Lynch Syndrome - Hereditary Nonpolyposis Colorectal Cancer (HNPCC)

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.

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Clinical Overview

Key Points

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 Deficiency

Presence of mismatch repair (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

Functions as a surrogate marker for MMR deficiency
- Microsatellite instability (MSI) is caused by the loss of MMR activity

Screening and Diagnostic Testing

Screening and Diagnostic Testing for LS
Test	Test Interpretation
Initial testing^a 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).
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 Sources: Based on NCCN, 2016 and AGA, 2015; U.S. Multi-Society Task Force on Colorectal Cancer, 2014; ASCP/CAP/AMP/ASCO, 2017

Diagnosis

Indications for Testing

All colorectal cancer (CRC) and/or endometrial tumors

Laboratory Testing

For additional information regarding testing strategies, refer to

Key Points for this topic
Lynch Syndrome Testing (HNPCC) algorithm
National Comprehensive Cancer Network (NCCN) guidelines, Genetic/Familial High Risk Assessment (2016), page LS-2, for algorithm

Prognosis

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

Screening

Refer to Key Points for discussion of screening tests
For further discussion of Lynch syndrome screening, please refer to the following references
- National Comprehensive Cancer Network (NCCN) guidelines, Genetic/Familial High Risk Assessment (2016)
- American Society of Clinical Oncology (ASCO) (2015)
- European Society for Medical Oncology (ESMO) (2013)
- U.S. Preventive Services Task Force (USPSTF) (2016)

Monitoring

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

Background

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^a
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
^aMutations include point mutations and large genomic deletions or rearrangements

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
- Prostate – ~30%
- Ovarian – 11-24%
- Gastric – 6-13%
- Urinary tract – 1-7%
- Small bowel – 3-6%
- Hepatobiliary tract – 1-4%
- Brain/CNS – 1-3%
- Sebaceous neoplasms – 1-9%
- 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

ARUP Lab Tests

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

Definitive diagnosis of LS requires additional targeted MMR germline molecular studies

Do not use in endometrial cancer

Refer to Test Fact Sheet for limitations

Definitive diagnosis of LS requires additional targeted MMR germline mutation studies

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

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

Recommended test to 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

When a relative has a previously identified pathogenic sequence variant, refer to familial mutation targeted sequencing test

Refer to Test Fact Sheet for full list of genes tested

Refer to Test Fact Sheet for limitations

Hereditary Gastrointestinal Cancer Panel, Sequencing and Deletion/Duplication 2013449

Method: Massively Parallel Sequencing/Exonic Oligonucleotide-based CGH Microarray/Sequencing/Multiplex Ligation-dependent Probe Amplification

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

Refer to Test Fact Sheet for limitations

Mismatch Repair by Immunohistochemistry with Reflex to MLH1 Promoter Methylation 2005270

Method: Qualitative Immunohistochemistry/Qualitative Real-time Polymerase Chain Reaction

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

First-line screening test for LS

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

~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

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

10-15% 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

Microsatellite Instability (MSI), HNPCC/Lynch Syndrome, by PCR 0051740

Method: Polymerase Chain Reaction/Fragment Analysis

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

Refer to Test Fact Sheet for full list of limitations

HNPCC/Lynch Syndrome (MLH1) Sequencing and Deletion/Duplication 0051650