Hereditary Cancer Panel Comprehensive
GTR Test Accession: Help GTR000530120.4
CAP
INHERITED DISEASECANCERINHERITED DISEASE SUSCEPTIBILITY ... View more
Last updated in GTR: 2020-01-23
Last annual review date for the lab: 2024-02-07 LinkOut
At a Glance
Diagnosis; Mutation Confirmation; Pre-symptomatic; ...
Hereditary breast ovarian cancer syndrome; Ataxia-telangiectasia syndrome; Attenuated familial adenomatous polyposis; ...
APC (5q22.2), ATM (11q22.3), BARD1 (2q35), BMPR1A (10q23.2), BRCA1 (17q21.31), ...
Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
The Hereditary Cancer Panel (HCP) is a genetic test designed …
This assay meets the sensitivity and specificity of combined Sanger …
Avoidance of invasive testing; Establish or confirm diagnosis; Guidance for management; ...
Ordering Information
Offered by: Help
Molecular Genetics Laboratory
View lab's website
View lab's test page
Test short name: Help
HCP Comprehensive
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Licensed Physician
Contact Policy: Help
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: Help
Please complete the requisition available on the website and ensure it is signed by the referring physician.
Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Custom Deletion/Duplication Testing
Custom Sequence Analysis
Test additional service: Help
Custom mutation-specific/Carrier testing
Test development: Help
Test developed by laboratory (no manufacturer test name)
Informed consent required: Help
Decline to answer
Test strategy: Help
Methodology: All coding exons and 20 bp of flanking non-coding 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 … View more
View citations (1)
  • Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn. 2016;18(5):657-667. doi:10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 02. PMID: 27376475.
Pre-test genetic counseling required: Help
Decline to answer
Post-test genetic counseling required: Help
Decline to answer
Recommended fields not provided:
Conditions Help
Total conditions: 39
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 30
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 4
Method Category Help
Test method Help
Instrument
Deletion/duplication analysis
Multiplex Ligation-dependent Probe Amplification (MLPA)
Deletion/duplication analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina MiSeq/NextSeq
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina MiSeq/NextSeq
Targeted variant analysis
Bi-directional Sanger Sequence Analysis
Applied Biosystems 3730 capillary sequencing instrument
Clinical Information
Test purpose: Help
Diagnosis; Mutation Confirmation; Pre-symptomatic; Predictive; Prognostic; Recurrence; Risk Assessment
Clinical validity: Help
This assay meets the sensitivity and specificity of combined Sanger sequencing and MLPA copy number analysis, >99%
View citations (1)
  • Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn. 2016;18(5):657-667. doi:10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 02. PMID: 27376475.
Target population: Help
The Hereditary Cancer Panel (HCP) is a genetic test designed to help assess the cancer predisposition risk for a number of common heritable cancers including: breast, ovarian, gastric, colorectal, pancreatic, melanoma, prostate, and endometrial cancers. The Hereditary Cancer Panel (HCP) includes 30 genes, . Mutations in these genes are associated … View more
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
All coding exons and 20 bp of flanking non-coding 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; … View more

Will the lab re-contact the ordering physician if variant interpretation changes? Help
No. The laboratory will re-visit variant interpretation when requested by the referring physician.
Recommended fields not provided:
Technical Information
Test Procedure: Help
Methodology: All coding exons and 20 bp of flanking non-coding 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 … View more
View citations (1)
  • Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn. 2016;18(5):657-667. doi:10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 02. PMID: 27376475.
Test Confirmation: Help
Mutations identified are repeated if necessary in an independent assay using either Sanger sequence, MLPA, Q-PCR or other.
Test Comments: Help
.
Availability: Help
Tests performed
Entire test performed in-house

Test performance comments
Testing performed in a modern purpose built facility that exceeds clinical standards
Analytical Validity: Help
This assay meets the sensitivity and specificity of combined Sanger sequencing and MLPA copy number analysis, >99%
View citations (1)
  • Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn. 2016;18(5):657-667. doi:10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 02. PMID: 27376475.
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Formal PT program

PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP

Description of PT method: Help
2 trials of 3 samples annually
VUS:
Software used to interpret novel variations Help
(SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; and Alamut Visual).

Laboratory's policy on reporting novel variations Help
Variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868), if necessary, 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 request. Variants detected in the 5’ UTR … View more
Recommended fields not provided:
Regulatory Approval
FDA Review: Help
Category: FDA exercises enforcement discretion
Additional Information

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.