MLH1, MSH2, and MSH6 Sequencing and Deletion/Duplication Analysis for Hereditary Non-Polyposis Colorectal Cancer (HNPCC) and HNPCC-like Syndromes
HEREDITARY NON-POLYPOSIS COLORECTAL CANCER (HNPCC)
Gene: MLH1 at 3p21.3
MSH2 at 2p22-p21
MSH6 at 2p16
Methodology: Bi-directional DNA sequencing of 19 coding exons and splice
sites of MLH1, 16 coding exons and splice sites of MSH2, and/or 10 exons
and splice sites of MSH6. Deletion/duplication analysis by MLPA for MLH1
and/or MSH2 is also available.
Clinical Sensitivity: Variable. Mutations in MLH1 and MSH2 account for
approximately 90% of mutations HNPCC families. Sequencing detects
~ 90-95% of MLH1 mutations and 50-80% of MSH2 mutations. MLH1 deletions
are identified in about 5-10% of patients and MSH2 deletions in 17-50%.
Mutations in MSH6 are rare.
Turn-Around-Times:
|
MLH1, MSH2, and MSH6 Gene Sequencing: |
4 weeks (total) |
|
MLH1 and MSH2 Gene Sequencing: |
4 weeks (total) |
|
MLH1 or MSH2 or MSH6 Gene Sequencing: |
3 weeks (per gene) |
|
Deletion/Duplication Analysis
for MSH1 or MSH2: |
3 weeks (per gene) |
|
Deletion/Duplication Analysis
for MSH1 and MSH2: |
3 weeks (total) |
|
MLH1/MSH2 Gene Sequencing and
Deletion/Duplication Analysis: |
4 weeks (per gene) |
|
Familial Known Mutation (Sequencing): |
2 weeks |
|
Familial Known Mutation
(Deletion/Duplication Analysis): |
3 weeks |
Sample Requirements: 7cc's blood in an K3EDTA (purple top) tube
Costs:
- MLH1, MSH2, and MSH6 Gene Sequencing: $2,700
- MLH1 and MSH2 Gene Sequencing: $1,800
- MLH1 or MSH2, or MSH6 Gene Sequencing: $900
- MLH1 or MSH2 Deletion/Duplication Analysis: $600
- MLH1 and MSH2 Deletion/Duplication Analysis: $800
- Familial Known Mutation Test (Sequencing): $250
- Familial Known Mutation Test (Deletion/Duplication Analysis):
same price as MLH1 or MSH2 Deletion/Duplication Analysis
listed above
How to order test |
BROCHURE PDF
Resources | Clinical Services
Background:
Hereditary Non-Polyposis Colorectal Cancer (HNPCC), also known as Lynch syndrome, confers an increased risk of colon cancer in addition to cancers of the endometrium, stomach, ovaries, small bowel, hepatobiliary epithelium, skin, and brain. HNPCC is implicated in 3-5% of all cases of colon cancer. For an individual with HNPCC, the lifetime risk for developing colorectal cancer has been reported to be approximately 80%. Two-thirds of these cancers occur in the proximal colon. The typical age of onset of colorectal cancer in individuals with HNPCC is younger (as early as 44 years) than the general population. These individuals are therefore less likely to be detected by routine colon cancer screening practices.
HNPCC is caused by mutation in a class of genes known as DNA mismatch repair genes which consists of MLH1, MSH2, MSH6, and PMS2. Germline mutations in MLH1 and MSH2 account for approximately 90% of detected mutations in families with HNPCC where as mutations in MSH6 account for about 7%-10%, and PMS2 mutations in fewer than 5% of families with HNPCC. The majority of individuals with HNPCC have inherited the condition from a parent but new (de novo) mutations, although extremely rare, have been reported.
Tumor cells with defective mismatch repair gene function exhibit an inconsistent number of microsatellite nucleotide repeats when compared to normal tissue, a characteristic referred to as "microsatellite instability" or "MSI'. These tumors often also exhibit the loss of at least one of the DNA mismatch repair proteins by immunohistochemistry (IHC). MSI and IHC, as well as clinical criteria (Classic Amsterdam, Amsterdam II, Bethesda, Modified Bethesda), can be used to both identify individuals with an increased likelihood of having HNPCC. If an individual does not meet Amsterdam criteria, then it is recommended that MSI and IHC screening be pursued prior to genetic testing.
