Lynch Syndrome - Hereditary Nonpolyposis Colorectal Cancer (HNPCC)

Primary Author: Samowitz, Wade S., MD.
  • Key Points
  • Diagnosis
  • Algorithms
  • Screening
  • Monitoring
  • Background
  • Lab Tests
  • References
  • Related Topics
  • Videos

Lynch syndrome (LS) is an autosomal dominant inherited cancer syndrome that predisposes an individual to colorectal, endometrial, gastric, ovarian, upper urinary tract, and other cancers. Several organizations recommend universal screening of all colorectal cancer (CRC) specimens (American Gastroenterological Association [AGA], 2015; American Society of Clinical Oncology [ASCO], 2015; European Society for Medical Oncology [ESMO], 2013; National Comprehensive Cancer Network [NCCN], 2016; American Society for Clinical Pathology [ASCP]/College of American Pathologists [CAP]/Association for Molecular Pathology [AMP]/American Society of Clinical Oncology [ASCO], 2017) and all endometrial cancer patients (up to age 50, NCCN, 2016) for LS. In most situations, it is most effective to first evaluate specimens from suspected LS patients with immunohistochemistry (IHC) or polymerase chain reaction (PCR), as only 2-4% of CRCs are LS-associated (NCCN, 2016). However, if strong suspicion exists (eg, family history, cancer at a young age), it is reasonable to proceed to single or full-panel genetic testing.

Mismatch repair (MMR) deficiency

  • Presence of MMR deficiency helps identify patients who may have LS – MMR testing should be ordered in all patients with CRC (ASCP/CAP/AMP/ASCO, 2017)
    • MMR deficiency also occurs in ~15% of sporadic CRCs
  • Definitive diagnosis of LS requires differentiating colorectal tumors with MMR deficiency due to a sporadic somatic event from colorectal tumors with MMR deficiency due to an LS germline mutation
  • MMR genes in which LS-causing mutations can occur
    • MLH1
    • MSH2
    • MSH6
    • PMS2
    • EPCAM (deletions causing methylation of MSH2)

Microsatellite instability (MSI)

  • Functions as a surrogate marker for MMR deficiency
    • MSI is caused by the loss of MMR activity

Screening and diagnostic testing for LS

Screening and Diagnostic Testing

Initial testinga

Typically, IHC or PCR testing is used initially to eliminate expense of full gene sequencing for the vast majority of tumors that lack MMR deficiency. Both tests are sensitive and usually produce concordant results. However, it is reasonable to proceed to germline multigene analysis instead if strong suspicion of LS exists (eg, family history, cancer at a young age).

Test

Test Interpretation

IHC  

  • 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 mutational testing
  • 5-10% false-negative rate (NCCN, 2016)
  • Isolated PMS2 loss has been associated with germline MLH1 mutation

IHC Result

Likely Gene Mutation

MLH1, PMS2 loss

MLH1

MSH2, MSH6 loss

MSH2

MSH6

MSH6

PMS2

PMS2

BRAF V600E or MLH1 promoter methylation

  • When MLH1 loss is identified using IHC, perform prior to LS mutation analysis (ASCP/CAP/AMP/ASCO, 2017)
  • Loss of MLH1 is either due to acquired hypermethylation in sporadic tumors or a germline mutation in LS
    • BRAF mutations are uncommon in LS but common in sporadic CRC of MSI pathway
  • NOTE: BRAF testing is not appropriate for endometrial cancer; use only MLH1 promoter methylation testing

If BRAF or MLH1 hypermethylation is positive

  • LS unlikely; probably sporadic colorectal cancer
  • LS gene mutation analysis not necessary unless high suspicion for LS still exists

PCR (panel of 5 mononucleotide microsatellites)

  • Detects expansion or contraction of microsatellite repeats in the tumor
  • Does not detect which specific MMR protein is deficient
  • Patient tumor tissue is compared to normal tissue
  • Highest sensitivity 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 or more markers with instability

