GTR Test Accession:
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GTR000530120.4
CAP
Last updated in GTR: 2020-01-23
View version history
GTR000530120.4, last updated: 2020-01-23
GTR000530120.3, last updated: 2019-01-23
GTR000530120.2, last updated: 2016-04-07
GTR000530120.1, last updated: 2016-04-05
Last annual review date for the lab: 2024-02-07
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At a Glance
Test purpose:
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Diagnosis;
Mutation Confirmation;
Pre-symptomatic; ...
Conditions (39):
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Hereditary breast ovarian cancer syndrome;
Ataxia-telangiectasia syndrome;
Attenuated familial adenomatous polyposis
more...
Genes (30):
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Methods (4):
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Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
Target population: Help
The Hereditary Cancer Panel (HCP) is a genetic test designed …
Clinical validity:
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This assay meets the sensitivity and specificity of combined Sanger …
Clinical utility:
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Avoidance of invasive testing;
Establish or confirm diagnosis;
Guidance for management; ...
Ordering Information
Offered by:
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Test short name:
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HCP Comprehensive
Specimen Source:
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- Cell culture
- Isolated DNA
- Peripheral (whole) blood
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Licensed Physician
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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Please complete the requisition available on the website and ensure it is signed by the referring physician.
Order URL
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Custom Deletion/Duplication Testing
Custom Sequence Analysis
Confirmation of research findings
Custom Deletion/Duplication Testing
Custom Sequence Analysis
Test additional service:
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Custom mutation-specific/Carrier testing
Test development:
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Test developed by laboratory but exempt from FDA oversight (eg. NYS CLEP approved, offered within a hospital or clinic)
Informed consent required:
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Decline to answer
Test strategy:
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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:
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Decline to answer
Post-test genetic counseling required:
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Decline to answer
Recommended fields not provided:
Test Order Code,
Lab contact for this test
Conditions
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Total conditions: 39
Condition/Phenotype | Identifier |
---|
Test Targets
Genes
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Total genes: 30
Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
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Methodology
Total methods: 4
Method Category
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Test method
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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:
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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.
Clinical utility:
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Avoidance of invasive testing
Establish or confirm diagnosis
Guidance for management
Predictive risk information for patient and/or family members
Establish or confirm diagnosis
Guidance for management
Predictive risk information for patient and/or family members
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 …
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Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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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
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?
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No. The laboratory will re-visit variant interpretation when requested by the referring physician.
No. The laboratory will re-visit variant interpretation when requested by the referring physician.
Recommended fields not provided:
Are family members with defined clinical status recruited to assess significance of VUS without charge?,
Is research allowed on the sample after clinical testing is complete?,
Sample negative report,
Sample positive report
Technical Information
Test Procedure:
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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:
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Mutations identified are repeated if necessary in an independent assay using either Sanger sequence, MLPA, Q-PCR or other.
Test Comments:
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.
Availability:
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Tests performed
Entire test performed in-house
Test performance comments
Testing performed in a modern purpose built facility that exceeds clinical standards
Entire test performed in-house
Test performance comments
Testing performed in a modern purpose built facility that exceeds clinical standards
Analytical Validity:
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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?
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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
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
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(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
(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:
Assay limitations,
Description of internal test validation method,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Category:
FDA exercises enforcement discretion
Additional Information
Suggested reading:
Clinical resources:
Molecular resources:
Practice guidelines:
Consumer resources:
IMPORTANT NOTE:
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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.