What you need to know about Lynch Syndrome testing

Lynch syndrome, also known as hereditary non-polyposis colorectal cancer, is an inherited disorder that increases the risk of developing certain types of cancer. Individuals with Lynch syndrome (LS) have an elevated risk of colorectal cancer (up to 65%), endometrial (uterine) cancer (up to 46%), gastric cancer, kidney and ureter cancer, brain cancer, small bowel cancer, bladder cancer, biliary tract cancer, sebaceous neoplasms (a type of skin cancer), and ovarian cancer².

Lynch syndrome is caused by pathogenic or likely pathogenic variants in MLH1, MSH2, MSH6, PMS2, and EPCAM. These genes are called mismatch repair (MMR) genes and are responsible for fixing DNA errors that occur during the replication process. When functioning normally, these genes help prevent cancer from occurring. However, when someone has a pathogenic or likely pathogenic variant in one of these genes, their risk for cancer increases. LS is inherited in a dominant manner, which means that first degree blood relatives of affected individuals are at 50% risk of having LS. When someone is identified to have LS, it is important for them to share this information with at-risk relatives so they can pursue testing.

There are three sets of guidelines that exist to help providers determine who should consider genetic testing for LS. This includes the Amsterdam criteria and Bethesda guidelines that assess a person’s family history and/or personal history of cancer^9,10. However, most clinicians and payors follow the National Comprehensive Cancer Network (NCCN) guidelines. While the specific guidelines may change from year-to-year, they generally recommend considering testing a patient under the following circumstances⁴:

• An individual diagnosed with LS related cancer under the age of 50.
  
• An individual diagnosed with multiple LS related cancers.
  
• Family history of first- and/or second-degree relatives with LS related cancer(s).
  
• Personal history of a tumor with MMR deficiency at any age.
  

There are multiple strategies to test an individual for LS. For individuals with cancer, screening the tumor is often the best first step. There are two common methods to screen the tumor: 1) immunohistochemistry staining (IHC) and 2) microsatellite instability testing (MSI).

1.  IHC stains for the presence (+) or absence (-) of the protein products of four of the five LS MMR genes in an individual’s tumor (MLH1, PMS2, MSH2, MSH6). If the staining indicates an MMR deficiency, it’s suggestive there is a variant in the individual’s tumor, or a germline variant present. Depending on the staining pattern, follow up tumor testing may be recommended.

a.  The most common abnormal tumor staining pattern is absent MLH1 and PMS2¹.

i.  For colon cancers, most tumors with this staining pattern are due to the acquired BRAF V600E variant in the tumor⁷.

ii.  For all other cancers, or when colon cancers are BRAF V600E negative, another common cause is hypermethylation of the MLH1 promoter. When MLH1 and PMS2 are absent on IHC its strongly recommended to complete BRAF and/or hypermethylation analysis on the tumor before moving on to germline testing.

The table below reviews the possible outcomes and possible etiology of IHC tumor testing. Highlighted rows show when LS is suggested. For all cases, a sporadic cancer cannot be ruled out.

2. MSI testing looks to see if a Lynch Syndrome tumor has high microsatellite instability, a known property of Lynch Syndrome cancers. Approximately 80% of Lynch Syndrome tumors are MSI-High⁸.

If IHC or MSI indicate a higher possibility for LS, follow up genetic testing is recommended to confirm the diagnosis. At this point, full sequencing and deletion and duplication analysis can be completed on all five LS genes. Generally, the recommendation is to look at all five genes, even if the patient had abnormal IHC suggesting one gene more likely than others⁵.

For affected individuals with abnormal tumor screening but normal genetic test results, here are possible explanations for that result:

1. They do not have LS, and MMR somatic changes are present in the tumor is present.
   
2. They have LS due to a variant that cannot be detected by current technology.
   
3. In rare cases, individuals with MLH1 hypermethylation in their tumor, who are under age 55, may have constitutional MLH1 hypermethylation. In most cases MLH1 hypermethylation is a tumor specific finding, but rarely is a systemic occurrence which is known as constitutional MLH1 hypermethylation³. Further testing an individual’s blood for MLH1 methylation can be completed to determine if the individual may have this epigenetic hypermethylation throughout their body, and therefore, at higher risk to develop LS tumors. It’s important to note that testing for constitutional MLH1 hypermethylation should be considered only after a person has had negative Lynch Syndrome genetic testing.

Affected and unaffected individuals with a strong personal or family history suggestive of LS should consider germline genetic testing. It is important to note that MMR IHC and MSI are screening tools and can miss individuals with LS⁶. It is recommended that affected family members be tested first to determine if a hereditary cause for cancer in the family can be identified. If no affected family members are available for testing, unaffected individuals should consider genetic testing through a gene panel, one that includes at least all five MMR genes. Panel testing may also be considered as a variant may be present outside of the five Lynch Syndrome genes. LS testing can be complicated. Local genetic counselors, genetics professionals, and laboratories are available to help providers identify the best testing options for patients. 

