GTR Test Accession:
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GTR000597346.3
Last updated in GTR: 2024-04-15
View version history
GTR000597346.3, last updated: 2024-04-15
GTR000597346.2, last updated: 2024-03-25
GTR000597346.1, last updated: 2022-01-31
Last annual review date for the lab: 2024-05-28
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At a Glance
Test purpose:
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Diagnosis;
Predictive
Conditions (1):
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Hereditary gastrointestinal cancer and/or polyposis syndrome
Genes (26):
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Methods (1):
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Molecular Genetics - Sequence analysis of the entire coding region: Next-Generation (NGS)/Massively parallel sequencing (MPS)
Target population: Help
Evaluation for patients with a personal or family history suggestive …
Clinical validity:
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Not provided
Clinical utility:
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Establish or confirm diagnosis;
Guidance for management;
Guidance for selecting a drug therapy and/or dose; ...
Ordering Information
Offered by:
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Test short name:
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CRCGP
Specimen Source:
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- Peripheral (whole) blood
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Dentist
- Licensed Physician
- Nurse Practitioner
- Physician Assistant
- Public Health Mandate
- Registered Nurse
Lab contact:
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Megan Hoenig, MS, MPH, Certified Genetic counselor, CGC, Genetic Counselor
GCMolgen@mayo.edu
1-800-533-1710
GCMolgen@mayo.edu
1-800-533-1710
Contact Policy:
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Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
How to Order:
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https://www.mayocliniclabs.com/test-catalog/Specimen/614571
Order URL
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
OrderCode: FMTT
OrderCode: FMTT
Test development:
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Test developed by laboratory (no manufacturer test name)
Informed consent required:
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Based on applicable state law
Pre-test genetic counseling required:
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Decline to answer
Post-test genetic counseling required:
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Decline to answer
Recommended fields not provided:
Test strategy
Conditions
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Total conditions: 1
Condition/Phenotype | Identifier |
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Test Targets
Genes
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Total genes: 26
Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
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Methodology
Total methods: 1
Method Category
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Test method
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Instrument
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina NovaSeq 6000
Clinical Information
Test purpose:
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Diagnosis;
Predictive
Clinical utility:
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Establish or confirm diagnosis
Guidance for management
Guidance for selecting a drug therapy and/or dose
Predictive risk information for patient and/or family members
View citations (1)
- NCCN Guidelines Insights: Genetic/Familial High-Risk Assessment: Colorectal, Version 2.2019. Gupta S, et al. J Natl Compr Canc Netw. 2019;17(9):1032-1041. doi:10.6004/jnccn.2019.0044. PMID: 31487681.
Guidance for management
View citations (1)
- NCCN Guidelines Insights: Genetic/Familial High-Risk Assessment: Colorectal, Version 2.2019. Gupta S, et al. J Natl Compr Canc Netw. 2019;17(9):1032-1041. doi:10.6004/jnccn.2019.0044. PMID: 31487681.
Guidance for selecting a drug therapy and/or dose
View citations (1)
- NCCN Guidelines Insights: Genetic/Familial High-Risk Assessment: Colorectal, Version 2.2019. Gupta S, et al. J Natl Compr Canc Netw. 2019;17(9):1032-1041. doi:10.6004/jnccn.2019.0044. PMID: 31487681.
Predictive risk information for patient and/or family members
View citations (1)
- NCCN Guidelines Insights: Genetic/Familial High-Risk Assessment: Colorectal, Version 2.2019. Gupta S, et al. J Natl Compr Canc Netw. 2019;17(9):1032-1041. doi:10.6004/jnccn.2019.0044. PMID: 31487681.
Target population:
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Evaluation for 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 …
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View citations (5)
- Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL, . Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405-24. doi:10.1038/gim.2015.30. Epub 2015 Mar 05. PMID: 25741868.
