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HelpTest Code MISC2MAYOCRCGP Hereditary Gastrointestinal Cancer Panel, Varies
Ordering Guidance
Customization of this panel and single gene analysis for any gene present on this panel are available. For more information see CGPH / Custom Gene Panel, Hereditary, Next-Generation Sequencing, Varies.
Targeted testing for familial variants (also called site-specific or known mutations testing) is available for the genes on this panel. For more information see FMTT / Familial Variant, Targeted Testing, Varies. To obtain more information about this testing option, call 800-533-1710.
Shipping Instructions
Necessary Information
Prior Authorization is available, but not required, for this test. If proceeding with the prior authorization process, submit the required form with the specimen.
Specimen Required
Patient Preparation: A previous bone marrow transplant from an allogenic donor will interfere with testing. For instructions for testing patients who have received a bone marrow transplant, call 800-533-1710.
Specimen Type: Whole blood
Container/Tube:
Preferred: Lavender top (EDTA) or yellow top (ACD)
Acceptable: Green top (Sodium heparin)
Specimen Volume: 3 mL
Collection Instructions:
1. Invert several times to mix blood.
2. Send whole blood specimen in original tube. Do not aliquot.
Specimen Stability Information: Ambient 4 days/Refrigerated 4 days/Frozen 4 days
Additional Information:
1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for samples received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.
2. To ensure minimum volume and concentration of DNA is met, the preferred volume of blood must be submitted. Testing may be canceled if DNA requirements are inadequate.
Specimen Type: Saliva
Patient Preparation: Patient should not eat, drink, smoke, or chew gum 30 minutes prior to collection.
Supplies: Saliva Swab Collection Kit (T786)
Specimen Volume: 1 Swab
Collection Instructions: Collect and send specimen per kit instructions.
Specimen Stability Information: Ambient (preferred) 30 days, Refrigerated 30 days
Additional information: Due to lower quantity/quality of DNA yielded from saliva, some aspects of the test may not perform as well as DNA extracted from a whole blood sample. When applicable, specific gene regions that were unable to be interrogated will be noted in the report. Alternatively, additional specimen may be required to complete testing.
Forms
1. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file.
-Informed Consent for Genetic Testing (T576)
-Informed Consent for Genetic Testing (Spanish) (T826)
2. Molecular Genetics: Inherited Cancer Syndromes Patient Information Sheet (T519)
3. Hereditary Gastrointestinal Cancer Panel Prior Authorization Ordering Instructions
4. If not ordering electronically, complete, print, and send a Oncology Test Request (T729) with the specimen.
Secondary ID
614571Useful For
Evaluating patients with a personal or family history suggestive of a hereditary gastrointestinal cancer or hereditary polyposis syndrome
Establishing a diagnosis of a hereditary gastrointestinal cancer syndrome or hereditary polyposis syndrome allowing for targeted cancer surveillance based on associated risks
Identifying genetic variants associated with increased risk for gastrointestinal cancer and polyposis, allowing for predictive testing and appropriate screening of at-risk family members
Testing Algorithm
First-tier testing may be considered/recommended. For more information see Lynch Syndrome Testing Algorithm.
Special Instructions
- Molecular Genetics: Inherited Cancer Syndromes Patient Information
- Informed Consent for Genetic Testing
- Hereditary Gastrointestinal Cancer Panel Prior Authorization Ordering Instructions
- Lynch Syndrome Testing Algorithm
- Informed Consent for Genetic Testing (Spanish)
- Targeted Genes and Methodology Details for Hereditary Gastrointestinal Cancer Panel
Method Name
Sequence Capture and Next-Generation Sequencing (NGS), Polymerase Chain Reaction (PCR), Sanger Sequencing and/or Multiplex Ligation-Dependent Probe Amplification (MLPA)
Reporting Name
Hereditary GI Cancer PanelSpecimen Type
VariesSpecimen Minimum Volume
Whole blood: 1 mL; Saliva: See Specimen Required
Specimen Stability Information
| Specimen Type | Temperature | Time |
|---|---|---|
| Varies | Varies | |
Reject Due To
All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.Clinical Information
Colorectal cancer occurs in approximately 4% to 6% of individuals in the general population.(1) In some cases, individuals with a personal or family history of colorectal cancer, gastric cancer, or polyposis may be at increased risk of cancer due to a hereditary cancer syndrome.(2,3) Evaluation of the genes on this panel may be useful for families with a history of colorectal cancer, gastric cancer, polyposis, or gastrointestinal cancers to determine cancer risk, surveillance recommendations, and targeted treatments.(2-4)
