HNPCC / Lynch syndrome DNA Analysis
Hereditary Non-Polyposis Colon Cancer (HNPCC), also known as Lynch syndrome, is an autosomal dominant syndrome that predisposes to malignancy, including lifetime risk of up to 80% for early onset of colorectal cancer.
PrintHereditary Non-Polyposis Colon Cancer (HNPCC), also known as Lynch syndrome, is an autosomal dominant syndrome that predisposes to malignancy, including lifetime risk of up to 80% for early onset of colorectal cancer.
Individuals affected with HNPCC are also at increased risk for developing tumors in the ovaries, endometrium, stomach, small intestine, hepatobiliary tract, upper urinary tract, brain and skin.
Ambry offers the most comprehensive testing for Lynch syndrome available, including analysis of MLH1, MSH2, MSH6, EPCAM and PMS2 as well as tumor testing. Our flexible options allow the provider to choose the most appropriate testing for their patient. Ambry's most comprehensive test includes analysis of MLH1, MSH2, MSH6, and EPCAM, and it is capable of detecting >99% of described mutations in these genes. HNPCC/Lynch Syndrome CONCURRENT analyzes all four genes concurrently, and the result is available in 14-21 days. HNPCC/Lynch Syndrome SEQUENCE is a two-step reflexive test option for these four genes that provides comprehensive testing while minimizing cost. Concurrent gene sequencing and deletion/duplication analysis of the PMS2 gene is also available as a separate test. Ambry is currently the only lab to offer PMS2 deletion/duplication analysis. Gene-specific analysis is available, as well as specific mutation testing for individual gene mutations known to be in the family.
Ambry also offers HNPCC/Lynch Syndrome screening by tumor testing, including analysis of MMR proteins by IHC, microsatellite instability testing by PCR, MLH1 hypermethylation analysis, and testing for the BRAF V600E mutation. For detailed information about tumor testing, please see HNPCC/Lynch Syndrome Tumor Analysis.
Colorectal cancer (CRC) is the third leading cause of cancer-related deaths, with an estimated 142,000 new cases diagnosed annually. While the majority CRC cases are sporadic, 5-10% of cases can be due to an inherited condition.2 The most common inherited form of colorectal cancer is Hereditary Non-Polyposis Colon Cancer (HNPCC), and it is estimated to cause 2-5% of all CRC cases. HNPCC, also known as Lynch syndrome, is an autosomal dominant syndrome with a predisposition to CRC and other malignancies. Affected individuals have a lifetime risk of up to 80% for CRC, 20-60% risk of endometrial cancer, as well as other tumors.7
This hereditary predisposition to malignancies is caused by germ-line mutations in the DNA mismatch repair (MMR) genes, which form heterodimers between MLH1 with PMS2, and MSH6 with MSH2.5 An estimated 90% of mutations are found in the MLH1 and MSH2 genes, 7-10% are in the MSH6 gene, and much less frequently seen in the PMS2 gene(<5%).7 Mutations in MSH6 and PMS2 tend to result in an attenuated expression of HNPCC with an older age of onset.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 who have microsatellite instability (MSI) and absence of the MSH2 protein in their tumors.19
Comprehensive analysis of the MLH1, MSH2, MSH6, PMS2 and EPCAM genes is recommended for diagnostic testing of HNPCC.17 Routine surveillance is available for those found to carry an HNPCC 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 not generally recommended.
