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Leber's Hereditary Optic Neuropathy
Clinical Genetic Test
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offered by
Molecular Genetics Laboratory
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GTR Test Accession: Help GTR000501208.5
CAP
INHERITED DISEASECARDIOVASCULARDYSMORPHOLOGY ... View more
Last updated in GTR: 2024-02-07
View version history
Last annual review date for the lab: 2024-02-07 LinkOut
At a Glance
Test purpose: Help
Diagnosis; Mutation Confirmation
Conditions (1): Help
Leber optic atrophy
Genes (3): Help
MT-ND1 (); MT-ND4 (); MT-ND6 ()
Methods (2): Help
Molecular Genetics - Sequence analysis of the entire coding region: Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
Target population: Help
Not provided
Clinical validity: Help
Not provided
Clinical utility: Help
Establish or confirm diagnosis
Ordering Information
Offered by: Help
Molecular Genetics Laboratory
View lab's website
View lab's test page
Test short name: Help
LHON
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Licensed Physician
Test Order Code: Help
Leber's Hereditary Optic Neuropathy (LHON)
LOINC codes: Help
**LOINC codes notice
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
Complete and physician signed requisition required with pedigree and clear clinical diagnosis. Requisition available on lab website if required. Please draw 6 ml EDTA whole blood and ship by overnight courier to the lab address(weekdays only)
Order URL
Test service: Help
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
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 intronic sequence of ND1, ND4 and ND6, are enriched using an LHSC custom targeted hybridization protocol (Roche Nimblegen), followed by high throughput sequencing (Illumina). This chemistry and analysis pipeline provides a highly sensitive and specific detection of sequence and copy number alterations … 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: 1
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 3
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 2
Method Category Help
Test method Help
Instrument
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina MiSeq/NextSeq
Targeted variant analysis
PCR with RFLP analysis
Clinical Information
Test purpose: Help
Diagnosis; Mutation Confirmation
Clinical utility: Help
Establish or confirm diagnosis
View citations (1)

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 genes have >1000x mean read depth coverage, with a minimum 200x coverage at a single nucleotide resolution. Mitochondrial DNA testing is validated for … View more

Are family members with defined clinical status recruited to assess significance of VUS without charge? Help
Decline to answer.

Will the lab re-contact the ordering physician if variant interpretation changes? Help
No. Requests for re-interpretation of a VUS over time must be initiated by the ordering physician.
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: Help
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). This chemistry and analysis pipeline provides a highly sensitive and specific detection of sequence and copy number alterations in a single assay that … 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: Help
All 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’ … View more
Availability: Help
Tests performed
Entire test performed in-house

Test performance comments
Testing is performed in a licensed purpose built facility located in a major regional medical health care facility
Analytical Validity: Help
This assay has been validated at a level of sensitivity equivalent to the Sanger sequencing and standard copy number analysis (>99%; PMID: 27376475, 28818680).
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
VUS:
Software used to interpret novel variations Help
Alamut Visual, Polyphen2, AGVGD, SIFT, relevant databases

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), 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 … View more
Recommended fields not provided:
Assay limitations, Description of internal test validation method, Description of PT method, Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review: Help
Category: FDA exercises enforcement discretion
Additional Information

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.