Lynch Syndrome - Hereditary Nonpolyposis Colorectal Cancer (HNPCC)

Last Literature Review: October 2022 Last Update:

Lynch syndrome (LS), also known as hereditary nonpolyposis colorectal cancer (HNPCC), is an inherited cancer syndrome that predisposes an individual to early-onset colorectal cancer, 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

Who should be tested for Lynch syndrome?

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 (available at 

When should germline genetic testing for Lynch syndrome be performed?

In most situations, it is cost-effective to perform somatic testing for microsatellite instability (MSI) by polymerase chain reaction (PCR) and/or mismatch repair (MMR) protein deficiency by immunohistochemistry (IHC) before germline testing, 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 for LS exists (eg, family history, cancer at a young age), it is reasonable to bypass MSI testing and proceed directly to molecular germline genetic testing.

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). However, if strong suspicion exists (eg, family history, 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, see the Lynch Syndrome (HNPCC) Testing algorithm.

Cancer Specimen (Somatic) Screening Tests for LS
TestUse and Characteristics
Mismatch repair by immunohistochemistry

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

Pattern of protein loss directs germline testing (see Diagnosis)

Microsatellite instability by PCR

Useful when IHC testing is negative despite high clinical suspicion

Does not detect which MMR protein is deficient

BRAF V600E by PCR/pyrosequencing

Use when MLH1 loss is identified by IHC; perform before germline testing (see Diagnosis)

If either BRAF V600E variant or MLH1 promoter methylation is positive, cancer is likely sporadic CRC

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

MLH1 promoter methylation by real-time PCR/fluorescence resonance energy transfer
Sources: NCCN, 2021 ; Rubenstein, 2015 ; NCCN, 2022 ; Sepulveda, 2017 ; NCCN, 2022 ; 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 can 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.

ARUP Laboratory Tests

Screening (Somatic)

Diagnosis (Germline)

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

For additional test information, refer to the Hereditary Gastric Cancer Panel, Sequencing and Deletion/Duplication Test Fact Sheet


Additional Resources

Medical Experts



Picture of Nicole Leonard, MD
Nicole Leonard, MD
Anatomic and Clinical Pathology Resident, University of Utah School of Medicine and ARUP Laboratories


Anna P. Matynia, MD
Associate Professor of Pathology (Clinical), University of Utah
Medical Director, Molecular Oncology, ARUP Laboratories