry (IHC) has been shown to detect all heterozygotes for mutations in mismatch repair genes (23/23), while each method alone missed 2/23 cases. Similar results have been seen in other studies. A combined approach of IHC and MSI testing of tumors is ideal.

Lynch syndrome is inherited in an autosomal dominant manner. The majority of individuals diagnosed with Lynch syndrome have inherited the condition from a parent. However, because of incomplete penetrance, variable age of cancer development, cancer risk reduction as a result of screening or prophylactic surgery, or early death, not all individuals with a Lynch syndrome gene mutation have a parent who had cancer.


This test is indicated for:

  • Identification of individuals at risk for Lynch syndrome by analysis of tumor tissue for the presence or absence of microsatellite instability
  • Use before imuunohistochemistry and genetic testing to identify the mismatch gene involved


A multiplex PCR-based method is used to amplify a panel of 13 microsatellite markers, which includes the NCI recommended markers (BAT25, BAT26, NR21, NR22, NR24, D2S123, D17S250, D5S346, D18S35, D1S2883) for both the normal and tumor tissue. The amplified products are electrophoresed on ABI3100 and analyzed using the ABI Genemapper software.

Results are scored as follows MSI-H (High): > 40% markers positive; MSI-L (Low): <40% markers positive; MSS (Stable): No markers unstable.

MSI-high = greater than 40% marker instability; MSI-low = less than 40% marker instability; MSI-stable = 0% marker instability

Additional Specimen Collection/Handling Instructions Required for this Test

If sending colorectal tumor tissue, both a paraffin block and H&E-stained slides are required. Submit only 1 of the following specimen types

Type: Whole Blood
Specimen Requirements:
In EDTA (purple top) or ACD (yellow top) tube: 5-10 ml

Specimen Collection and Shipping: Refrigerate until time of shipment. Ship sample within 5 days of collection at room temperature with overnight delivery.

Type: Colorectal Tumor Tissue
Specimen Requirements:
Paraffin block AND H&E-stained slides.

Specimen Collection and Shipping: Ship sample at room temperature with overnight delivery.


  • Immunohistochemistry for the MLH1, MSH2, MSH6, and PMS2 proteins is available individually, and as a panel.
  • Sequence analysis of the MLH1, MSH2, MSH6, and PMS2 genes is available as a panel or individually.
  • Deletion/duplication analysis of the MLH1, MSH2, and MSH6 genes is available as a panel or individually for those individuals in whom sequence analysis is negative