  • Consider gene mutation testing
  • IHC can be used to target specific mutation testing

Indeterminate – 1 marker with instability

  • Instability in even 1 mononucleotide repeat can be associated with LS – suggest IHC

Stable – no markers detected with instability

  • Very low risk of LS
  • Add IHC and possibly gene mutation testing if high suspicion of LS exists

Direct gene analysis (germline multigene analysis panel or single gene analysis available)

Consider single gene testing when

  • IHC result indicates gene to target
  • Mutation is known

Consider germline multigene panel if strong suspicion exists

  • Family history of hereditary cancer syndrome
  • Cancer at a young age

Mutational testing of MMR genes is gold standard for diagnosing LS

aRefer to Lynch Syndrome Testing (HNPCC) algorithm

Based on NCCN, 2016 and AGA, 2015; US Multi-Society Task Force on Colorectal Cancer, 2014; ASCP/CAP/AMP/ASCO, 2017

Indications for Testing

All colorectal cancer (CRC) and/or endometrial tumors

Laboratory Testing

Prognosis

Patients with mismatch repair (MMR)-deficient CRC have improved prognosis compared to stage-matched patients without MMR deficiency

  • Recommend frequent monitoring for patients diagnosed with Lynch syndrome (LS)
  • For further discussion of LS monitoring, please refer to National Comprehensive Cancer Network (NCCN) guidelines, Genetic/Familial High Risk 

Colorectal cancer (CRC) exhibits the characteristics of familial clustering in ~10-15% of cases. The most common cause of hereditary CRC is Lynch syndrome (LS), also known as hereditary nonpolyposis colorectal cancer (HNPCC). LS is caused by a germline mutation in one of the genes within the DNA mismatch repair (MMR) system.

Epidemiology

  • Prevalence
    • 1/440 individuals in general population (American Gastroenterological Association [AGA], 2015)
    • 2-4% of CRC (National Comprehensive Cancer Network [NCCN], 2016)
  • Age at presentation – mutation dependent (44-66 years mean)
    • >75% risk of developing CRC by 70 years
  • Sex – M:F, equal

Inheritance

  • Autosomal dominant with incomplete penetrance
  • Germline mutations in 1 of 4 DNA MMR genes
    • MLH1
    • MSH2
      • Small percentage of MSH2 inactivation is due to EPCAM deletions (included with MSH2 testing)
    • MSH6
    • PMS2
    • Inheritance of homozygous mutations for any of the above is termed biallelic MMR deficiency (BMMR-D)
  • MMR gene mutations

Mutations include point mutations and large genomic deletions or rearrangements

Common mutations

~90% of mutations in LS

MLH1 (mutL homolog1)

MSH2 (mutS homolog 2)

Less common mutations

MSH6 (mutS homolog 6)

PMS2 (postmeiotic segregation increased 2)

Heterodimeric complexes

Obligatory expression partners

  • MLH1 and PMS2
    • MLH1 mutation usually leads to concomitant PMS2 expression loss due to PMS2 degradation
  • MSH2 and MSH6
    • MSH2 mutation usually leads to concomitant MSH6 expression loss due to MSH6 degradation
  • MSH6 or PMS2 losses or mutations are usually not associated with any other loss

Clinical Presentation

  • Early onset of proximal (right side) CRC – often <50 years
    • Multiple metachronous and synchronous tumors are common
  • Early-onset extra colonic tumors – risk depends on mutation present (the following lifetime risk estimates apply to individuals with MLH1 and MSH2 pathogenic variants; risks for variants in MSH6 or PMS2 may be lower)
    • CRC – 52-82%
    • Endometrial – 25-60%
      • Some patients may present with endometrial tumor rather than colon tumor; some MSH6 germline-mutated families present with mainly endometrial tumors
    • Ovarian – 4-24%
    • Gastric – 6-13%
    • Urinary tract – 1-7%
    • Small bowel – 3-6%
    • Hepatobiliary tract – 1-4%
    • Brain/CNS – 1-3%
    • Pancreatic – 1-6% (MLH1 and MSH2 only)
  • Penetrance – variable; patients may present with tumors at older age
    • Especially true for MSH6 and PMS2
    • Universal screening will identify these tumors and patients will not be mistakenly classified as sporadic CRC
Tests generally appear in the order most useful for common clinical situations. Click on number for test-specific information in the ARUP Laboratory Test Directory.

