GTR Test Accession:
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GTR000518846.9
Last updated in GTR:
2018-11-15
View version history
GTR000518846.9,
last updated:
2018-11-15
GTR000518846.8,
last updated:
2018-03-06
GTR000518846.7,
last updated:
2014-12-23
GTR000518846.6,
last updated:
2014-12-04
GTR000518846.5,
last updated:
2014-12-03
GTR000518846.4,
last updated:
2014-12-02
GTR000518846.3,
last updated:
2014-11-28
GTR000518846.2,
last updated:
2014-11-07
GTR000518846.1,
registered in GTR:
2014-09-29
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 (1):
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Autosomal dominant optic atrophy classic form
Genes (1):
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OPA1 (3q29)
Methods (2):
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Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...
Target population: Help
For patients suspected to this particular and patients with positive …
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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OPA1
Specimen Source:
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- Amniocytes
- Amniotic fluid
- Buccal swab
- Cell culture
- Chorionic villi
- Cord blood
- Fetal blood
- Fibroblasts
- Fresh tissue
- Frozen tissue
- Isolated DNA
- Peripheral (whole) blood
- Saliva
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Physician
- Physician Assistant
Test Order Code:
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OPA1
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
Maternal cell contamination study (MCC)
Uniparental Disomy (UPD) Testing
Confirmation of research findings
Custom Deletion/Duplication Testing
Maternal cell contamination study (MCC)
Uniparental Disomy (UPD) Testing
Test additional service:
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Custom Prenatal Testing
Custom mutation-specific/Carrier testing
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:
Lab contact for this test
Conditions
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Total conditions: 1
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;
Prognostic;
Risk Assessment;
Screening
Target population:
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For patients suspected to this particular and patients with positive familial history for this disease, gene sequence analysis is recommended as the first step in mutation identification.
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)
Are family members with defined clinical status recruited to assess significance of VUS without charge?
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Carrier testing is performed with a reduced pricing rate and in selected cases at no cost after contact with the lab.
Carrier testing is performed with a reduced pricing rate and in selected cases at no cost after contact with the lab.
Will the lab re-contact the ordering physician if variant interpretation changes?
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Not provided.
Not provided.
Recommended fields not provided:
Clinical validity,
Clinical utility,
Are family members with defined clinical status recruited to assess significance of VUS without charge?,
Will the lab re-contact the ordering physician if variant interpretation changes?,
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 visualised 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 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
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 number of PCR fragments, and the error rate is less than 0.01% (99.99% accuracy). Also We had performed MLPA large numbers of samples, and NGS (used for increasing number of genes and panels in cardiogenetics, metabolic diseases, ophthalmogenetics and … 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 number of PCR fragments, and the error rate is less than 0.01% (99.99% accuracy). Also We had performed MLPA large numbers of samples, and NGS (used for increasing number of genes and panels in cardiogenetics, metabolic diseases, ophthalmogenetics and … 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:
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
Reviews:
Clinical resources:
Molecular 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.