The most common hereditary colon cancer syndrome is Lynch syndrome, accounting for about 2% to 4% of all colon cancer cases.(2) Lynch syndrome is associated with germline variants in the mismatch repair genes, MLH1, MSH2, MSH6, PMS2, or deletions of the EPCAM gene.(2,3) It is predominantly characterized by significantly increased risks for colorectal and endometrial cancer.(2,3) The lifetime risk for colorectal cancer is highly variable and dependent on the gene involved.(2,3) Other malignancies within the tumor spectrum include gastric cancer, ovarian cancer, hepatobiliary and upper tract urothelial carcinomas, and small bowel cancer.(2,3)
Although rare, individuals and families with polyposis may also be at risk for a hereditary polyposis syndrome, such as familial adenomatous polyposis (FAP).(2) FAP is caused by variants in the APC gene and characterized by numerous adenomatous polyps.(2) The presence of extracolonic manifestations is variable and includes gastric and duodenal polyps, ampullary polyps, osteomas, dental abnormalities (unerupted teeth), congenital hypertrophy of the retinal pigment epithelium (CHRPE), benign cutaneous lesions, desmoid tumors, hepatoblastoma, and extracolonic cancers.(2)
Other genes are also known to cause to hereditary colorectal cancer, gastric cancer, polyposis, and gastrointestinal cancers.(2) The risk for developing cancer associated with these syndromes varies.(2) Some individuals with a disease-causing variant in one of these genes develop multiple primary cancers.(2)
The National Comprehensive Cancer Network and the American Cancer Society provide recommendations regarding the medical management of individuals with hereditary gastrointestinal cancer syndromes.(2,4)
Reference Values
An interpretive report will be provided.
Interpretation
All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(5) Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.
Method Description
Next-generation sequencing (NGS) and/or Sanger sequencing are performed to test for the presence of variants in coding regions and intron/exon boundaries of the genes analyzed, as well as some other regions that have known disease-causing variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At least 99% of the bases are covered at a read depth over 30X. Sensitivity is estimated at above 99% for single nucleotide variants, above 94% for deletions-insertions (delins) less than 40 base pairs (bp), above 95% for deletions up to 75 bp and insertions up to 47 bp. NGS, multiplex ligation-dependent probe amplification (MLPA), and/or a polymerase chain reaction (PCR)-based quantitative method is performed to test for the presence of deletions and duplications in the genes analyzed. PCR and gel electrophoresis is performed to test for the presence of the 10 megabase inversion of coding exons 1-7 of the MSH2 gene.
There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. For details regarding the targeted genes analyzed and specific gene regions not routinely covered, see Targeted Genes and Methodology Details for Hereditary Gastrointestinal Cancer Panel.(Unpublished Mayo method)
Confirmation of select reportable variants may be performed by alternate methodologies based on internal laboratory criteria.
Genes analyzed: APC (including promoters 1A and 1B), ATM, AXIN2, BMPR1A, CDH1, CHEK2, CTNNA1, EPCAM (copy number variants only), GREM1 (upstream enhancer region duplication only), KIT, MLH1, MLH3, MSH2, MSH3, MSH6, MUTYH, NTHL1, PDGFRA, PMS2, POLD1, POLE, PTEN (including promoter), RNF43, SMAD4, STK11, and TP53
Day(s) Performed
Varies
Report Available
21 to 28 daysPerforming Laboratory
Mayo Clinic Laboratories in Rochester
Test Classification
This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.CPT Code Information
81435
LOINC Code Information
| Test ID | Test Order Name | Order LOINC Value |
|---|---|---|
| CRCGP | Hereditary GI Cancer Panel | 97656-3 |
| Result ID | Test Result Name | Result LOINC Value |
|---|---|---|
| 614695 | Test Description | 62364-5 |
| 614696 | Specimen | 31208-2 |
| 614697 | Source | 31208-2 |
| 614698 | Result Summary | 50397-9 |
| 614699 | Result | 82939-0 |
| 614700 | Interpretation | 69047-9 |
| 614701 | Resources | 99622-3 |
| 614702 | Additional Information | 48767-8 |
| 614703 | Method | 85069-3 |
| 614704 | Genes Analyzed | 48018-6 |
| 614705 | Disclaimer | 62364-5 |
| 614706 | Released By | 18771-6 |
Prior Authorization
Insurance preauthorization is available for this testing; forms are available.
Patient financial assistance may be available to those who qualify. Patients who receive a bill from Mayo Clinic Laboratories will receive information on eligibility and how to apply.