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GTR Home > Tests > Hereditary Cancer Panel Comprehensive

Overview

Test name

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Hereditary Cancer Panel Comprehensive (HCP Comprehensive)

Purpose of the test

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This is a clinical test intended for Help: Diagnosis, Mutation Confirmation, Pre-symptomatic, Predictive, Prognostic, Recurrence, Risk Assessment

Condition

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Click Indication tab for more information.

How to order

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Please complete the requisition available on the website and ensure it is signed by the referring physician.
Order URL Help: http://www.lhsc.on.ca/lab/molegen/hcp.htm

Specimen source

Cell culture
Isolated DNA
Peripheral (whole) blood

Methodology

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Molecular Genetics
DDeletion/duplication analysis
Multiplex Ligation-dependent Probe Amplification (MLPA)Next-Generation (NGS)/Massively parallel sequencing (MPS)
  • Illumina MiSeq/NextSeq
CSequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
  • Illumina MiSeq/NextSeq
TTargeted variant analysis
Bi-directional Sanger Sequence Analysis
  • Applied Biosystems 3730 capillary sequencing instrument

Summary of what is tested

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Clinical utility

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Not provided

Clinical validity

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This assay meets the sensitivity and specificity of combined Sanger sequencing and MLPA copy number analysis, >99%

Citations

Not provided

Testing strategy

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All coding exons and 20 bp of flanking intronic sequence are enriched using an LHSC custom targeted hybridization protocol (Roche Nimblegen), followed by high throughput sequencing (Illumina). Sequence variants and copy number changes are assessed and interpreted using clinically validated algorithms and commercial software (SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; and Alamut Visual). All exons have >1000x mean read depth coverage, with a minimum 200x coverage at a single nucleotide resolution. This assay meets the sensitivity and specificity of combined Sanger sequencing and MLPA copy number analysis. All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon reques 000 Please complete the requisition available on the website and ensure it is signed by the referring physician.

Test services

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  • Clinical Testing/Confirmation of Mutations Identified Previously
  • Confirmation of research findings
  • Custom Deletion/Duplication Testing
  • Custom Sequence Analysis
  • Custom mutation-specific/Carrier testing

Suggested reading

  • USPSTF, 2019
    Risk Assessment, Genetic Counseling, and Genetic Testing for BRCA1/2-Related Cancer in Women: A Systematic Review for the U.S. Preventive Services Task Force
  • USPSTF, 2013
    Risk Assessment, Genetic Counseling, and Genetic Testing for BRCA-Related Cancer: Systematic Review to Update the U.S. Preventive Services Task Force Recommendation (See 2019 Update)
  • Phillips et al., 2013
    Tamoxifen and risk of contralateral breast cancer for BRCA1 and BRCA2 mutation carriers.
  • Domchek et al., 2010
    Association of Risk-Reducing Surgery in BRCA1 or BRCA2 Mutation Carriers with Cancer Risk and Mortality
  • NCI PDQ, Cancer Genetics Counseling
    Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version

Practice guidelines

  • NICE, 2023
    UK NICE Clinical Guideline CG164, Familial breast cancer: classification, care and managing breast cancer and related risks in people with a family history of breast cancer, 2023
  • NICE, 2023
    UK NICE Clinical guideline (CG122), Ovarian cancer: recognition and initial management, 2023
  • NCCN, 2022
    NCCN Clinical Practice Guidelines in Oncology, Genetic/Familial High-Risk Assessment: Breast, Ovarian, and Pancreatic version 2.2022
  • ACMG ACT, 2019
    American College of Medical Genetics and Genomics, Genomic Testing (Secondary Findings) ACT Sheet, BRCA1 and BRCA2 Pathogenic Variants (Hereditary Breast and Ovarian Cancer), 2019

IMPORTANT NOTE: NIH does not independently verify information submitted to the GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in the 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.