Lynch Syndrome/Hereditary Nonpolyposis Colorectal Cancer
- 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
See Related Tests
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 (NCCN, Colorectal, 2018)
- Universal screening for LS in individuals with endometrial cancer (NCCN, Uterine Neoplasms, 2018)
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 (NCCN, Uterine Neoplasms, 2018; Chadwick, 2001)
- 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 (NCCN, 2018)
- 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% (NCCN, 2018)
- 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
- High MSI (MSI-H)
- Limitations
- 10-15% of sporadic CRCs are also MSI-H (NCCN, 2018)
- 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% (NCCN, 2018)
- 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
- Normal - MMR proteins are normally expressed
- 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
- BRAF V600E detected
Germline Genetic Studies (MLH1, MSH2, MSH6, PMS2, or EPCAM)
- Sensitivity/specificity
- Proportion of LS attributed to pathogenic variants in specific MMR gene
- MLH1 – 50% (Smith 2016)
- MSH2 – 40% (Smith 2016)
- MSH6 – 7-10% (Miyaki 1997; Berends 2002; Petomaki 2003)
- PMS2 – <5% (Senter 2008)
- EPCAM – ~1-3% (Kuiper 2011)
- Analytical sensitivity/specificity – 99%
- Proportion of LS attributed to pathogenic variants in specific MMR gene
- 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
- Positive – 1 pathogenic variant detected
- 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
- Not evaluated
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Last Update: February 2019
Screening Studies (Requires Pathological Tissue)