1. Adar T, Rodgers LH, Shannon KM, Yoshida M, Ma T, Mattia A, Lauwers GY, Iafrate AJ, Hartford NM, Oliva E, Chung DC. Universal screening of both endometrial and colon cancers increases the detection of Lynch syndrome. Cancer. 2018 Aug 1;124(15):3145-3153. doi: 10.1002/cncr.31534. Epub 2018 May 11. PMID: 29750335.
2. Dominguez-Valentin M, Haupt S, Seppälä TT,Mortality by age, gene and gender in carriers of pathogenic mismatch repair gene variants receiving surveillance for early cancer diagnosis and treatment: a report from the prospective Lynch syndrome database. EClinicalMedicine. 2023 Mar 20;58:101909. doi: 10.1016/j.eclinm.2023.101909. PMID: 37181409; PMCID: PMC10166779.
3. Hitchins MP, Dámaso E, Alvarez R, Zhou L, Hu Y, Diniz MA, Pineda M, Capella G, Pearlman R, Hampel H. Constitutional MLH1 Methylation Is a Major Contributor to Mismatch Repair-Deficient, MLH1-Methylated Colorectal Cancer in Patients Aged 55 Years and Younger. J Natl Compr Canc Netw. 2023 Jul;21(7):743-752.e11. doi: 10.6004/jnccn.2023.7020. PMID: 37433431.
4. National Comprehensive Cancer Network. Genetic/Famililal High-Risk Assessment: Colorectal (Version 2.2023). http://www.nccn.org/professionals/physician_gls/pdf/bone.pdf. Accessed April 10, 2019.
5. Pan S, Cox H, Willmott J, Mundt E, Gorringe H, Landon M, Bowles KR, Coffee B, Roa BB, Mancini-DiNardo D. Discordance between germline genetic findings and abnormal tumor immunohistochemistry staining of mismatch repair proteins in individuals with suspected Lynch syndrome. Front Oncol. 2023 Jan 30;13:1069467. doi: 10.3389/fonc.2023.1069467. PMID: 36793599; PMCID: PMC9923021.
6. Riedinger CJ, Esnakula A, Haight PJ, Suarez AA, Chen W, Gillespie J, Villacres A, Chassen A, Cohn DE, Goodfellow PJ, Cosgrove CM. Characterization of mismatch-repair/microsatellite instability-discordant endometrial cancers. Cancer. 2024 Feb 1;130(3):385-399. doi: 10.1002/cncr.35030. Epub 2023 Sep 26. PMID: 37751191; PMCID: PMC10843110.
7. Roth RM, Hampel H, Arnold CA, Yearsley MM, Marsh WL, Frankel WL. A modified Lynch syndrome screening algorithm in colon cancer: BRAF immunohistochemistry is efficacious and cost beneficial. Am J Clin Pathol. 2015 Mar;143(3):336-43. doi: 10.1309/AJCP4D7RXOBHLKGJ. PMID: 25696791.
8. Roudko V, Cimen Bozkus C, Greenbaum B, Lucas A, Samstein R, Bhardwaj N. Lynch Syndrome and MSI-H Cancers: From Mechanisms to "Off-The-Shelf" Cancer Vaccines. Front Immunol. 2021 Sep 24;12:757804. doi: 10.3389/fimmu.2021.757804. PMID: 34630437; PMCID: PMC8498209.
9. Umar A, Boland CR, Terdiman JP, Syngal S, de la Chapelle A, Rüschoff J, Fishel R, Lindor NM, Burgart LJ, Hamelin R, Hamilton SR, Hiatt RA, Jass J, Lindblom A, Lynch HT, Peltomaki P, Ramsey SD, Rodriguez-Bigas MA, Vasen HF, Hawk ET, Barrett JC, Freedman AN, Srivastava S. Revised Bethesda Guidelines for hereditary nonpolyposis colorectal cancer (Lynch syndrome) and microsatellite instability. J Natl Cancer Inst. 2004 Feb 18;96(4):261-8. doi: 10.1093/jnci/djh034. PMID: 14970275; PMCID: PMC2933058.
10. Vasen H, Watson P, Mecklin J, Lynch H. New Clinical Criteria for Hereditary Nonpolyposis Colorectal Cancer (HNPCC, Lynch Syndrome) Proposed by the International Collaborative Group on HNPCC☆. Gastroenterology. 1999;116(6):1453-6. doi:10.1016/s0016-5085(99)70510-x