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Lynch syndrome (LS), also known as hereditary nonpolyposis colorectal cancer (HNPCC), is an inherited cancer syndrome that predisposes an individual to colorectal, endometrial, gastric, ovarian, upper urinary tract, and other cancers. The risk of developing one of these cancers and the age of onset vary, depending on the associated gene. LS results from pathogenic variants in the DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2. In certain cases, a deletion of the promoter region of the EPCAM gene leads to MSH2 inactivation, and thus LS. Testing for LS includes screening for MMR deficiency in patients with colorectal cancer (CRC) or endometrial tumors, as well as diagnostic germline genetic testing in patients with a personal and/or family history suggestive of LS.
Quick Answers for Clinicians
Several organizations recommend universal screening for Lynch syndrome (LS) in all patients with endometrial cancer or colorectal cancer (CRC). - Germline genetic testing is generally recommended for patients with an early cancer diagnosis, positive family history, and/or abnormal tumor testing results. The National Comprehensive Cancer Network (NCCN) has published specific criteria for LS screening.
In most situations, it is cost-effective to perform somatic testing for mismatch repair (MMR) protein deficiency by immunohistochemistry (IHC) and/or microsatellite instability (MSI) by polymerase chain reaction (PCR) before germline testing, given that only a small percentage of colorectal and endometrial cancer cases are Lynch syndrome (LS) associated. , Both tests are sensitive and usually produce concordant results. If these tests reveal that a tumor is MMR deficient or has MSI, follow-up somatic molecular testing and/or germline genetic testing should be performed. However, if strong suspicion for LS exists (e.g., due to family history or cancer at a young age) or tissue availability is limited, it is reasonable to bypass MSI testing and proceed directly to molecular germline genetic testing. ,
Indications for Testing
Testing for LS is indicated in individuals with:
- Colon or endometrial cancer -
- A personal or family history suggestive of LS
- A relative with a known LS-associated pathogenic gene variant
- An identified pathogenic/likely pathogenic (P/LP) variant in tumor tissue that has clinical implications if also detected in the germline
Laboratory Testing
Screening of Cancer Specimens
In most situations, it is most effective to first perform somatic testing, i.e., to evaluate specimens with immunohistochemistry (IHC) or polymerase chain reaction (PCR) testing for MMR protein deficiency/microsatellite instability (MSI). However, if strong suspicion exists (e.g., due to family history or cancer at a young age), it is reasonable to proceed directly to germline genetic testing.
For more detailed interpretive information about the screening tests for LS, refer to the Lynch Syndrome (HNPCC) Testing algorithm.
Test | Use and Characteristics | |
---|---|---|
MMR by IHC | Use as initial test when screening cancer specimen for Lynch syndrome Stains for protein expression of 4 MMR genes (MLH1, MSH2, MSH6, and PMS2) Eliminates the expense of full gene sequencing for the majority of tumors that lack MMR deficiency The pattern of protein loss directs germline testing (refer to the Diagnosis section) | |
MSI by PCR | Useful when IHC testing is negative despite high clinical suspicion Does not detect which MMR protein is deficient | |
BRAF V600E by PCR (in cases of CRC; not applicable for endometrial cancer) | Use when the absence of MLH1 expression is identified by IHC; perform before germline testinga (refer to the Diagnosis section) If either BRAF V600E variant or MLH1 promoter methylation is positive, cancer is likely sporadic CRC | |
MLH1 promoter methylation by real-time PCR/fluorescence resonance energy transfer | BRAF V600E and MLH1 promoter methylation testing may be ordered together as a reflex test BRAF V600E testing is not appropriate for endometrial cancer; use only MLH1 promoter methylation testing | |
aIf loss of MLH1 expression is concurrent with loss of MSH2 or MSH6 expression, germline genetic analysis is appropriate. Sources: NCCN, 2025 ; Rubenstein, 2015 ; ESMO, 2019 ; NCCN, 2024 ; Sepulveda, 2017 ; NCCN, 2025 ; Giardiello, 2014 |
Diagnosis
Molecular germline genetic testing can be used for definitive diagnosis of LS. Genetic testing can be used in patients with suggestive screening results or if strong suspicion exists based on personal and/or family history. Germline gene analysis can take the form of single gene testing or a multigene panel.
