GTR Test Accession:
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GTR000570468.1
Registered in GTR:
2020-01-29
View version history
GTR000570468.1,
registered in GTR:
2020-01-29
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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Pontocerebellar hypoplasia type 2B
Genes (1):
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TSEN2 (3p25.2)
Methods (1):
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Molecular Genetics - Sequence analysis of the entire coding region: Bi-directional Sanger Sequence Analysis
Target population: Help
Not provided
Clinical validity:
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Not provided
Clinical utility:
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Not provided
Ordering Information
Offered by:
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Specimen Source:
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- Buccal swab
- Cell culture
- Chorionic villi
- Fibroblasts
- Isolated DNA
- Peripheral (whole) blood
Who can order: Help
- Genetic Counselor
- Licensed Physician
How to Order:
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Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Custom Sequence Analysis
Custom Sequence Analysis
Informed consent required:
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No
Test strategy:
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Simultaneous bi-directional sequencing of all coding/selected exons
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,
Contact policy,
Test development
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: 1
Method Category
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Test method
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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
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,
Clinical utility,
Target population,
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 visualised on a capillary sequencer. Sequencing is performed separately in both the forward …
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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
DNA sequencing - Sanger (Full version)
Yes
Method used for proficiency testing: Help
Formal PT program
PT Provider: Help
European Molecular Genetics Quality Network, EMQN
Description of PT method: Help
DNA sequencing - Sanger (Full version)
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
Alamut (Interactive Biosoftware), including AGVGD, PolyPhen-2, SIFT and MutationTaster for missense predictions and MAXEntScan, NNSPLICE, GeneSplicer and Human Splicing Finder for splice predictions
Recommended fields not provided:
Test Confirmation,
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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Not provided
Additional Information
Clinical resources:
Molecular resources:
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.