Lynch Syndrome - Hereditary Nonpolyposis Colorectal Cancer (HNPCC)

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 varies, depending on the associated gene. LS results from pathogenic variants of the DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2. In certain cases, a deletion 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

How does Lynch syndrome present clinically?

Lynch syndrome (LS) often presents with early-onset colorectal cancer (CRC), in many cases before 50 years of age. Multiple tumors are common. Extracolonic tumors may also arise, depending on the specific causative pathogenic variant. Common extracolonic tumors include endometrial, prostate, ovarian, gastric, urinary tract, small bowel, hepatobiliary, brain/central nervous system, and pancreatic tumors, as well as sebaceous neoplasms. 

Who should be tested for Lynch syndrome?

Several organizations recommend universal screening for Lynch syndrome (LS) in all patients with colorectal cancer (CRC) -  or endometrial cancer.  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 (available at 

When should molecular germline genetic testing for Lynch syndrome be performed?

In most situations, it is cost-effective to first test for microsatellite instability (MSI) by polymerase chain reaction (PCR) and/or mismatch repair (MMR) protein deficiency by immunohistochemistry (IHC), given that only 2-4% of colorectal cancer cases are Lynch syndrome (LS) associated.   Both tests are sensitive and usually produce concordant results. If these tests reveal that a tumor has MSI or is MMR deficient, molecular germline genetic testing should be performed. However, if strong suspicion exists (eg, family history, cancer at a young age), it is reasonable to bypass MSI testing and proceed directly to molecular germline genetic testing.

Should BRAF testing be used for endometrial cancer specimens when screening for Lynch syndrome?

BRAF V600E testing is not appropriate for follow-up testing of endometrial cancer specimens with MLH1 loss by immunohistochemistry (IHC); only MLH1 promoter methylation testing should be performed. In colorectal cancer (CRC) specimens with MLH1 loss by IHC, BRAF V600E and MLH1 promoter methylation testing can be performed to determine the likelihood of Lynch syndrome (LS). See Screening of Cancer Specimens and the Lynch Syndrome (HNPCC) Testing Algorithm for more information.

Indications for Testing

Laboratory testing for LS is used to:

  • Screen for LS in all CRC specimens - 
  • Screen for LS in all endometrial tumors 
  • Diagnose LS in patients with a suggestive personal or family history of tumors and/or cancer

Laboratory Testing

Screening of Cancer Specimens

In most situations, it is most effective to first perform somatic testing, ie, to evaluate specimens from patients with suspected LS with immunohistochemistry (IHC) or polymerase chain reaction (PCR) testing for MMR protein deficiency or microsatellite instability (MSI). This eliminates the expense of full gene sequencing for the majority of tumors that lack MMR deficiency, given that only 2-4% of CRCs are LS associated.   Both IHC and PCR tests are sensitive and usually produce concordant results. However, if strong suspicion exists (eg, family history, cancer at a young age), it is reasonable to proceed directly to germline genetic testing. 

Cancer Specimen (Somatic) Screening Tests for LS
Test Characteristics Test Interpretation

Involves staining of tumor tissue for protein expression of 4 MMR genes known to be mutated in LS (MLH1, MSH2, MSH6, and PMS2)

Pattern of protein loss identified on IHC directs germline testing

5-15% false-negative rate 

NOTE: Loss of MLH1 may be due to acquired hypermethylation in sporadic tumors or a germline mutation in LSa; see the Lynch Syndrome (HNPCC) Testing Algorithm for additional information

IHC Result Likely Gene Mutationa
MLH1, PMS2 loss MLH1 or, rarely, PMS2
MSH2, MSH6 loss MSH2 or, rarely, MSH6
MSI by PCR (panel of 5 or more mononucleotide microsatellites)

Use to detect expansion or contraction of microsatellite repeats in the tumor

Does not detect which specific MMR protein is deficient

Patient tumor tissue is compared with normal tissue

Highest sensitivity is achieved when PCR is combined with IHC

Useful for MSI testing when IHC testing is negative despite high clinical suspicion of LS

Determination of MSI
High (≥2 markers, or ≥30% of markers in an expanded panel, with instability):
  • Consider germline testing
  • IHC can be used to target specific LS gene for testing
Low (1 marker, or <30% of markers in an expanded panel, with instability):
  • IHC suggested
  • Instability in even 1 mononucleotide repeat can be associated with LS
Stable (no markers detected with instability):
  • Very low risk of LS
  • Add IHC and consider germline gene testing if suspicion for LS is high
BRAF V600E or MLH1 promoter methylation

When MLH1 loss is identified using IHC, perform before LS mutation analysis 

Loss of MLH1 may be due to acquired hypermethylation in sporadic tumors or a germline mutation in LS

NOTES: The BRAF V600E variant is uncommon in LS but common in sporadic CRC of the MSI pathway

BRAF V600E testing is not appropriate for endometrial cancer; use only MLH1 promoter methylation testing

Additional BRAF testing may be appropriate for sporadic CRC (see Colorectal Cancer topic)

If BRAF V600E or MLH1 hypermethylation is positive:
  • LS unlikely; probably sporadic CRC
  • Germline LS gene analysis is not necessary unless suspicion for LS is still high

aRefer to Lynch Syndrome (HNPCC) Testing Algorithm.

NCCN, National Comprehensive Cancer Network

Sources: NCCN, 2020 ; Rubenstein, 2015 ; NCCN, 2020 ; Sepulveda, 2017 ; NCCN, 2021 ; Giardiello, 2014 


Molecular germline genetic testing is the gold standard for the 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 may be considered when IHC results indicate that a specific LS gene should be targeted. Consider a multigene panel if strong suspicion exists for LS or other hereditary cancer syndromes due to a suggestive personal and/or family history.  

The diagnosis of LS is established by 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 (see ARUP test code 2001961).


Patients with MMR-deficient CRC have an improved prognosis compared with stage-matched patients without MMR deficiency.

ARUP Laboratory Tests

Screening (Somatic)

Preferred screening test for LS in individuals with CRC

Do not use in endometrial cancer

First-line screening test for LS

Screening test for LS

Recommended reflex test to differentiate between LS and sporadic CRC in tumors showing loss of MLH1

Used within LS reflex testing pathway (for CRC specimens only)

Preferred reflex screening test for LS in non-CRC tumors (eg, endometrial carcinoma)

Recommended test to distinguish between LS and sporadic non-CRC tumors with loss of MLH1

Diagnosis (Germline)

Recommended test for individuals with a personal and/or family history consistent with Lynch syndrome when documentation of a causative familial variant is not available

For additional test information, refer to the Lynch Syndrome Panel, Sequencing and Deletion/Duplication Test Fact Sheet

Use to confirm a diagnosis of hereditary gastrointestinal (GI) cancer in individuals with a personal or family history of GI cancer and/or polyposis 

Lynch Syndrome Panel is preferred for the diagnosis of LS 

For additional test information, refer to the Hereditary Gastrointestinal Cancer Panel Test Fact Sheet

Useful when a pathogenic familial variant identifiable by sequencing is known

Order if negative germline sequencing studies have been performed previously at another laboratory or if there is a known familial deletion or duplication


Additional Resources

Medical Experts



Anna P. Matynia, MD
Associate Professor of Pathology (Clinical), University of Utah
Section Chief, Molecular Genetics and Genomics; Medical Director, Molecular Oncology, ARUP Laboratories