Mismatch Repair by Immunohistochemistry with Reflex to BRAF Codon 600 Mutation and MLH1 Promoter Methylation 2002327
Method: Qualitative Immunohistochemistry/Qualitative Real-time Polymerase Chain Reaction

Recommended Use 

Preferred screening test for Lynch syndrome (LS) in individuals with colorectal cancer (CRC)

Reflex pattern – if MLH1 IHC is abnormal, evaluations of BRAF codon 600 and, possibly, MLH1 methylation are performed

Clinical sensitivity – 90%

Do not use in endometrial cancer

Limitations 

~10% of individuals with LS will have IHC tests which show normal staining of the MMR proteins

Because correlation of microsatellite instability (MSI) with IHC is not 100%, direct testing of MSI by PCR may be helpful

Screens for LS only and does not evaluate other hereditary causes of CRC or endometrial cancer

Follow-up 

Definitive diagnosis of LS requires additional targeted MMR germline mutation studies

Gastrointestinal Hereditary Cancer Panel, Sequencing and Deletion/Duplication, 16 Genes 2013449
Method: Massively Parallel Sequencing/Exonic Oligonucleotide-based CGH Microarray/Sequencing/Multiplex Ligation-dependent Probe Amplification

Recommended Use 

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

Includes all 4 MMR genes known to cause LS

Preferred test for individuals with suspected LS or another hereditary GI cancer syndrome

Analysis of specific genes included in this panel may be available individually at ARUP Laboratories

For more information, refer to Additional Technical Information document

Mismatch Repair by Immunohistochemistry with Reflex to MLH1 Promoter Methylation 2005270
Method: Qualitative Immunohistochemistry/Qualitative Real-time Polymerase Chain Reaction

Recommended Use 

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

Reflex pattern – if MLH1 expression is lost, MLH1 methylation is performed

Clinical sensitivity – 90%

Limitations 

~10% of individuals with LS will have IHC tests that show normal staining of MMR proteins

Because correlation of MSI with IHC is not 100%, direct testing of MSI by PCR may be helpful

Screens for LS only and does not evaluate other hereditary causes of CRC or endometrial cancer

Mismatch Repair by Immunohistochemistry 0049302
Method: Qualitative Immunohistochemistry

Recommended Use 

First-line screening test for LS

Highly recommended prior to ordering MMR germline mutation analysis gene testing – results direct subsequent genetic diagnostic testing

Clinical sensitivity – 90%

Limitations 

~10% of individuals with LS will have IHC tests that show normal staining of MMR proteins

Because correlation of MSI with IHC is not 100%, direct testing of MSI by PCR may be helpful

Screens for LS only and does not evaluate other hereditary causes of CRC or endometrial cancer

Microsatellite Instability (MSI), HNPCC/Lynch Syndrome, by PCR 0051740
Method: Polymerase Chain Reaction/Fragment Analysis

Recommended Use 

First-line screening test for LS; directs subsequent genetic diagnostic testing for LS

Clinical sensitivity – 90%

Limitations 

15% of sporadic CRCs are also MSI-H

Preoperative chemoradiation of rectal cancer

  • May complicate IHC interpretation and/or decrease tumor mass
  • May make MSI testing difficult – evaluation of pretreatment biopsies will avoid this limitation

Screens for LS only and does not evaluate other hereditary causes of CRC or endometrial cancer

HNPCC/Lynch Syndrome (MLH1) Sequencing and Deletion/Duplication 0051650
Method: Polymerase Chain Reaction/Sequencing/Multiplex Ligation-dependent Probe Amplification