- Smith RA, Andrews KS, Brooks D, Fedewa SA, Manassaram-Baptiste D, Saslow D, Wender RC. Cancer screening in the United States, 2019: A review of current American Cancer Society guidelines and current issues in cancer screening. CA Cancer J Clin. 2019;69(3):184-210. doi:10.3322/caac.21557. Epub 2019 Mar 15. PMID: 30875085.
- NCCN Guidelines Insights: Genetic/Familial High-Risk Assessment: Colorectal, Version 2.2019. Gupta S, et al. J Natl Compr Canc Netw. 2019;17(9):1032-1041. doi:10.6004/jnccn.2019.0044. PMID: 31487681.
- Howlader N, Noone AM, Krapcho M (eds). SEER Cancer Statistics Review, 1975-2018, National Cancer Institute. Bethesda, MD, https://seer.cancer.gov/csr/1975_2018/, based on November 2020 SEER data submission, posted to the SEER web site, April 2021.
- Idos G, Valle L. Lynch Syndrome. In: Adam MP, Ardinger HH, Pagon RA, et al, eds. GeneReviews (Internet). University of Washington, Seattle; 2004. Updated February 2, 2021. Accessed May 4, 2021 Available at www.ncbi.nlm.nih.gov/books/NBK1211/
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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All detected variants are evaluated according to the most recent American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) recommendations. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.
All detected variants are evaluated according to the most recent American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) recommendations. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.
Are family members with defined clinical status recruited to assess significance of VUS without charge?
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Yes. Contact lab for details
Yes. Contact lab for details
Will the lab re-contact the ordering physician if variant interpretation changes?
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No. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time.
No. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time.
Research:
Is research allowed on the sample after clinical testing is complete?
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Research testing is only performed under IRB approved protocol with an opt-out policy in place.
Research testing is only performed under IRB approved protocol with an opt-out policy in place.
Recommended fields not provided:
Clinical validity,
Sample negative report,
Sample positive report
Technical Information
Test Procedure:
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Next generation sequencing (NGS) and/or Sanger sequencing is 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 pathogenic variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At …
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Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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At least 99% of the bases are covered at a read depth >30X. Sensitivity is estimated at >99% for single nucleotide variants, >94% for indels up to 39 base pairs, >95% for deletions up to 75 base pairs and insertions up to 47 base pairs.
Assay limitations:
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Clinical Correlations Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete. If testing was performed because of a clinically significant family history, it is often useful to first test …
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Proficiency testing (PT):
Is proficiency testing performed for this test?
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Yes
Method used for proficiency testing: Help
Alternative Assessment
Description of PT method: Help
Platform covered
Description of internal test validation method: Help
This test was laboratory developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements
Yes
Method used for proficiency testing: Help
Alternative Assessment
Description of PT method: Help
Platform covered
Description of internal test validation method: Help
This test was laboratory developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements
VUS:
Software used to interpret novel variations
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Variants may be analyzed using any combination of the following: Alamut, REVEL, Polyphen-2, SIFT, AGVGD, MutationTaster, SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, SpliceAI, gene-specific online databases, ISCA, UCSC Genome Browser
Laboratory's policy on reporting novel variations Help
All novel alterations and copy number variants are evaluated for potential pathogenicity and included in the written report, accordingly.
Variants may be analyzed using any combination of the following: Alamut, REVEL, Polyphen-2, SIFT, AGVGD, MutationTaster, SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, SpliceAI, gene-specific online databases, ISCA, UCSC Genome Browser
Laboratory's policy on reporting novel variations Help
All novel alterations and copy number variants are evaluated for potential pathogenicity and included in the written report, accordingly.
Recommended fields not provided:
Test Confirmation,
Citations to support assay limitations,
Citations to support internal test validation method,
Citations for Analytical validity,
PT Provider,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Category:
FDA exercises enforcement discretion
Additional Information
Reviews:
Clinical resources:
Consumer resources:
IMPORTANT NOTE:
NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading.
NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice.
Patients and consumers
with specific questions about a genetic test should contact a health care provider or a genetics professional.