Lynch Syndrome

Lynch syndrome, previously known as hereditary non-polyposis colorectal cancer (HNPCC), is caused by mutations in the mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2, and EPCAM. Lynch syndrome is the most common hereditary form of colorectal cancer. It affects about 1 in 440 individuals in the U.S.

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Lynch syndrome, previously known as hereditary non-polyposis colorectal cancer (HNPCC), is caused by mutations in the mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2, and EPCAM. Lynch syndrome is the most common hereditary form of colorectal cancer. It affects about 1 in 440 individuals in the U.S.

Lynch syndrome is an autosomal dominant syndrome that predisposes to malignancy, including a lifetime colorectal cancer risk of up to 82%. Lynch syndrome is also associated with an increased risk for uterine, ovarian, stomach, small bowel, hepatobiliary tract, upper urinary tract, brain, pancreatic, and sebaceous cancers.

Ambry offers the most comprehensive testing for Lynch syndrome available, including analyses of five genes: MLH1, MSH2, MSH6, PMS2, EPCAM. Analysis for the MSH2 inversion of exons 1-7 is also available. Our flexible options allow clinicians to choose the most appropriate testing approach for their patients: concurrent analyses of all five genes, two-step sequential analyses, gene-specific analysis, or specific site analysis.

Disease Name 
Colorectal cancer
HNPCC (hereditary non-polyposis colorectal cancer)
Lynch syndrome
Muir-Torre syndrome
Turcot syndrome
Uterine cancer
Disease Information 

Lynch syndrome is an autosomal dominant hereditary cancer syndrome that causes increased risk for several types of cancer, primarily colorectal and uterine (also known as endometrial) cancer. Other associated cancers include, stomach, ovarian, small bowel, hepatobiliary tract, upper urinary tract, brain, pancreatic, and sebaceous neoplasms. 
 

Lynch syndrome is caused by germline mutations in the DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2, and EPCAM.5 An estimated 90% of mutations are found in the MLH1 and MSH2 genes, 7-10% are in the MSH6 gene, and (<5%) are detected in the PMS2 gene.7 More recent data suggests that mutations in MSH6 and PMS2 may result in a milder form of Lynch syndrome with an older age of onset and/or lower cancer risks than MLH1 and MSH2.8 EPCAM (also known as TACSTD1) is the epithelial cell adhesion molecule located upstream of MSH2. Gross deletions disrupting the 3’ end of EPCAM lead to inactivation of the adjacent MSH2 gene through methylation induction of its promoter.18,20 Germline deletions encompassing this region have been reported in 19-30% of individuals with microsatellite instability (MSI) and absence of the MSH2 protein in their tumors identified by immunohistochemistry (IHC).19

Ambry Lynch Syndrome Test Description % of described mutations7,13
Lynch syndrome CONCURRENT

Concurrent gene sequence and deletion/duplication analyses of MLH1, MSH2, MSH6, and PMS2 plus EPCAM deletion/duplication and MSH2 inversion analyses

>99%
Lynch syndrome SEQUENTIAL Step 1: Gene sequence and deletion/duplication analyses of MLH1, MSH2, and MSH6 plus EPCAM deletion/duplication and MSH2 inversion analyses. If negative, then reflex to:
Step 2: PMS2 gene sequence and deletion/duplication analyses
>99%
MLH1 Concurrent gene sequence and deletion/duplication analyses of MLH1 40-50%
MSH2 + EPCAM Concurrent gene sequence and deletion/duplication analyses of MSH2, EPCAM deletion/duplication, and MSH2 inversion analyses 20-40%
MSH6 Concurrent gene sequence and deletion/duplication analyses of MSH6 7-10%
EPCAM EPCAM deletion/duplication analysis 1-3%
PMS2 Concurrent gene sequence and deletion/duplication analyses of PMS2 <5%

 

Testing Benefits & Indication 

Comprehensive analyses of the MLH1, MSH2, MSH6, PMS2 and EPCAM genes are recommended for Lynch syndrome diagnostic testing.17 Specific cancer surveillance protocols and risk-reducing surgical options are available for individuals found to carry a Lynch syndrome mutation, which can help reduce mortality by 60%.16 Testing is available for at risk family members; however, testing individuals younger than 18 years of age is generally not recommended.