Single gene testing can be considered when IHC results indicate that a specific LS gene should be targeted. Consider a germline multigene panel if strong suspicion exists for LS or other hereditary cancer syndromes due to a suggestive personal and/or family history. Ideally, germline genetic testing should be performed in the context of formalized genetic counseling, with an affected family member tested first. This enables targeted genetic testing for any causative variant(s) identified in affected family members. Panel testing may be important to consider in patients who were tested previously using only single gene analysis (e.g., MLH1 or MSH2 only). ,
The diagnosis of LS is established by the identification of a pathogenic variant in one of the MMR genes (MLH1, MSH2, MSH6, or PMS2) or an EPCAM deletion. Both sequencing and deletion/duplication analysis are necessary to identify all detectable pathogenic variants in MMR genes. If a pathogenic sequencing variant in an LS gene has already been identified in the family, targeted testing for the familial variant may be available. Ruling out a germline variant in patients with MMR deficiency or MSI (excluding MLH1 hypermethylation) is important, as it prevents intensive surveillance of Lynch-associated tumors in relatives otherwise identified as potentially at risk.
It is important to note that sequencing performed on somatic tumor tissue will not detect some variants (e.g., deletions/duplications, splicing variants) that are clinically actionable.
ARUP Laboratory Tests
Qualitative Immunohistochemistry
Qualitative Immunohistochemistry
Capillary Electrophoresis/Polymerase Chain Reaction (PCR)
Massively Parallel Sequencing
Real-Time Polymerase Chain Reaction/Fluorescence Resonance Energy Transfer (FRET)
Massively Parallel Sequencing/Sequencing/Multiplex Ligation-Dependent Probe Amplification (MLPA)
Massively Parallel Sequencing/Sequencing/Multiplex Ligation-dependent Probe Amplification
For additional test information, refer to the Hereditary Gastric Cancer Panel, Sequencing and Deletion/Duplication Test Fact Sheet
Massively Parallel Sequencing/Sequencing/Multiplex Ligation-dependent Probe Amplification
Massively Parallel Sequencing/Sequencing/Multiplex Ligation-Dependent Probe Amplification (MLPA)
Massively Parallel Sequencing
Multiplex Ligation-Dependent Probe Amplification (MLPA)
References
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GeneReviews - Lynch Syndrome
Idos G, Valle L. Lynch syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews. University of Washington, Seattle. Last revision Feb 2021; accessed Apr 2025.
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NCCN - genetic/familial high-risk-colorectal, endometrial, gastric v4.2024
National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology: genetic/familial high-risk assessment—colorectal, endometrial, and gastric. Version 4.2024. Updated Apr 2025; accessed Apr 2025.
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Rubenstein JH, Enns R, Heidelbaugh J, et al. American Gastroenterological Association Institute guideline on the diagnosis and management of Lynch syndrome. Gastroenterology. 2015;149(3):777-782; quiz e16-17.
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Stoffel EM, Mangu PB, Gruber SB, et al. 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. J Clin Oncol. 2015;33(2):209-217.
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Stjepanovic N, Moreira L, Carneiro F, et al. Hereditary gastrointestinal cancers: ESMO clinical practice guidelines for diagnosis, treatment and follow-up. Ann Oncol. 2019;30(10):1558-1571.
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NCCN - colorectal cancer screening v1.2024
National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology: colorectal cancer screening. Version 1.2024. Updated Feb 2024; accessed Apr 2025.
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Sepulveda AR, Hamilton SR, Allegra CJ, et al. 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 the American Society of Clinical Oncology. J Clin Oncol. 2017;35(13):1453-1486.
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NCCN - colon cancer v2.2025
National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology: colon cancer. Version 2.2025. Updated Mar 2025; accessed Apr 2025.
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Giardiello FM, Allen JI, Axilbund JE, et al. Guidelines on genetic evaluation and management of Lynch syndrome: a consensus statement by the US Multi-Society Task Force on colorectal cancer. Gastroenterology. 2014;147(2):502-526.
For additional test information, refer to the Lynch Syndrome Panel, Sequencing and Deletion/Duplication Test Fact Sheet