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 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.