GTR Test Accession:
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GTR000529452.5
CAP
Last updated in GTR: 2024-02-07
View version history
GTR000529452.5, last updated: 2024-02-07
GTR000529452.4, last updated: 2023-02-08
GTR000529452.3, last updated: 2019-01-23
GTR000529452.2, last updated: 2017-02-07
GTR000529452.1, last updated: 2016-02-17
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;
Pre-symptomatic; ...
Conditions (46):
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Charcot-Marie-Tooth disease; AMYLOIDOSIS, LEPTOMENINGEAL, TRANSTHYRETIN-RELATED; Charcot-Marie-Tooth Neuropathy Type 2H/2K; ...
Genes (34):
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AARS1 (16q22.1), AIFM1 (Xq26.1), DNAJB2 (2q35), DYNC1H1 (14q32.31), EGR2 (10q21.3), ...
Methods (2):
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Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...
Target population: Help
Charcot-Marie-Tooth (CMT) disease is a genetically and clinically heterogeneous group …
Clinical validity:
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Not provided
Clinical utility:
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Avoidance of invasive testing;
Establish or confirm diagnosis;
Guidance for management; ...
Ordering Information
Offered by:
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Test short name:
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CMT
Specimen Source:
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- Cell culture
- Isolated DNA
- Peripheral (whole) blood
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Licensed Physician
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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Please complete the requisition available on the website and ensure it is signed by the referring physician.
Order URL
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Custom Deletion/Duplication Testing
Custom Sequence Analysis
Confirmation of research findings
Custom Deletion/Duplication Testing
Custom Sequence Analysis
Test additional service:
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Custom Prenatal Testing
Custom mutation-specific/Carrier testing
Custom mutation-specific/Carrier testing
Test development:
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Test developed by laboratory (no manufacturer test name)
Informed consent required:
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Decline to answer
Test strategy:
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All coding exons and 20 bp of flanking non-coding 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.
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: 46
| Condition/Phenotype | Identifier |
|---|
Test Targets
Genes
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Total genes: 34
| 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
Multiplex Ligation-dependent Probe Amplification (MLPA)
Applied Biosystems 3730 capillary sequencing instrument
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;
Pre-symptomatic;
Predictive;
Prognostic
Clinical utility:
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Avoidance of invasive testing
Establish or confirm diagnosis
Guidance for management
Predictive risk information for patient and/or family members
Establish or confirm diagnosis
Guidance for management
Predictive risk information for patient and/or family members
Target population:
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Charcot-Marie-Tooth (CMT) disease is a genetically and clinically heterogeneous group of inherited disorders of the peripheral nervous system characterised by progressive loss of muscle tissue and touch sensation across various parts of the body. CMT type 1 (CMT1) is a demyelinating peripheral neuropathy characterized by distal muscle weakness and atrophy, …
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View citations (1)
- Bird TD. Charcot-Marie-Tooth Hereditary Neuropathy Overview. 1998 Sep 28 [updated 2024 Apr 25]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Amemiya A, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024. PMID: 20301532.
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 (SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; and Alamut Visual). All exons have >300x mean read depth coverage, with a minimum 100x coverage at a single nucleotide resolution. This assay meets the sensitivity and … View more
Sequence variants and copy number changes are assessed and interpreted using clinically validated algorithms and commercial software (SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; and Alamut Visual). All exons have >300x mean read depth coverage, with a minimum 100x coverage at a single nucleotide resolution. This assay meets the sensitivity and … 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,
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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All coding exons and 20 bp of flanking non-coding 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
Test Platform:
None/not applicable
Test Confirmation:
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Variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868), if necessary, 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. Variants detected in the 5’ UTR …
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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 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
Method used for proficiency testing: Help
Formal PT program
PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
Description of PT method: Help
Methodology covered by CAP surveys of NGS based methods
No
Method used for proficiency testing: Help
Formal PT program
PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
Description of PT method: Help
Methodology covered by CAP surveys of NGS based methods
VUS:
Software used to interpret novel variations
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(SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; and Alamut Visual).
Laboratory's policy on reporting novel variations Help
Variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868), if necessary, 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. Variants detected in the 5’ UTR … View more
(SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; and Alamut Visual).
Laboratory's policy on reporting novel variations Help
Variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868), if necessary, 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. Variants detected in the 5’ UTR … View more
Recommended fields not provided:
Assay limitations,
Description of internal test validation method,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Category:
FDA exercises enforcement discretion
Additional Information
Clinical 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.