Lynch Syndrome/Hereditary Nonpolyposis Colorectal Cancer

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

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

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
  • 90%  
• 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