Life Time Cancer Risk (up to age 70 years)1, 9, 10
| Cancer Type | General Population Risk | HNPCC Mutation Carrier Lifetime Risk |
| Colon | 5.5% | Up to 80% |
| Endometrium | 2.7% | 20-60% |
| Stomach | <1% | 11-19% |
| Ovary | <1% | 9-12% |
| Hepatobiliary tract | <1% | 2-7% |
| Urinary tract | <1% | 4-5% |
| Small Bowel | <1% | 1-4% |
| Brain/central nervous system | <1% | 1-3% |
The Ambry CONCURRENT and Ambry SEQUENCE: HNPCC are the most comprehensive test options, detecting >99% of mutations in the MLH1, MSH2, MSH6 and EPCAM genes. Testing is arranged into two steps to maximize yield and minimize cost. Other sequence and deletion/duplication analysis options are also described below:
| Ambry HNPCC/Lynch Synrome Test | Description | % of all HNPCC mutations7,13 |
| HNPCC/Lynch Syndrome CONCURRENT |
Concurrent MLH1, MSH2, and MSH6 genes sequence and deletion/duplication analysis and EPCAM deletion/duplication analysis |
~97% |
| HNPCC/Lynch Syndrome SEQUENCE | Step 1: Concurrent MLH1 and MSH2 gene sequence analysis. If negative then reflex to Step 2: Concurrent MSH6 gene sequence and MLH1, MSH2, MSH6 and EPCAM deletion/duplication analysis | ~97% |
| MLH1 | Concurrent gene sequence and deletion/duplication analysis of the MLH1 gene | 40-50% |
| MSH2+EPCAM/TACSTD1 | Concurrent gene sequence and deletion/duplication analysis of the MLH2 gene and deletion analysis of exons 3, 8, 9 and 3’ end of the EPCAM/TACSTD1 gene | 20-40% |
| MSH6 | Concurrent gene sequence and deletion/duplication analysis of the MLH6 gene | 7-10% |
| EPCAM/TACSTD1 | Deletion analysis of exons 3, 8, 9 and 3’ end of the EPCAM gene | 1-3% |
| PMS2 | Concurrent gene sequence and deletion/duplication analysis of the PMS2 gene | ~5% |
These Ambry Tests include full gene sequence analysis performed by PCR-based double-stranded automated sequencing in the sense and antisense directions for: (1) exons 1-19 of the MLH1 gene plus the 5’UTR region (c.1-337 to -194), (2) exons 1-16 of the MSH2 gene plus the 5’UTR region (c.1-318 to -69), (3) exons 1-10 of the MSH6 gene, and (4) exons 1-15 of the PMS2 gene. In addition, all full-gene sequence analysis includes at least 20 bases into the 5’ and 3’ ends of all the introns. Testing also includes deletion/duplication analysis of MLH1, MSH2, MSH6, and PMS2, as well as analysis of exons 3, 8, 9, and the 3’ end of the EPCAM gene. Germline testing does not include methlyation status of the MLH1 promoter region. Specific mutation analysis for individual MLH1, MSH2, MSH6, PMS2 or EPCAM mutations known to be in the family is available.
Tumor testing for microsatellite instability (MSI), mismatch repair proteins by immunohistochemistry (IHC), MLH1 hypermethylation, and BRAF V600E mutation is also available (see HNPCC/Lynch Tumor Analysis).
Clinical sensitivity for HNPCC testing using gene sequence and deletion/duplication analysis is ~50% in MLH1, ~40% in MSH2, 7-10% in MSH6, and <5% in PMS2.7,13 For individuals with tumors exhibiting microsatellite instability and absence of the MSH2 protein by immunohistochemistry, the detection rate of deletions in the EPCAM gene is 19-30%.19 Overall, it is estimated that EPCAM mutations account for 1-3% of all HNPCC mutations. Analytical sensitivity for all genes is greater than 99% with the exception of PMS2 (60-70% of described mutations).
Blood: Collect 3-5 cc from adult or 2 cc minimum from child into EDTA purple-top tube (first choice) or ACD yellow-top tube (second choice). Store at room temperature or refrigerate. Ship at room temperature.
Saliva: Collect 2 ml into Oragene™ DNA Self-Collection container. Store and ship at room temperature.
DNA: Send 20 µg in TE at 50-100 ng/µl. Store frozen and ship on ice or dry ice.