HNPCC has a broad spectrum of clinical manifestations. In addition to classic HNPCC, two HNPCC-related syndromes are recognized, Turcot syndrome and Muir-Torre syndrome. Turcot syndrome is characterized by colorectal cancer or colorectal adenomas in addition to tumors of the central nervous system, usually glioblastomas. Individuals with Muir-Torre Muir-Torre can have any of the above HNPCC-related cancers in addition to sebaceous neoplasms of the skin such as adenomas, epitheliomas, carcinomas, and keratoacanthomas.
In addition to confirming the diagnosis of HNPCC, genetic testing allows for early identification and diagnosis of individuals at greatest risk for developing colorectal cancer, prior to the expression of typical clinical manifestations. The identification of a specific mutation can significantly impact the clinical management of these patients and facilitates the screening of their family members. Predictive testing for HNPCC mutations may be offered to unaffected, but at-risk, family members of HNPCC patients. If an at-risk individual is shown not to carry the familial mutation (genotype negative), they can be definitively diagnosed as unaffected with HNPCC and reassured that neither they nor their offspring will be at higher risk compared to the general population to develop this disorder. The need for serial follow up by colonoscopy is also obviated. However, if an at-risk family member is found to carry the mutation (genotype positive), then they can receive appropriate and early intervention and treatment.
Synonyms (OMIM #120435):
- COLON CANCER, FAMILIAL NONPOLYPOSIS, TYPE 1; FCC1
- COCA1
- LYNCH SYNDROME I
| Gene |
Protein |
OMIM# |
Locus |
| MLH1 |
DNA mismatch repair protein MLH1 |
120436 |
3p21.3 |
| MSH2 |
DNA mismatch repair protein MSH2 |
609309 |
2p22-p21 |
| MSH6 |
DNA mismatch repair protein MSH6 |
600678 |
2p16 |
- Clinical Features (variable, and may not occur in every patient):
- HNPCC:
- Colonic polyps (usually number 10-20)
- Colon cancer (age of onset 44-61 years)
- Extracolonic manifestations:
- Endometrial
- Ovarian
- Gastric
- Small bowel: duodenum and jejunum
- Hepatobiliary tract
- Upper urinary tract
- Brain/CNS
- Skin
- Turcot syndrome
- Colonic polyposis
- CNS tumors, usually glioblastomas
- PMS2 mutations more commonly observed
- Muir-Torre syndrome
- Sebaceous neoplasms of the skin (adenomas, epitheliomas, carcinomas, and keratoacanthomas)
- Any of the above HNPCC-related tumors
- Mutations in MSH2 more commonly reported than MLH1
Inheritance Pattern: Autosomal dominant
- The presence of a pathogenic mutation in one copy of MLH1, MSH2, or MSH6 is sufficient to cause HNPCC.
- First-degree relatives of an affected individual with an identified pathogenic mutation have a 50% (or 1 in 2) chance of inheriting the same mutation.
- Reduced penetrance and variable expressivity exists.
- De novo mutations have been reported but the incidence is unknown and expected to be extremely low.
Test Indications:
- Individuals with a clinical diagnosis of HNPCC based on Amsterdam, Bethesda, or other clinical criteria.
- Individuals with a colon tumor identified as having microsatellite instability (MSI; also referred to as MSI high).
- Individuals with a colon tumor exhibiting absence of MLH1, MSH2, or MSH6 protein by immunohistochemistry.
- Predictive testing for at-risk family members (parents, siblings, and children) of an individual diagnosed with HNPCC and an identified MLH1, MSH2 or MSH6 mutation.
Test Outcomes:
- The detection of one pathogenic mutation in MLH1, MSH2, or MSH6 confirms a diagnosis of HNPCC. A positive test result confirms a diagnosis of HNPCC in a symptomatic individual. If a familial mutation is known, a positive test result confirms the presence of the mutation in an asymptomatic family member.