Lynch syndrome genetic testing may be warranted for individuals with a personal and/or family history of any of the following:

• Colorectal or uterine cancer diagnosed under age 50
• An individual with more than one Lynch syndrome cancer (e.g. colorectal & uterine cancer or two separate colorectal cancers)
• Three or more close relatives with colorectal, uterine, ovarian, or other Lynch syndrome cancers (on the same side of the family)
• Known Lynch syndrome mutation in the family
• MSI and/or IHC results indicate MMR deficiency in the tumor

Test Description 

MLH1 coding exons 1-19, MSH2 coding exons 1-16, MSH6 coding exons 1-10, and PMS2 coding exons 1-15, and well into the 5’ and 3’ ends of all the introns and untranslated regions are analyzed by sequencing. Gross deletion/duplication analysis determines gene copy number for all coding exons of MLH1, MSH2, MSH6, and PMS2, and coding exon 9 of EPCAM. Clinically significant intronic findings beyond 5 base pairs are always reported. Intronic variants of unknown or unlikely clinical significance are not reported beyond 5 base pairs from the splice junction. Genomic deoxyribonucleic acid (gDNA) is isolated from the patient’s specimen using standardized methodology and quantified. Sequence enrichment of the targeted coding exons and adjacent intronic nucleotides is carried out by a bait-capture methodology, using long biotinylated oligonucleotide probes followed by polymerase chain reaction (PCR) and next generation sequencing (NGS). Sanger sequencing is performed for any regions missing or with insufficient read depth coverage for reliable heterozygous variant detection. Reportable small insertions and deletions, potentially homozygous variants, variants in regions complicated by pseudogene interference, and single nucleotide variant calls not satisfying 100x depth of coverage and 40% het ratio thresholds are verified by Sanger sequencing.21 Gross deletion/duplication analysis of MLH1, MSH2, MSH6, and PMS2 using read-depth from NGS data and EPCAM using multiplex ligation-dependent probe amplification (MLPA) is also performed. Any copy number changes detected by NGS are confirmed by targeted chromosomal microarray and/or MLPA.  If a deletion is detected in exons 13, 14, or 15 of PMS2, double stranded sequencing of the appropriate exon(s) of the pseudogene, PMS2CL, will be performed to determine if the deletion is located in the PMS2 gene or pseudogene. If a deletion is detected in exon 9 of EPCAM, deletion/duplication analysis of coding exons 3 and 8 of EPCAM will be performed. For EPCAM, only gross deletions encompassing the 3’ end of the gene are reported.

Mutation Detection Rate 

Clinical sensitivity is described in the table above. Ambry's Lynch syndrome testing can detect >99.9% of described mutations in the included genes, when present (analytic sensitivity).

Specimen Requirements 

Complete specimen requirements are available here or by downloading the PDF found above on this page.

Turnaround Time 
Test Code Test Name CALENDAR DAYS
8517 Lynch Syndrome Concurrent (not available for Medicare patients):
Gene sequence and deletion/duplication analyses of MLH1, MSH2, MSH6,
and PMS2 plus EPCAM deletion/duplication and MSH2 inversion analyses
14-21
8515 Lynch Syndrome Sequential
Step 1: Gene sequence and deletion/duplication analyses of MLH1, MSH2,
and MSH6 plus EPCAM deletion/duplication and MSH2 inversion analyses
Step 2: PMS2 gene sequence and deletion duplication analyses
* Running steps 1 and 2 could have a hi TAT of 42 days

14-21

14-21
8508 MLH1 gene sequence and deletion/duplication analyses 14-21
8510 MSH2 gene sequence and deletion/duplication analyses plus
EPCAM deletion/duplication and MSH2 inversion analyses
14-21
2226 MSH2 inversion 7-14
8512 MSH6 gene sequence and deletion/duplication analyses 14-21
4646 PMS2 gene sequence and deletion/duplication analyses 14-21
Click here Specific Site Analysis for any Lynch syndrome gene 7-14