Recommended Use 

Detect germline MLH1 variants

Use in MMR-deficient carcinoma with suggestive IHC results (loss of MLH1 and PMS2 proteins), negative for the BRAF codon 600 pathogenic variant, and with normal MLH1 methylation studies

Limitations 

Regulatory region and deep intronic pathogenic variants and causes of hereditary CRC or endometrial cancer other than LS are not evaluated

Diagnostic errors can occur due to rare sequence variations

HNPCC/Lynch Syndrome (MSH2) Sequencing and Deletion/Duplication 0051654
Method: Polymerase Chain Reaction/Sequencing/Multiplex Ligation-dependent Probe Amplification

Recommended Use 

Detect germline MSH2 variants

Use in MMR-deficient carcinoma with suggestive IHC results (loss of MSH2 and MSH6 proteins)

Includes evaluation of EPCAM exon 9 deletions

Limitations 

Regulatory region and deep intronic pathogenic variants and causes of hereditary CRC or endometrial cancer other than LS are not evaluated

Diagnostic errors can occur due to rare sequence variations

HNPCC/Lynch Syndrome (MSH6) Sequencing and Deletion/Duplication 0051656
Method: Polymerase Chain Reaction/Sequencing/Multiplex Ligation-dependent Probe Amplification

Recommended Use 

Detect germline MSH6 variants

Use in MMR-deficient carcinoma with suggestive IHC results (isolated loss of MSH6 protein)

Limitations 

Regulatory region and deep intronic pathogenic variants and causes of hereditary CRC or endometrial cancer other than LS are not evaluated

Diagnostic errors can occur due to rare sequence variations

HNPCC/Lynch Syndrome (PMS2) Sequencing and Deletion/Duplication 0051737
Method: Polymerase Chain Reaction/Sequencing/Multiplex Ligation-dependent Probe Amplification

Recommended Use 

Detect germline PMS2 variants

Use in MMR-deficient carcinoma with suggestive IHC results (isolated loss of PMS2 protein)

Limitations 

Regulatory region and deep intronic pathogenic variants and causes of hereditary CRC or endometrial cancer other than LS are not evaluated

Diagnostic errors can occur due to rare sequence variations

BRAF Codon 600 Mutation Detection with Reflex to MLH1 Promoter Methylation 0051750
Method: Polymerase Chain Reaction/Pyrosequencing

Recommended Use 

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

Reflex pattern – if no BRAF mutation is detected, MLH1 promoter methylation is evaluated

Analytic sensitivity – methylation levels >10% are reported as positive

BRAF Codon 600 Mutation Detection by Pyrosequencing 2002498
Method: Polymerase Chain Reaction/Pyrosequencing

Recommended Use 

Detect activating BRAF mutations at codon 600, which can indicate resistance to anti-EGFR therapy in CRC

This test is also used within the LS reflex testing pathway (for CRC specimens only)

Clinical sensitivity – activating BRAF mutation found in ~10% of CRCs

Limitations 

Limit of detection

  • MassARRAY and pyrosequencing − 10% mutant alleles
    • MassARRAY and pyrosequencing – oncogenic mutations outside of codon 600 will not be detected; MassARRAY only detects BRAF V600E mutation, whereas pyrosequencing can detect any BRAF codon 600 variants
  • NGS – 5% mutant alleles

HNPCC/Lynch Syndrome Deletion/Duplication 2001728
Method: Polymerase Chain Reaction/Multiplex Ligation-dependent Probe Amplification

Recommended Use 

Order if sequencing studies have been performed previously at another laboratory

Order if there is a known familial deletion or duplication

Both sequencing and deletion/duplication testing are necessary to detect all pathogenic variants in MMR genes

Requires permission from ARUP's Genetic Counselors (800-242-2787, x2141) before ordering

Guidelines

Balmana J, Balaguer F, Cervantes A, Arnold D, ESMO Guidelines Working Group. Familial risk-colorectal cancer: ESMO Clinical Practice Guidelines. Ann Oncol. 2013; 24 Suppl 6: vi73-80. PubMed

Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group. Recommendations from the EGAPP Working Group: genetic testing strategies in newly diagnosed individuals with colorectal cancer aimed at reducing morbidity and mortality from Lynch syndrome in relatives. Genet Med. 2009; 11(1): 35-41. PubMed

Giardiello FM, Allen JI, Axilbund JE, Boland R, Burke CA, Burt RW, Church JM, Dominitz JA, Johnson DA, Kaltenbach T, Levin TR, Lieberman DA, Robertson DJ, Syngal S, Rex DK, US Multi-Society Task Force on Colorectal Cancer. 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): 502-26. PubMed

Hampel H, Bennett RL, Buchanan A, Pearlman R, Wiesner GL, Guideline Development Group, American College of Medical Genetics and Genomics Professional Practice and Guidelines Committee and National Society of Genetic Counselors Practice Guidelines Committee. A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. Genet Med. 2015; 17(1): 70-87. PubMed

NCCN Clinical Practice Guidelines in Oncology, Colorectal Cancer Screening. National Comprehensive Cancer Network. Fort Washington, PA [Accessed: Feb 2017]

NCCN Clinical Practice Guidelines in Oncology, Genetic/Familial High-Risk Assessment: Colorectal. National Comprehensive Cancer Network. Fort Washington, PA [Accessed: Feb 2017]

NCCN Clinical Practice Guidelines in Oncology, Uterine Neoplasms. National Comprehensive Cancer Network. Fort Washington, PA [Accessed: Jul 2016]

Protocol for the Examination of Specimens from Patients with Primary Carcinoma of the Colon and Rectum. Based on AJCC/UICC TNM, 7th ed. Protocol web posting date: Oct 2013. College of American Pathologists (CAP). Northfield, IL [Revised Jan 2016; Accessed: Jun 2017]

Rubenstein JH, Enns R, Heidelbaugh J, Barkun A, Clinical Guidelines Committee. American Gastroenterological Association Institute Guideline on the Diagnosis and Management of Lynch Syndrome. Gastroenterology. 2015; 149(3): 777-82; quiz e16-7. PubMed

Sepulveda AR, Hamilton SR, Allegra CJ, Grody W, Cushman-Vokoun AM, Funkhouser WK, Kopetz SE, Lieu C, Lindor NM, Minsky BD, Monzon FA, Sargent DJ, Singh VM, Willis J, Clark J, Colasacco C, Rumble B, Temple-Smolkin R, Ventura CB, Nowak JA. 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; JCO2016719807. PubMed

Stoffel EM, Mangu PB, Gruber SB, Hamilton SR, Kalady MF, Lau MW, Lu KH, Roach N, Limburg PJ, American Society of Clinical Oncology, European Society of Clinical Oncology. 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): 209-17. PubMed

Vasen HF, Möslein G, Alonso A, Bernstein I, Bertario L, Blanco I, Burn J, Capella G, Engel C, Frayling I, Friedl W, Hes FJ, Hodgson S, Mecklin J, Møller P, Nagengast F, Parc Y, Renkonen-Sinisalo L, Sampson JR, Stormorken A, Wijnen J. Guidelines for the clinical management of Lynch syndrome (hereditary non-polyposis cancer). J Med Genet. 2007; 44(6): 353-62. PubMed

General References

Bedeir A, Krasinskas AM. Molecular diagnostics of colorectal cancer. Arch Pathol Lab Med. 2011; 135(5): 578-87. PubMed

Boland R, Goel A. Microsatellite instability in colorectal cancer. Gastroenterology. 2010; 138(6): 2073-2087.e3. PubMed

Djordjevic B, Broaddus RR. Role of the clinical pathology laboratory in the evaluation of endometrial carcinomas for Lynch syndrome. Semin Diagn Pathol. 2014; 31(3): 195-204. PubMed

Geiersbach KB, Samowitz WS. Microsatellite instability and colorectal cancer. Arch Pathol Lab Med. 2011; 135(10): 1269-77. PubMed

