Clinical Genetic Test
offered by
GTR Test Accession:
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GTR000593379.2
Last updated in GTR:
2023-07-31
View version history
GTR000593379.2,
last updated:
2023-07-31
GTR000593379.1,
registered in GTR:
2023-07-17
Last annual review date for the lab: 2024-07-12
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At a Glance
Test purpose:
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Diagnosis;
Predictive;
Prognostic; ...
Conditions (34):
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Cole-Carpenter syndrome 2;
Adult hypophosphatasia;
Bone mineral density quantitative trait locus 18
more...
Genes (26):
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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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- Peripheral (whole) blood
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Physician
- Nurse Practitioner
- Physician Assistant
Test Order Code:
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3001607
View other test codes
View other test codes
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.
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:
How to Order,
Lab contact for this test,
Test strategy,
Test development
Conditions
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Total conditions: 34
| Condition/Phenotype | Identifier |
|---|
Test Targets
Genes
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Total genes: 26
| 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)
* Instrument: Not provided
Clinical Information
Test purpose:
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Diagnosis;
Predictive;
Prognostic;
Risk Assessment;
Screening
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Multiple methodologies are utilized to classify a VUS. General knowledge regarding the gene and types of disease-associated mutations is reviewed. Population frequency is used to determine the incidence in which the variant is present in the general population as well as in specific ethnicities. Computational prediction programs are used to … View more
Multiple methodologies are utilized to classify a VUS. General knowledge regarding the gene and types of disease-associated mutations is reviewed. Population frequency is used to determine the incidence in which the variant is present in the general population as well as in specific ethnicities. Computational prediction programs are used to … View more
Are family members with defined clinical status recruited to assess significance of VUS without charge?
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Yes.
Yes.
Will the lab re-contact the ordering physician if variant interpretation changes?
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Yes. For significant changes to variant classification, an amended report is sent to the ordering facility and ARUP Laboratories will attempt to contact the provider. Clinicians are encouraged to continue to analyze the literature and re-contact the laboratory if a reclassification may be warranted.
Yes. For significant changes to variant classification, an amended report is sent to the ordering facility and ARUP Laboratories will attempt to contact the provider. Clinicians are encouraged to continue to analyze the literature and re-contact the laboratory if a reclassification may be warranted.
Recommended fields not provided:
Clinical validity,
Clinical utility,
Target population,
Is research allowed on the sample after clinical testing is complete?,
Sample negative report,
Sample positive report
Technical Information
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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The analytical sensitivity of this test is approximately 99% for single nucleotide variants (SNVs) and greater than 93% for insertions/duplications/deletions from 1-10 base pairs in size. Variants greater than 10 base pairs may be detected, but the analytical sensitivity may be reduced.
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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The software utilized varies depending on the gene and variant type. Some examples of computational prediction programs ARUP Laboratories uses are SIFT, Polyphen2, Mutation Taster, NetGene and NNSplice. The evidence of pathogenicity generated by these computer prediction programs is considered weak.
Laboratory's policy on reporting novel variations Help
ARUP Laboratories complies with New York regulations for all variants reported. If a VUS is incidentally detected using a mutation panel or in an ACMG-recommended gene via exome sequencing, it will not be reported (in agreement with ACMG recommendations for standards for interpretation and reporting of sequence variations). Please see … View more
The software utilized varies depending on the gene and variant type. Some examples of computational prediction programs ARUP Laboratories uses are SIFT, Polyphen2, Mutation Taster, NetGene and NNSplice. The evidence of pathogenicity generated by these computer prediction programs is considered weak.
Laboratory's policy on reporting novel variations Help
ARUP Laboratories complies with New York regulations for all variants reported. If a VUS is incidentally detected using a mutation panel or in an ACMG-recommended gene via exome sequencing, it will not be reported (in agreement with ACMG recommendations for standards for interpretation and reporting of sequence variations). Please see … View more
Recommended fields not provided:
Test Confirmation,
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:
Molecular resources:
Consumer 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.