GTR Test Accession:
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GTR000593088.3
CAP
Last updated in GTR: 2023-05-10
View version history
GTR000593088.3, last updated: 2023-05-10
GTR000593088.2, last updated: 2022-12-02
GTR000593088.1, last updated: 2022-05-31
Last annual review date for the lab: 2024-05-28
LinkOut
At a Glance
Methods (3):
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Molecular Genetics - Deletion/duplication analysis: Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
Target population: Help
Individuals with a diagnosis of an epilepsy or seizure disorder
Clinical validity:
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Not provided
Clinical utility:
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Establish or confirm diagnosis
Ordering Information
Offered by:
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Test short name:
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EPPAN
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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Emily Lauer, MS, CGC, 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/overview/616550#Specimen
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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No
Post-test genetic counseling required:
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No
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: 318
Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
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Methodology
Total methods: 3
Method Category
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Test method
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Instrument
Deletion/duplication analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina NovaSeq 6000
Mutation scanning of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina NovaSeq 6000
Targeted variant analysis
Trinucleotide repeat by PCR or Southern Blot
Applied Biosystems 3730 capillary sequencing instrument
Clinical Information
Test purpose:
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Diagnosis
Clinical utility:
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Establish or confirm diagnosis
View citations (1)
- Hebbar M, Mefford HC. Recent advances in epilepsy genomics and genetic testing. F1000Res. 2020;9. doi:10.12688/f1000research.21366.1. Epub 2020 Mar 12. PMID: 32201576.
Target population:
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Individuals with a diagnosis of an epilepsy or seizure disorder
View citations (1)
- Hebbar M, Mefford HC. Recent advances in epilepsy genomics and genetic testing. F1000Res. 2020;9. doi:10.12688/f1000research.21366.1. Epub 2020 Mar 12. PMID: 32201576.
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. NGS and/or a polymerase chain reaction (PCR)-based quantitative method is performed to test for the presence of deletions and duplications in the genes analyzed. Additionally, …
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Test Confirmation:
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Confirmation of select reportable variants may be performed by alternate methodologies based on internal laboratory criteria. PCR-based methods and/or Sanger sequencing is used to confirm variants detected by NGS when appropriate
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
Formal PT program
PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
Yes
Method used for proficiency testing: Help
Formal PT program
PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
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, gene-specific online databases, ISCA, UCSC Genome Browser
Laboratory's policy on reporting novel variations Help
All novel variants 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, gene-specific online databases, ISCA, UCSC Genome Browser
Laboratory's policy on reporting novel variations Help
All novel variants and copy number variants are evaluated for potential pathogenicity and included in the written report, accordingly.
Recommended fields not provided:
Citations to support assay limitations,
Description of internal test validation method,
Citations for Analytical validity,
Description of PT method,
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:
Practice guidelines:
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.