GTR Test Accession:
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GTR000576329.8
Last updated in GTR: 2023-12-05
View version history
GTR000576329.8, last updated: 2023-12-05
GTR000576329.7, last updated: 2023-07-06
GTR000576329.6, last updated: 2023-01-31
GTR000576329.5, last updated: 2022-02-06
GTR000576329.4, last updated: 2021-02-07
GTR000576329.3, last updated: 2020-05-29
GTR000576329.2, last updated: 2020-05-03
GTR000576329.1, last updated: 2020-04-05
Last annual review date for the lab: 2024-01-30
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At a Glance
Test purpose:
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Diagnosis
Conditions (52):
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Dyssynergia; Ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia; Ataxia, spastic, childhood-onset, autosomal recessive, with optic atrophy and intellectual disability; ...
Human genome
Genes (52):
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AFG3L2 (18p11.21), ANO10 (3p22.1-21.33), APTX (9p21.1), ATM (11q22.3), ATN1 (12p13.31), ...
Methods (3):
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Molecular Genetics - Deletion/duplication analysis: Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
Target population: Help
Patients with clinical features of ataxia.
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
- Saliva
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Physician
Test Order Code:
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NR002
View other test codes
View other test codes
CPT codes:
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Lab contact:
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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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Genomic UnityⓇ Comprehensive Ataxia Analysis orders are initiated at https://www.variantyx.com/resources/provider-resources/order-forms/. Following submission, a clinical coordinator will get in touch to send a blood or saliva sample collection kit if required and facilitate collection of the test requisition and informed consent forms.
Order URL
Order URL
Informed consent required:
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Yes
Test strategy:
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When results are not positive, there is an option to reflex up to Genomic Unity Exome Analysis or Genomic Unity Exome Plus Analysis, and Genomic Unity Whole Genome Analysis
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 development
Conditions
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Total conditions: 52
| Condition/Phenotype | Identifier |
|---|
Test Targets
Chromosomal regions/Mitochondria
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Total chromosomal regions/mitochondria: 1
| Chromosomal region/Mitochondrion | Associated condition |
|---|
Genes
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Total genes: 52
| Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
|---|
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)
Mutation scanning of select exons
Tandem repeat expansion analysis
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
* Instrument: Not provided
Clinical Information
Test purpose:
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Diagnosis
Target population:
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Patients with clinical features of ataxia.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Variants are categorized as pathogenic, likely pathogenic or a variant of uncertain significance (VUS) utilizing the American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines as published by Richards et al 2015.
Variants are categorized as pathogenic, likely pathogenic or a variant of uncertain significance (VUS) utilizing the American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines as published by Richards et al 2015.
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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The patient's DNA is sequenced using whole genome sequencing conducted on an Illumina platform at 30X mean mappable coverage. The relevant region(s) of DNA are subsequently isolated in-silico for analysis.
Test Confirmation:
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Due to the variable nature of repetitive sequences and sequence-specific differences in detection and repeat evaluation, orthogonal confirmation is performed on a case-by-case basis in a third party CLIA/CAP lab.
Test Comments:
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This test includes full sequence and del/dup analysis of 54 recessive and dominant genes as well as repeat expansion analysis of 16 loci: AATN1, ATXN1, ATXN2, ATXN3, ATXN7, ATXN8OS, ATXN10, CACNA1A, FGF14, FMR1, FXN, GLS, NOP56, PPP2R2B, RFC1 and TBP genes.
Availability:
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Tests performed
Entire test performed in-house
Test performance comments
Specimen preparation, clinical grade sequencing, data processing, analysis, interpretation, diagnosis and report generation is performed by Variantyx.
Entire test performed in-house
Test performance comments
Specimen preparation, clinical grade sequencing, data processing, analysis, interpretation, diagnosis and report generation is performed by Variantyx.
Analytical Validity:
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The Genomic Unity® Comprehensive Ataxia Analysis is designed to identify genetic variants that correlate with hereditary ataxias. This analysis includes sequence analysis (single nucleotide variants, deletions/insertions, and characterized intronic variants), copy number variants, duplications/deletions, mobile element insertions, and inversions in a panel of 51 genes, and short tandem repeat expansions …
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Assay limitations:
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The false negative rate for repeat expansions has not been determined.
Proficiency testing (PT):
Is proficiency testing performed for this test?
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Yes
Method used for proficiency testing: Help
Intra-Laboratory
Yes
Method used for proficiency testing: Help
Intra-Laboratory
VUS:
Software used to interpret novel variations
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Proprietary Variantyx Genomic Intelligence platform
Laboratory's policy on reporting novel variations Help
Test results will only be released to the ordering healthcare provider and additional healthcare provider(s) indicated on the test requisition form.
Proprietary Variantyx Genomic Intelligence platform
Laboratory's policy on reporting novel variations Help
Test results will only be released to the ordering healthcare provider and additional healthcare provider(s) indicated on the test requisition form.
Recommended fields not provided:
Citations to support 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
Reviews:
Clinical 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.