GTR Test Accession:
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GTR000500450.5
Last updated in GTR: 2018-11-15
View version history
GTR000500450.5, last updated: 2018-11-15
GTR000500450.4, last updated: 2018-03-06
GTR000500450.3, last updated: 2015-02-06
GTR000500450.2, last updated: 2014-12-04
GTR000500450.1, last updated: 2013-11-28
Last annual review date for the lab: 2024-04-16
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At a Glance
Test purpose:
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Diagnosis;
Mutation Confirmation;
Pre-symptomatic; ...
Conditions (3):
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Long QT syndrome 1;
Jervell and Lange-Nielsen syndrome 1;
Short QT syndrome type 2
Genes (1):
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KCNQ1 (11p15.5-15.4)
Methods (2):
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Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...
Target population: Help
Patients suspected to this particular and patients with a positive …
Clinical validity:
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Not provided
Clinical utility:
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Establish or confirm diagnosis;
Predictive risk information for patient and/or family members
Ordering Information
Offered by:
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Test short name:
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KCNQ1
Specimen Source:
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- Buccal swab
- Cell culture
- Cord blood
- Fibroblasts
- Frozen tissue
- Isolated DNA
- Peripheral (whole) blood
- Saliva
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Physician
- Physician Assistant
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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Using our website
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
Confirmation of research findings
Custom Deletion/Duplication Testing
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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No
Test strategy:
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Simultaneous bi-directional sequencing of all coding exons and MLPA
Pre-test genetic counseling required:
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Yes
Post-test genetic counseling required:
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Yes
Recommended fields not provided:
Test Order Code,
Lab contact for this test
Conditions
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Total conditions: 3
Condition/Phenotype | Identifier |
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Test Targets
Genes
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Total genes: 1
Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
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Methodology
Total methods: 2
Method Category
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Test method
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Instrument
Deletion/duplication analysis
Multiplex Ligation-dependent Probe Amplification (MLPA)
Applied Biosystems 3730 capillary sequencing instrument
Sequence analysis of the entire coding region
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;
Screening
Clinical utility:
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Establish or confirm diagnosis
Predictive risk information for patient and/or family members
Predictive risk information for patient and/or family members
Target population:
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Patients suspected to this particular and patients with a positive family history for the disease.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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The 5-classes classification method (Alamut)
The 5-classes classification method (Alamut)
Will the lab re-contact the ordering physician if variant interpretation changes?
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Yes.
Yes.
Recommended fields not provided:
Clinical validity,
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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DNA is extracted from the patient specimen, PCR amplification and sequence analysis of the entire coding region/ or indicated exons plus additional flanking intronic or other non-coding sequence. Sanger sequencing is carried out and the sequence is visualized on a capillary sequencer. Sequencing is performed separately in both the forward …
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Test Confirmation:
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Confirmation of identified mutations is done in an independent experiment.
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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This test detects >99% of described mutations
Assay limitations:
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All coding sequences, including the flanking intron sequences are analyzed using direct sequencing. With this method we can detect point mutations and small deletions or insertions. The presence of larger deletions or duplications are analyzed by MLPA. Mutations outside the analyzed regions will not be detected.
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
European Molecular Genetics Quality Network, EMQN
Description of PT method: Help
For Proficiency Testing, both external and internal, we have Sanger-sequenced extensive numbers of PCR fragments, and the error rate is less than 0.01% (99.99% accuracy). We also have performed MLPA of large numbers of samples with the maximal possible technical accuracy (>99.8%). Technical specificity for methods used in our laboratory … View more
Yes
Method used for proficiency testing: Help
Formal PT program
PT Provider: Help
European Molecular Genetics Quality Network, EMQN
Description of PT method: Help
For Proficiency Testing, both external and internal, we have Sanger-sequenced extensive numbers of PCR fragments, and the error rate is less than 0.01% (99.99% accuracy). We also have performed MLPA of large numbers of samples with the maximal possible technical accuracy (>99.8%). Technical specificity for methods used in our laboratory … View more
VUS:
Software used to interpret novel variations
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Alamut (Interactive Biosoftware), including AGVGD, PolyPhen-2, SIFT and MutationTaster for missense predictions and MAXEntScan, NNSPLICE, GeneSplicer and Human Splicing Finder for splice predictions
Laboratory's policy on reporting novel variations Help
Our laboratory reports class 3 (unknown pathogenicity), class 4 (likely pathogenic) and class 5 (certainly pathogenic) variants.
Alamut (Interactive Biosoftware), including AGVGD, PolyPhen-2, SIFT and MutationTaster for missense predictions and MAXEntScan, NNSPLICE, GeneSplicer and Human Splicing Finder for splice predictions
Laboratory's policy on reporting novel variations Help
Our laboratory reports class 3 (unknown pathogenicity), class 4 (likely pathogenic) and class 5 (certainly pathogenic) variants.
Recommended fields not provided:
Citations to support assay limitations,
Description of internal test validation method,
Citations for Analytical validity,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Category:
Not Applicable
Additional Information
Clinical resources:
Molecular resources:
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.