Lynch Syndrome/Hereditary Nonpolyposis Colorectal Cancer

Screening Studies (Requires Pathological Tissue)

  • First-line screening test for newly diagnosed CRC, endometrial carcinoma, and LS
  • Highly recommended prior to ordering germline MMR gene testing
    • Directs subsequent genetic diagnostic testing
  • Testing for CRC and other solid tumors to qualify patients for certain immune checkpoint inhibitor treatment
  • First-line screening test for newly diagnosed CRC, endometrial carcinoma, and LS
  • Directs subsequent genetic diagnostic testing for LS
  • Testing for CRC and other solid tumors to qualify patients for certain immune checkpoint inhibitor treatment
  • Screening for HNPCC/LS 
  • If MLH1 IHC is abnormal, evaluations of BRAF codon 600 and, possibly, MLH1 methylation are performed
  • Definitive diagnosis of LS requires additional targeted MMR germline molecular studies
  • Do not use in endometrial cancer
  • Recommended reflex test to differentiate between LS and sporadic CRC in tumors showing loss of MLH1
  • If no BRAF variant is detected, MLH1 promoter methylation is evaluated
  • Reflex screening test for LS in non-CRC tumors (eg, endometrial carcinoma)
  • If MLH1 expression is lost, MLH1 methylation is performed

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

Diagnostic Germline Genetic Studies

  • Specimen: peripheral blood
  • Germline genetic testing is available for all 4 MMR genes known to cause LS, either separately or as part of the hereditary gastrointestinal (GI) cancer panel (see Related Tests)
  • 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 promoter methylation studies
  • 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 and 10 Mb inversion of MSH2 exons 1-7
  • Detect germline MSH6 variants
  • Use in MMR-deficient carcinoma with suggestive IHC results (isolated loss of MSH6 protein)
  • Detect germline PMS2 variants
  • Use in MMR-deficient carcinoma with suggestive IHC results (isolated loss of PMS2 protein)
  • Useful when a pathogenic familial variant identifiable by sequencing is known
  • A copy of a relative’s lab report is REQUIRED
  • Use to assess for large deletion/duplication previously identified in a family member
  • A copy of a relative’s lab report is REQUIRED

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.

Indications for Ordering

Microsatellite instability (MSI) and/or immunohistochemistry (IHC) tumor analyses

  • Universal screening for LS in all individuals with newly diagnosed CRC 
  • Universal screening for LS in individuals with endometrial cancer 

Germline MMR gene testing

  • Order following abnormal screening test result
  • Confirms diagnosis of LS

Disease Overview

Incidence

  • Accounts for 2-4% of CRC and ~1-2% of endometrial cancers  
  • Most common hereditary CRC syndrome
  • Most common cause of hereditary endometrial cancer

Risk Estimates

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%
  • Prostate: ~30%
  • Ovarian: 11-24%
  • Gastric: 6-13%
  • Hepatobiliary tract: 1-4%
  • Urinary tract: 1-7%
  • Small bowel: 3-6%
  • Brain/central nervous system: 1-3%
  • Sebaceous neoplasms: 1-9%
  • Pancreatic: 1-6% (MLH1 and MSH2 only)

Genetics

Genes Tested

MLH1, MSH2, MSH6, PMS2, and EPCAM

Inheritance

Autosomal dominant

Test Interpretation

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

Sensitivity/Specificity

  • Clinical sensitivity: 90%  
  • Analytical sensitivity/specificity: >99%

Results

  • High MSI (MSI-H)
    • MMR deficiency, either sporadic or LS
  • Indeterminate MSI (MSI-I)
    • Instability in even one mononucleotide repeat can be associated with LS.
    • Follow-up IHC studies are recommended.
  • Microsatellite stable (MSS)
    • LS unlikely

Limitations

  • 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.

Mismatch Repair by IHC

Sensitivity/Specificity

  • Clinical sensitivity: 90%  

Results

  • Normal: MMR proteins are normally expressed.
    • MMR deficiency is unlikely.
    • LS unlikely
  • Abnormal: MMR protein expression is abnormal.
    • Loss of expression of one or more proteins is highly predictive of MMR deficiency.
    • Absence of both MLH1 and PMS2:
      • MLH1 germline pathogenic variant is possible.
      • Consider MLH1 methylation ± BRAF V600E studies.
      • If methylation and BRAF studies are negative, follow with MLH1 germline genetic testing.
    • Absence of PMS2 only:
      • PMS2 germline pathogenic variant likely
      • Consider PMS2 germline testing.
      • If PMS2 testing does not identify a germline pathogenic variant, consider MLH1 germline testing.
    • Absence of both MSH2 and MSH6:
      • MSH2 germline pathogenic variant likely
      • Consider MSH2 germline testing.
    • Absence of MSH6 only:
      • MSH6 germline pathogenic variant likely
      • Consider MSH6 germline testing.
      • If MSH6 testing does not identify a germline pathogenic variant, consider MSH2 germline testing.

Limitations

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

BRAF Codon 600 Mutation Detection with Reflex to MLH1 Promoter Methylation

Sensitivity/Specificity

  • Analytical sensitivity: Methylation levels >10% are reported as positive.

Results

  • BRAF V600E detected
    • Presence in MMR-deficient CRC indicates the tumor is probably sporadic and not associated with LS.
    • Further germline testing is not typically indicated.
  • MLH1 promoter methylation detected
    • Presence in an MSI CRC indicates the tumor is probably sporadic and not associated with LS.
    • Further germline testing is not typically indicated.
  • No variants detected
    • In MSI-H tumors with loss of MLH1 protein by IHC, MLH1 germline testing is indicated.

Germline Genetic Studies (MLH1, MSH2, MSH6, PMS2, or EPCAM)

Sensitivity/Specificity

  • Proportion of LS attributed to pathogenic variants in specific MMR gene:
    • MLH1: 50% 
    • MSH2: 40% 
    • MSH6: 7-10%   
    • PMS2: <5% 
    • EPCAM: ~1-3% 
  • Analytical sensitivity/specificity: 99%

Results

  • Positive: one pathogenic variant detected
    •  Predicted to be causative for LS
  • Negative: no pathogenic variants detected
    • Diagnosis of LS unlikely, but not excluded
  • Inconclusive: variant detected, but whether it is benign or pathogenic is unknown

Limitations

  • Not evaluated:
    • Regulatory region and deep intronic variants
    • Sequence variants and large deletion/duplications in genes other than MLH1, MSH2, MSH6, and PMS2
    • Sequence variants in EPCAM
    • Large deletions/duplications in EPCAM, other than exon 9
    • Large gene inversions, other than the MSH2 10 Mb exons 1-7 inversion
    • Causes of hereditary CRC or endometrial cancer other than LS
  • Diagnostic errors can occur due to rare sequence variations.

References

Additional Resources
  • GeneReviews - Lynch Syndrome

    Kohlmann W, Gruber SB. Lynch syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, editors. GeneReviews, University of Washington; 1993-2021. [Last revision: Apr 2018; Accessed: Feb 2020]

    Online