Charcot Marie Tooth Panel
GTR Test Accession: Help GTR000529452.5
CAP
INHERITED DISEASENERVOUS SYSTEMMETABOLIC DISEASE ... View more
Last updated in GTR: 2024-02-07
Last annual review date for the lab: 2024-02-07 LinkOut
At a Glance
Diagnosis; Mutation Confirmation; Pre-symptomatic; ...
Charcot-Marie-Tooth disease; AMYLOIDOSIS, LEPTOMENINGEAL, TRANSTHYRETIN-RELATED; Charcot-Marie-Tooth Neuropathy Type 2H/2K; ...
AARS1 (16q22.1), AIFM1 (Xq26.1), DNAJB2 (2q35), DYNC1H1 (14q32.31), EGR2 (10q21.3), ...
Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...
Charcot-Marie-Tooth (CMT) disease is a genetically and clinically heterogeneous group …
Not provided
Avoidance of invasive testing; Establish or confirm diagnosis; Guidance for management; ...
Ordering Information
Offered by: Help
Molecular Genetics Laboratory
View lab's website
View lab's test page
Test short name: Help
CMT
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Licensed Physician
Lab contact: Help
Gavin Giles, MSc, Administrator
gavin.giles@lhsc.on.ca
+1-519-685-8500 x36339
Contact Policy: Help
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: Help
Please complete the requisition available on the website and ensure it is signed by the referring physician.
Order URL
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Custom Deletion/Duplication Testing
Custom Sequence Analysis
Test additional service: Help
Custom Prenatal Testing
Custom mutation-specific/Carrier testing
Test development: Help
Test developed by laboratory (no manufacturer test name)
Informed consent required: Help
Decline to answer
Test strategy: Help
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: Help
Decline to answer
Post-test genetic counseling required: Help
Decline to answer
Conditions Help
Total conditions: 46
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 34
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 2
Method Category Help
Test method Help
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
Clinical Information
Test purpose: Help
Diagnosis; Mutation Confirmation; Pre-symptomatic; Predictive; Prognostic
Clinical utility: Help
Target population: Help
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, … View more
View citations (1)
  • Bird TD. Charcot-Marie-Tooth Hereditary Neuropathy Overview. 1998 Sep 28 [updated 2024 Mar 14]. 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? Help
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? Help
Not provided.
Recommended fields not provided:
Technical Information
Test Procedure: Help
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: 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
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
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? Help
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 Help
(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:
Regulatory Approval
FDA Review: Help
Category: FDA exercises enforcement discretion
Additional Information

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