Overview
Test order codeHelpLaboratory's order or catalog code for the test (used in the order requisition form).: Mitochondrial Genome Sequencing MtDNA
Mitochondrial Genome Sequencing and Depletion/Integrity Panel (MtDNA)
This is a clinical test intended for HelpPurposes or indications for the test. Lab-provided.: Diagnosis, Drug Response, Mutation Confirmation, Predictive, Prognostic, Risk Assessment
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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 2-5ml EDTA whole blood or other appropriate tissues and ship by overnight courier to the lab address (weekdays only)
Order URL HelpLink to the laboratory webpage with information about how to order this test. Please note that clicking on this link will open a new tab in your internet browser.: http://www.lhsc.on.ca/palm/molecular/panels.html#genome
Specimen source
Bone marrow
Cell culture
Fibroblasts
Fresh tissue
Frozen tissue
Isolated DNA
Peripheral (whole) blood
Skin
Urine
White blood cell prep
- Molecular Genetics
- DDeletion/duplication analysis
- Next-Generation (NGS)/Massively parallel sequencing (MPS)
- CSequence analysis of the entire coding region
- Next-Generation (NGS)/Massively parallel sequencing (MPS)
- TTargeted variant analysis
- RT-qPCR
Summary of what is tested
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information.
Establish or confirm diagnosis
Guidance for management
Guidance for selecting a drug therapy and/or dose
Reproductive decision-making
Not provided
Mitochondrial regions of interest and all coding exons and 20 bp of flanking non--coding sequence of nuclear encoded genes 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; and Alamut Visual). Nuclear encoded genes have 300x or higher mean read depth coverage, with a minimum 100x coverage at a single nucleotide resolution. Mitochondrial genes have >1000x mean read depth coverage, with a minimum 500x coverage at a single nucleotide resolution. Test is validated for heteroplasmy detection sensitivity of 2-5%. Mitochondrial CNVs are routinely detectible to 15% heteroplasmy levels. LR-PCR is used to confirm mtDNA CNVs, and may be used to assess mitochondrial CNVs to 2-5% heteroplasmy levels. 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’ UTR and 3’ UTR of nuclear encoded genes are not reported unless there is evidence suggesting pathogenicity. Analysis includes copy number assessment for the mitochondrial DNA deletion syndrome (Kearns-Sayre syndrome). This assay has been validated at a level of sensitivity equivalent to the Sanger sequencing and standard copy number analysis (>99%; PMID: 27376475, 28818680). 000 Complete and physician signed requisition required with pedigree and clear clinical diagnosis. Requisition available on lab website if required. Please draw 2-5ml EDTA whole blood or other appropriate tissues and ship by overnight courier to the lab address (weekdays only)
- Clinical Testing/Confirmation of Mutations Identified Previously, comments
- Confirmation of research findings, comments
- Custom mutation-specific/Carrier testing