 

Genes 
EPCAM
MLH1
MSH2
MSH6
PMS2
References 
  1. ACS cancer reference information page. American Cancer Society Website. Available here. Updated March 5, 2008. Accessed March 11, 2009.
  2. Abdel-Rahman WM, et al. The genetics of HNPCC: application to diagnosis and screening. Crit Rev Oncol Hematol. 2006;53:208-220.
  3. Samowitz WS, et al. The colon cancer burden of genetically defined hereditary nonpolyposis colon cancer. Gastroenterology. 2001;4:830-838.
  4. Lucci-Codrisco E, et al. Hereditary nonpolyposis colorectal cancer and related conditions. Am J Med Genet A. 2003;122A(4):325-334. 
  5. Thibodeau SN, et al. Microsatellite instability in colorectal cancer: different mutator phenotypes and the principal involvement of hMLH1. Cancer Res. 1998;58(8):1713–1718.
  6. Peltomaki P. Role of DNA mismatch repair defects in the pathogenesis of human cancer. J Clin Oncol. 2003;21:1174-1179.
  7. Hedge MR and Roa BB. Genetic testing for hereditary nonpolyposis colorectal cancer (HNPCC). Curr Prot Hum Genet. 2009;10.
  8. Boland CR, et al. The biochemical basis of microsatellite instability and abnormal immunohistochemistry and clinical behavior in Lynch syndrome: from bench to bedside. Fam Cancer. 2007;7(1):41-52. 
  9. Aarnio M, et al. Cancer risk in mutation carriers of DNA-mismatch-repair genes. Int J Cancer. 1999;81:214-218.
  10. Aarnio M, et al. Life-time risk of different cancers in hereditary non-polyposis colorectal cancer (HNPCC) syndrome. Int J Cancer. 1995;64:430-433. 
  11. 11. Syngal S, et al. Sensitivity and specificity of clinical criteria for hereditary non-polyposis colorectal cancer associated mutations in MSH2 and MLH1. J Med Genet. 2000;37:641-645.
  12. Wahlberg SS, et al. Evaluation of microsatellite instability and immunohistochemistry for the prediction of germ-line MSH2 and MLH1 mutations in hereditary nonpolyposis colon cancer families. Cancer Res. 2002;62:3485-3492. 
  13. Charbonnier F, et al. Detection of exon deletions and duplications of the mismatch repair genes in hereditary nonpolyposis colorectal cancer families using multiplex polymerase chain reaction of short fluorescent fragments. Cancer Res. 2000;60:2760-2763. 
  14. Lynch HT and de la Chapelle A. Genetic susceptibility to non-polyposis colorectal cancer. J Med Genet. 1999;36:801-818.
  15. de Joung AE, et al. What is the appropriate screening protocol in Lynch syndrome?. Fam Cancer. 2006;5:373-378. 
  16. Jarvinen HJ, et al. Controlled 15-year trial on screening for colorectal cancer in families with hereditary nonpolyposis colorectal cancer. Gastroenterology. 2000;118:829-834. 
  17. Sankila R, et al. Better survival rates in patients with MLH1-associated hereditary colorectal cancer. Gastroenterology. 1996;110: 682-687. 
  18. Ligtenberg MJL, et al. Heritable somatic methylation and inactivation of MSH2 in families with Lynch syndrome due to deletion of the 3' exons of TACSTD1. Nature Genetics. 2009;41(1):112-117. 
  19. Niessen RC, et al. Germline hypermethylation of MLH1 and EPCAM deletions are a frequent cause of Lynch syndrome. Gene Chromo Cancer. 2009;48:737-744. 
  20. Kovacs ME, et al. Deletions removing the last exon of TACSTD1 constitute a distinct class of mutations predisposing to Lynch syndrome. Hum Mutat. 2009;30(2):197-20. 
  21. Mu W, et al. Sanger confirmation is required to achieve optimal sensitivity and specificity in next-generation sequencing panel testing. J Mol Diagn. 2016. 18(6):923-932.