GTR Test Accession:
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GTR000592401.2
NYS CLEP
Last updated in GTR:
2024-02-07
View version history
GTR000592401.2,
last updated:
2024-02-07
GTR000592401.1,
registered in GTR:
2023-02-08
Last annual review date for the lab: 2024-02-07
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At a Glance
Test purpose:
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Diagnosis;
Drug Response;
Mutation Confirmation; ...
Conditions (1):
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Epilepsy
Genes (166):
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Methods (2):
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Molecular Genetics - Deletion/duplication analysis: Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
Target population: Help
Epilepsy is a group of phenotypically and genetically heterogeneous diseases …
Clinical validity:
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Not provided
Clinical utility:
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Not provided
Ordering Information
Offered by:
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Test short name:
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Epilepsy
Specimen Source:
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- Amniocytes
- Amniotic fluid
- Bone marrow
- Cell culture
- Chorionic villi
- Cord blood
- Fetal blood
- Fibroblasts
- Fresh tissue
- Frozen tissue
- Isolated DNA
- Paraffin block
- Peripheral (whole) blood
- Plasma
- Urine
- White blood cell prep
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
Lab contact:
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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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Complete and physician signed requisition required with pedigree and clear clinical diagnosis. Requisition available on lab website if required. Please draw 4-10ml EDTA whole blood and ship by overnight courier to the lab address (weekdays only) Clinicians inside Ontario(Canada) must complete the OEGTP requisition to access this panel and receive …
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Comment: Requires prior phone contact to arrange for test development
Confirmation of research findings
Comment: Requires prior phone contact to arrange for test development
Custom Deletion/Duplication Testing
Comment: Available for any gene found on existing panels
Maternal cell contamination study (MCC)
Comment: Requires prior phone contact to arrange for consult
Comment: Requires prior phone contact to arrange for test development
Confirmation of research findings
Comment: Requires prior phone contact to arrange for test development
Custom Deletion/Duplication Testing
Comment: Available for any gene found on existing panels
Maternal cell contamination study (MCC)
Comment: Requires prior phone contact to arrange for consult
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 …
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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
Conditions
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Total conditions: 1
| Condition/Phenotype | Identifier |
|---|
Test Targets
Genes
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Total genes: 166
| Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
|---|
Methodology
Total methods: 2
Method Category
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Test method
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Instrument
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
Clinical Information
Test purpose:
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Diagnosis;
Drug Response;
Mutation Confirmation;
Predictive;
Prognostic;
Risk Assessment
Target population:
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Epilepsy is a group of phenotypically and genetically heterogeneous diseases that are characterized by recurrent and unprovoked seizures. It can develop at any age, but most commonly in early childhood, particularly in the first year of life. About two thirds of epilepsies have a genetic component, displaying two important features: …
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Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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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
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
Are family members with defined clinical status recruited to assess significance of VUS without charge?
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Decline to answer.
Decline to answer.
Will the lab re-contact the ordering physician if variant interpretation changes?
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No. Requests for re-interpretation of a VUS identified in this laboratory must be initiated by the ordering physician. The laboratory is not responsible for auditing mutation interpretations as they evolve over time.
No. Requests for re-interpretation of a VUS identified in this laboratory must be initiated by the ordering physician. The laboratory is not responsible for auditing mutation interpretations as they evolve over time.
Recommended fields not provided:
Clinical validity,
Clinical utility,
Is research allowed on the sample after clinical testing is complete?,
Sample negative report,
Sample positive report
Technical Information
Availability:
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Tests performed
Entire test performed in-house
Test performance comments
All testing is performed in a licensed facility in a teaching Hospital facility staffed by discipline specific licensed staff
Entire test performed in-house
Test performance comments
All testing is performed in a licensed facility in a teaching Hospital facility staffed by discipline specific licensed staff
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
NGS pipeline tested using other panels
Yes
Method used for proficiency testing: Help
NGS pipeline tested using other panels
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), are reported. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon request. Variants detected in the 5’ UTR and 3’ UTR are not reported unless there is … 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), are reported. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon request. Variants detected in the 5’ UTR and 3’ UTR are not reported unless there is … View more
Recommended fields not provided:
Test Confirmation,
Assay limitations,
Description of internal test validation method,
PT Provider,
Description of PT method,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Not provided
NYS CLEP Approval:
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Number:
Status: Exempt
Status: Exempt
Additional Information
Reviews:
Clinical resources:
Practice guidelines:
Consumer resources:
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Patients and consumers
with specific questions about a genetic test should contact a health care provider or a genetics professional.