Prenatal: Prenatal testing is not available. Testing Under 18 years of Age: Please call an Ambry Genetic Counselor to discuss your case
| Test Code | Technique | CPT Codes |
|---|---|---|
| 2200 | MLH1 Gene Sequence Analysis | 83891x1, 83894x17, 83898x16, 83904x17, 83909x17, 83912x1 |
| 2220 | MSH2 Gene Sequence Analysis | 83891x1, 83894x17, 83898x16, 83904x17, 83909x17, 83912x1 |
| 2240 | EPCAM Deletion / Duplication Analysis | 83891x1, 83894x1, 83900x1, 83901x9, 83909x1, 83912x1 |
| 2840 | MSH6 Gene Sequence Analysis | 83891x1, 83894x17, 83898x16, 83904x17, 83909x17, 83912x1 |
| 4640 | PMS2 Gene Sequence Analysis | 83891x1, 83894x19, 83898x18, 83904x27, 83909x27, 83912x1 |
| 4644 | PMS2 Deletion / Duplication Analysis | 83891x1, 83894x1, 83900x1, 83901x32, 83909x1, 83912x1 |
| 4646 | PMS2 Gene Sequence Analysis and Deletion / Duplication | 83891x1, 83894x20, 83898x18, 83900x1, 83901x32, 83904x27, 83909x28, 83912x2 |
| 8500 | HNPCC Reflex Option: MLH1 and MSH2 Sequence With Reflex to MSH6 Sequence and Deletion / Duplication for All Genes Including EPCAM | 83891x1, 83894x47, 83898x47, 83904x53, 83900x1, 83901x22, 83909x46, 83912x5 |
| 8504 | Step 1 (MLH1, MSH2) | 83891x1, 83894x31, 83898x31, 83904x31, 83909x31, 83912x2 |
| 8506 | Step 2 (MLH1, MSH2 Deletion / Duplication, MSH6 Sequence and EPCAM Deletion / Duplication) | 83891x1, 83894x16, 83898x17, 83904x17, 83900x2, 83901x22, 83909x17, 83912x3 |
| 8508 | MLH1 Gene Sequence Analysis and Deletion / Duplication | 83891x1, 83894x17, 83898x16, 83904x16, 83900x1, 83901x23, 83909x16, 83912x2 |
| 8510 | MSH2 Gene Sequence Analysis and Deletion / Duplication Including EPCAM | 83891x1, 83894x17, 83898x16, 83904x16, 83900x1, 83901x23, 83909x16, 83912x2 |
| 8512 | MSH6 Gene Sequence Analysis and Deletion / Duplication | 83891x1, 83894x17, 83898x16, 83904x16, 83900x1, 83901x23, 83909x16, 83912x2 |
| 8518 | HNPCC Concurrent MLH1 and MSH2 Sequence and to MSH6 Sequence and Deletion / Duplication for All Genes Including EPCAM | 83891x1, 83894x47, 83898x47, 83900x1, 83901x22, 83904x53, 83909x46, 83912x5 |
| 8700 | MMR Profile by IHC (MLH1, MSH2, MSH6, PMS2) | 88342x4 |
| 8702 | MSI by PCR | 83891x2, 83900x1, 83901x8, 83907x2, 83909x2, 88381x2, 83912x1 |
| 7978 | MLH1 Hypermethylation Analysis | 83898x3, 83904x1, 83896x2, 83907x1, 88381x1, 83912x1 |
| 7980 | BRAF SMA V600E Analysis | 83898x1, 83909x1, 83912x1, 99001x1 |
| 7982 | MLH1 Hypermethylation with BRAF (Analysis of V600E only) Analysis | 83896x4, 83898x5, 83904x1, 83907x2, 83912x4, 88381x2 |
| Call 2 | Any HNPCC Single Gene Deletion / Duplication Analysis | 83891x1, 83894x1, 83900x1, 83901x18, 83909x1, 83912x1 |
| Technique | Days |
|---|---|
| MLH1 Gene Sequence Analysis | 7-21 |
| MSH2 Gene Sequence Analysis | 7-21 |
| EPCAM Deletion / Duplication Analysis | 7-14 |
| MSH6 Gene Sequence Analysis | 7-21 |
| PMS2 Gene Sequence Analysis | 14-35 |
| PMS2 Deletion / Duplication Analysis | 7-14 |
| PMS2 Gene Sequence Analysis and Deletion / Duplication | 14-35 |
| HNPCC Reflex Option: MLH1 and MSH2 Sequence With Reflex to MSH6 Sequence and Deletion / Duplication for All Genes Including EPCAM | 7-35 |
| Step 1 (MLH1, MSH2) | 7-21 |
| Step 2 (MLH1, MSH2 Deletion / Duplication, MSH6 Sequence and EPCAM Deletion / Duplication) | 7-21 |
| MLH1 Gene Sequence Analysis and Deletion / Duplication | 7-21 |
| MSH2 Gene Sequence Analysis and Deletion / Duplication Including EPCAM | 7-21 |
| MSH6 Gene Sequence Analysis and Deletion / Duplication | 7-21 |
| HNPCC Concurrent MLH1 and MSH2 Sequence and to MSH6 Sequence and Deletion / Duplication for All Genes Including EPCAM | 14-21 |
| MMR Profile by IHC (MLH1, MSH2, MSH6, PMS2) | |
| MSI by PCR | |
| MLH1 Hypermethylation Analysis | |
| BRAF SMA V600E Analysis | |
| MLH1 Hypermethylation with BRAF (Analysis of V600E only) Analysis | |
| Any HNPCC Single Gene Deletion / Duplication Analysis | 7-14 |
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