Genetic Testing

MSI Testing - Microsatellite Instability Testing

The first step to testing for Lynch Syndrome is testing the tumor specimen for MSI or micro-satellite instability. MSI is stable in 90-95% of tumor specimens. This means the risk of Lynch Syndrome is low. However, if MSI is high, further testing for Lynch Syndrome is recommended. This first step costs about $500.

Microsatellites are repeated sequences of DNA. Microsatellite instability refers to an inconsistent length in these repeated DNA fragments. Finding this instability has been associated with colorectal, endometrial, ovarian and gastric cancers. The damaged mismatched repair gene in Lynch Syndrome causes a microsatellite repeat replication error to go unfixed. The replication error results in a frame shift mutation that inactivates or alters major tumor suppressor genes – This causes uncontrolled cell division and tumor growth. MSI testing has an 89% sensitivity for MLH1 and MSH2 testing and 77% sensitivity for MSH6 and PMS2. The specificity is 90.2% (from EWG). According to the Bethesda guidelines, MSI phenotype includes the presence of tumor infiltrating lymphocytes, mucinous histology, absence of dirty necrosis, histological heterogeneity.

IHC Testing – Immunohistochemical Testing

The next step is a blood test for IHC or Immunohistochemical testing. This tests if the protein products that the 4 common Lynch Syndrome cancer genes produce are found in the blood stream or not. If these protein products are absent, the risk for Lynch Syndrome increases. The MLH1 and PMS2 genes produce protein products that normally form a complex together. Likewise, the MSH2 and the MSH6 genes also make proteins that bind together. Therefore, for IHC testing, we are looking if there are low levels of either the MLH1/PMS2 or MSH2/MSH6 complexes. IHC testing normally costs around $500.

If the MLH1/PMS2 complex is not found (no methylation), it may be from Lynch Syndrome or secondary to the tumor itself. Sometimes tumors alter a protein by adding on an extra methyl group. This alters the identity and function of the protein. If a patient’s family history is strongly positive for Lynch and the MLH1/PMS2 protein complex is not found, then the person has Lynch Syndrome. However, if there is a weak family history for Lynch Syndrome, BRAF testing should be done.

BRAF Mutation Testing

BRAF tests for the V-600 E mutation in the BRAF gene. A BRAF test should be done if the MSI test is positive and the MSH1/PMS2 test is abnormal with  decreased proteins (no methylation). If the BRAF is positive (shows methylation), this lowers the risk of having Lynch Syndrome as the cause of the cancer. It is instead a different type of tumor causing an “epigenetic” effect. This occurs when the tumor alters the proteins after they are made, so they do not function properly. The BRAF mutation is associated with birth defects and the following cancers: non-Hodgkin lymphoma, colorectal cancer, malignant melanoma, papillary thyroid carcinoma, non-small cell lung carcinoma, and adenocarcinoma of lung. BRAF testing costs about $200-$300. If the BRAF testing is negative, testing should proceed for the MLH1 gene, to confirm Lynch Syndrome.

Genetic Counselors

After analyzing the results of the MSI, IHC, and BRAF testing, the next step is gene testing. Currently, there are commercial genetic tests for MSH2, MLH1, and MSH6 variants and these tests cost about $1,000 each. To keep costs down, the most cost effective approach is to perform these tests based on prior test results. For positive MSI testing with negative MLH1/PMS2 complex with a negative BRAF, testing for the MLH1 should be done. If the MSH2/MSH6 complex is low, test the MSH2 gene first. If that is normal, proceed with MSH6 testing.

Recently the price for genetic testing has decreased dramatically. While some labs still charge over $6,000 for a Lynch panel, it can be found for $500 or less.

Genetic Testing

Lynch Syndrome can be diagnosed with the Bethesda Guidelines or with genetic testing. Often, the diagnosis is confirmed utilizing a combination of these methods. Since a full genetic profile for Lynch Syndrome can cost over $4,000, consulting a genetic counselor, familiar with the nuances of Lynch Syndrome, can often save money. Once a specific abnormality is identified, screening family members can be done relatively inexpensively, usually for less than $350. Since Lynch Syndrome is an autosomal dominant genetic disorder, extensive genetic screening should go up and down the family tree, to identify all affected individuals. For this reason, genetic counselors are often a great resource to coordinate, test, counsel, and institute the proper screening procedures for affected family members.