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 (NCCN, Colorectal, 2018)
  • 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)
  • 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

Useful when a pathogenic familial variant identifiable by sequencing is known

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 1 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

  • Clinical sensitivity
  • Results
    • Normal - MMR proteins are normally expressed
      • MMR deficiency is unlikely
      • LS unlikely
    • Abnormal - MMR protein expression is abnormal
      • Loss of expression of 1 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

  • 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 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 not typically indicated
    • No variants detected
      • In MSI-H tumors with loss of MLH1 protein by IHC, MLH1 germline testing 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 – 1 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; 1993-2020. [Last Revision: Apr 2018; Accessed: Feb 2020]

    Online