Jasperson KW, Tuohy TM, Neklason DW, Burt RW. Hereditary and familial colon cancer. Gastroenterology. 2010; 138(6): 2044-58. PubMed

Legolvan MP, Taliano RJ, Resnick MB. Application of molecular techniques in the diagnosis, prognosis and management of patients with colorectal cancer: a practical approach. Hum Pathol. 2012; 43(8): 1157-68. PubMed

Lynch HT, Lynch PM, Lanspa SJ, Snyder CL, Lynch JF, Boland CR. Review of the Lynch syndrome: history, molecular genetics, screening, differential diagnosis, and medicolegal ramifications. Clin Genet. 2009; 76(1): 1-18. PubMed

Rybak C, Hall MJ. Interpretation of genetic testing for lynch syndrome in patients with putative familial colorectal cancer. J Natl Compr Canc Netw. 2011; 9(11): 1311-20. PubMed

Senter L. Genetic testing by cancer site: colon (nonpolyposis syndromes). Cancer J. 2012; 18(4): 334-7. PubMed

Sharma SG, Gulley ML. BRAF mutation testing in colorectal cancer. Arch Pathol Lab Med. 2010; 134(8): 1225-8. PubMed

References from the ARUP Institute for Clinical and Experimental Pathology®

Chadwick BE. Beyond cytomorphology: expanding the diagnostic potential for biliary cytology. Diagn Cytopathol. 2012; 40(6): 536-41. PubMed

Hegde M, Ferber M, Mao R, Samowitz W, Ganguly A, Working Group of the American College of Medical Genetics and Genomics (ACMG) Laboratory Quality Assurance Committee. ACMG technical standards and guidelines for genetic testing for inherited colorectal cancer (Lynch syndrome, familial adenomatous polyposis, and MYH-associated polyposis). Genet Med. 2014; 16(1): 101-16. PubMed

Patil DT, Bronner MP, Portier BP, Fraser CR, Plesec TP, Liu X. A five-marker panel in a multiplex PCR accurately detects microsatellite instability-high colorectal tumors without control DNA. Diagn Mol Pathol. 2012; 21(3): 127-33. PubMed

Slattery ML, Wolff RK, Curtin K, Fitzpatrick F, Herrick J, Potter JD, Caan BJ, Samowitz WS. Colon tumor mutations and epigenetic changes associated with genetic polymorphism: insight into disease pathways. Mutat Res. 2009; 660(1-2): 12-21. PubMed

Szankasi P, Reading S, Vaughn CP, Prchal JT, Bahler DW, Kelley TW. A quantitative allele-specific PCR test for the BRAF V600E mutation using a single heterozygous control plasmid for quantitation: a model for qPCR testing without standard curves. J Mol Diagn. 2013; 15(2): 248-54. PubMed

Tomsic J, Senter L, Liyanarachchi S, Clendenning M, Vaughn CP, Jenkins MA, Hopper JL, Young J, Samowitz W, de la Chapelle A. Recurrent and founder mutations in the PMS2 gene. Clin Genet. 2013; 83(3): 238-43. PubMed

Vaughn CP, Baker CL, Samowitz WS, Swensen JJ. The frequency of previously undetectable deletions involving 3' Exons of the PMS2 gene. Genes Chromosomes Cancer. 2013; 52(1): 107-12. PubMed

Walter AW, Ennis S, Best H, Vaughn CP, Swensen JJ, Openshaw A, Gripp KW. Constitutional mismatch repair deficiency presenting in childhood as three simultaneous malignancies. Pediatr Blood Cancer. 2013; 60(11): E135-6. PubMed

Medical Reviewers

Samowitz, Wade S., MD, Medical Director, Solid Tumor Molecular Diagnostics and Histology, and Staff Pathologist, Anatomic Pathology at ARUP Laboratories; Professor of Anatomic Pathology, University of Utah

Content Reviewed: 
June 2017

Last Update: October 2017