GTR Test Accession:
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GTR000529346.8
Last updated in GTR:
2021-02-02
View version history
GTR000529346.8,
last updated:
2021-02-02
GTR000529346.7,
last updated:
2020-06-02
GTR000529346.6,
last updated:
2019-05-30
GTR000529346.5,
last updated:
2017-09-25
GTR000529346.4,
last updated:
2017-07-17
GTR000529346.3,
last updated:
2017-05-04
GTR000529346.2,
last updated:
2017-04-17
GTR000529346.1,
registered in GTR:
2016-05-12
Last annual review date for the lab: 2021-02-05
Past due
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At a Glance
Methods (1):
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Molecular Genetics - Sequence analysis of the entire coding region: Next-Generation (NGS)/Massively parallel sequencing (MPS)
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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- Isolated DNA
- Peripheral (whole) blood
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Physician
- Nurse Practitioner
- Physician Assistant
- Registered Nurse
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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Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Custom Sequence Analysis
Result interpretation
Custom Sequence Analysis
Result interpretation
Test additional service:
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Custom Prenatal Testing
Custom mutation-specific/Carrier testing
Custom mutation-specific/Carrier testing
Informed consent required:
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Decline to answer
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,
Lab contact for this test,
Test strategy,
Test development
Conditions
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Total conditions: 39
| Condition/Phenotype | Identifier |
|---|
Test Targets
Genes
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Total genes: 38
| Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
|---|
Methodology
Total methods: 1
Method Category
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Test method
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Instrument
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina NextSeq 500
Clinical Information
Test purpose:
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Diagnosis;
Mutation Confirmation
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Variations are first classified based on frequency (according to databases such as 1000 Genomes and GnomAD). Rare variations are classified as VUS if: 1) the variation has not been reported previously and available information (effect prediction models, conservation scores and patient data) does not allow other classification; 2) there are … View more
Variations are first classified based on frequency (according to databases such as 1000 Genomes and GnomAD). Rare variations are classified as VUS if: 1) the variation has not been reported previously and available information (effect prediction models, conservation scores and patient data) does not allow other classification; 2) there are … View more
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,
Target population,
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 Confirmation:
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Potentially pathogenic findings are confirmed using another technology.
Test Comments:
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NGS panel covers the analysis of the entire coding region of 34 genes associated with Hereditary Spastic Paraplegia, and clinically relevant non-coding variants. CNV analysis is included in the panel.
Del/dup analysis of ATL1, NIPA1, SPAST, SPG7, REEP1 genes by MLPA.
Del/dup analysis of ATL1, NIPA1, SPAST, SPG7, REEP1 genes by MLPA.
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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Technical accuracy >99,8%
Proficiency testing (PT):
Is proficiency testing performed for this test?
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No
No
VUS:
Software used to interpret novel variations
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Alamut® Visual (includes splice site prediction tools, SIFT, PolyPhen2, MutationTaster, frequency data).
Laboratory's policy on reporting novel variations Help
Novel variations are interpreted in the context of the patient’s data as well as information known about the gene that it was found in. If possible association with patient’s phenotype is suspected, novel variations are reported with a short description of the possible effect and population frequencies.
Alamut® Visual (includes splice site prediction tools, SIFT, PolyPhen2, MutationTaster, frequency data).
Laboratory's policy on reporting novel variations Help
Novel variations are interpreted in the context of the patient’s data as well as information known about the gene that it was found in. If possible association with patient’s phenotype is suspected, novel variations are reported with a short description of the possible effect and population frequencies.
Recommended fields not provided:
Assay limitations,
Description of internal test validation method,
Citations for Analytical validity,
PT Provider,
Description of PT method,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Not provided
Additional Information
Clinical resources:
Molecular 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.