GTR Test Accession:
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GTR000552072.3
Last updated in GTR:
2024-02-07
View version history
GTR000552072.3,
last updated:
2024-02-07
GTR000552072.2,
last updated:
2023-02-08
GTR000552072.1,
registered in GTR:
2016-09-23
Last annual review date for the lab: 2024-02-07
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At a Glance
Test purpose:
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Diagnosis;
Mutation Confirmation;
Prognostic; ...
Conditions (1):
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Hereditary sensory and autonomic neuropathy type 1
Genes (1):
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SPTLC1 (9q22.31)
Methods (2):
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Molecular Genetics - Deletion/duplication analysis: 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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Establish or confirm diagnosis
Ordering Information
Offered by:
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Test short name:
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SPTLC1
Specimen Source:
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- Amniocytes
- Amniotic fluid
- Fibroblasts
- Isolated DNA
- Peripheral (whole) blood
Who can order: Help
- Genetic Counselor
- Health Care Provider
Test Order Code:
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SPTLC1
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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Complete and physician signed requisition required with pedigree and clear clinical diagnosis. Requisition available on lab website if required. Please draw 4-10ml EDTA whole blood and ship by overnight courier to the lab address (weekdays only)
Order URL
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Comment: Requires prior phone contact to arrange for test development
Confirmation of research findings
Comment: Requires prior phone contact to arrange for test development
Maternal cell contamination study (MCC)
Comment: Requires prior phone contact to arrange for consult
Comment: Requires prior phone contact to arrange for test development
Confirmation of research findings
Comment: Requires prior phone contact to arrange for test development
Maternal cell contamination study (MCC)
Comment: Requires prior phone contact to arrange for consult
Test additional service:
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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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Decline to answer
Test strategy:
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All coding exons and 20 bp of flanking intronic sequence are enriched using an LHSC custom targeted hybridization protocol (Roche Nimblegen), followed by high throughput sequencing (Illumina). Sequence variants and copy number changes are assessed and interpreted using clinically validated algorithms and commercial software (SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; …
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View citations (1)
- Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn. 2016;18(5):657-667. doi:10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 02. PMID: 27376475.
Pre-test genetic counseling required:
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Decline to answer
Post-test genetic counseling required:
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Decline to answer
Conditions
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Total conditions: 1
| Condition/Phenotype | Identifier |
|---|
Test Targets
Genes
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Total genes: 1
| Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
|---|
Methodology
Total methods: 2
Method Category
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Test method
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Instrument
Deletion/duplication analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina MiSeq/NextSeq
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Applied Biosystems 3730 capillary sequencing instrument
Illumina MiSeq/NextSeq
Illumina MiSeq/NextSeq
Clinical Information
Test purpose:
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Diagnosis;
Mutation Confirmation;
Prognostic;
Recurrence
Clinical utility:
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Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Sequence variants and copy number changes are assessed and interpreted using clinically validated algorithms and commercial software All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely … View more
Sequence variants and copy number changes are assessed and interpreted using clinically validated algorithms and commercial software All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely … View more
Are family members with defined clinical status recruited to assess significance of VUS without charge?
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Decline to answer.
Decline to answer.
Will the lab re-contact the ordering physician if variant interpretation changes?
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No. Requests for re-interpretation of a VUS identified in this laboratory must be initiated by the ordering physician. The laboratory is not responsible for auditing mutation interpretations as they evolve over time.
No. Requests for re-interpretation of a VUS identified in this laboratory must be initiated by the ordering physician. The laboratory is not responsible for auditing mutation interpretations as they evolve over time.
Recommended fields not provided:
Clinical validity,
Target population,
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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All coding exons and 20 bp of flanking intronic sequence are enriched using an LHSC custom targeted hybridization protocol (Roche Nimblegen), followed by high throughput sequencing (Illumina). Sequence variants and copy number changes are assessed and interpreted using clinically validated algorithms and commercial software (SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; …
View more
View citations (1)
- Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn. 2016;18(5):657-667. doi:10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 02. PMID: 27376475.
Test Confirmation:
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Mutations identified are repeated in an independent assay using either Sanger sequence or MLPA
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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This assay meets the sensitivity and specificity of combined Sanger sequencing and MLPA copy number analysis, >99%
View citations (1)
- Schenkel LC, Kerkhof J, Stuart A, Reilly J, Eng B, Woodside C, Levstik A, Howlett CJ, Rupar AC, Knoll JHM, Ainsworth P, Waye JS, Sadikovic B. Clinical Next-Generation Sequencing Pipeline Outperforms a Combined Approach Using Sanger Sequencing and Multiplex Ligation-Dependent Probe Amplification in Targeted Gene Panel Analysis. J Mol Diagn. 2016;18(5):657-667. doi:10.1016/j.jmoldx.2016.04.002. Epub 2016 Jul 02. PMID: 27376475.
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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SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; and Alamut Visual with HGMD
Laboratory's policy on reporting novel variations Help
All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon request.
SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; and Alamut Visual with HGMD
Laboratory's policy on reporting novel variations Help
All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon request.
Recommended fields not provided:
Assay limitations,
Description of internal test validation method,
PT Provider,
Description of PT method,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Category:
Not Applicable
Additional Information
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.