- A negative test result does not rule out the possibility that the individual has a genetic cause of HNPCC. Deletions of regions not covered by MLPA, regulatory mutations, and/or mutations in other genes could be responsible for the individual's clinical features.
Turn-Around-Times:
-
|
MLH1, MSH2, and MSH6 Gene Sequencing: |
4 weeks (total) |
-
|
MLH1 and MSH2 Gene Sequencing: |
4 weeks (total) |
-
|
MLH1 or MSH2 or MSH6 Gene Sequencing: |
3 weeks (per gene) |
-
|
Deletion/Duplication Analysis for MSH1 or MSH2: |
3 weeks (per gene) |
-
|
Deletion/Duplication Analysis for MSH1 and MSH2: |
3 weeks (total) |
-
|
MLH1/MSH2 Gene Sequencing and Deletion/Duplication Analysis: |
4 weeks (per gene) |
-
|
Familial Known Mutation (Sequencing): |
2 weeks |
-
|
Familial Known Mutation (Deletion/Duplication Analysis):
|
3 weeks |
Methodology: Bi-directional sequence analysis of 19 coding exons and splice sites of MLH1, 16 coding exons and splice sites of MSH2, and/or 10 coding exons and splice sites of MSH6. Gross deletions and duplications of the MLH1 and MSH2 genes are detected by Multiplex Ligation-dependent Probe Amplification (MLPA).
Analytical and Clinical Sensitivity: The gene sequencing assay is greater than 99.9% accurate in detecting mutations in the sequence analyzed. MLPA is greater than 98% accurate in detecting deletions and/or duplications at the analyzed locus. Mutation detection rates vary greatly depending on family history and other clinical criteria used in diagnosis. Germline mutations in MLH1 and MSH2 account for approximately 90% of mutations in families with HNPCC. The mutation detection rate by sequencing is approximately 90-95% for MLH1 and 50-80% of MSH2. Deletions are identified in MLH1 approximately 5-10% of the time and in MSH2, 17-50% of the time. Mutations in MSH6 are rare and detection rate is not known.
Cost and CPT codes:
MLH1, MSH2, and MSH6 Gene Sequencing
- Cost: $2,700
- CPT codes: 83891(1), 83894(1), 83898(70), 83904(70), 83909(1), 83912(1)
MLH1 and MSH2 Gene Sequencing
- Cost: $1,800
- CPT codes: 83891(1), 83894(1), 83898(35), 83904(35), 83909(1), 83912(1)
MLH1 Gene Sequencing
- Cost: $900
- CPT codes: 83891(1), 83894(1), 83898(19), 83904(19), 83909(1), 83912(1)
MSH2 Gene Sequencing
- Cost: $900
- CPT codes: 83891(1), 83894(1), 83898(16), 83904(16), 83909(1), 83912(1)
MSH6 Gene Sequencing
- Cost: $900
- CPT codes: 83891(1), 83894(1), 83898(10), 83904(10), 83909(1), 83912(1)
MLH1 Deletion/Duplication Analysis
- Cost: $600
- CPT codes: 83891(1), 83896(19), 83900(1), 83901(17), 83909(1), 83912(1)
MSH2 Deletion/Duplication Analysis
- Cost: $600
- CPT codes: 83891(1), 83896(17), 83900(1), 83901(15), 83909(1), 83912(1)
MLH1 and MSH2 Deletion/Duplication Analysis
- Cost: $800
- CPT codes: 83891(1), 83896(36), 83900(1), 83901(34), 83909(1), 83912(1)
Testing for Familial Known Mutation (Sequencing)
- Cost: $250
- CPT codes: 83891(1), 83894(1), 83898(1), 83904(1), 83909(1), 83912(1)
Testing for Familial Known Mutation (Deletion/Duplication Analysis)
- Same price and CPT codes as stated above for MLH1 or MSH2 Deletion/Duplication Analysis
References:
Gene Reviews: HNPCC: www.genetests.org
If you have any questions, please call the Laboratory for Molecular Medicine at 617-768-8500 or email us at LMM@partners.org
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