Mitochondrial Genome Sequencing and Depletion/Integrity Panel
- GTR Test IDHelpEach Test is a specific, orderable test from a particular laboratory, and is assigned a unique GTR accession number. The format is GTR00000001.1, with a leading prefix 'GTR' followed by 8 digits, a period, then 1 or more digits representing the version. When a laboratory updates a registered test, a new version number is assigned.: GTR000530224.5
- Last updated: 2023-02-08
- Test version history
Clinical testHelpIn the U.S., clinical tests must be performed under CLIA certification. When a lab uses the same methods for a test in both clinical and research settings, the test appears as two separate GTR records. for Inborn mitochondrial myopathy
Offered by Molecular Genetics Laboratory
Overview
Test name
HelpThe name the laboratory assigns the test. Used as the default title of the page specific to the test.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
Click Indication tab for more information.
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
Methodology
HelpThe assay's major method category (biochemical, cytogenetic or molecular genetics); method category (i.e. enzyme assay, chromosome breakage studies, targeted mutation analysis); methodology (i.e. the name of the method used) and instruments used when performing this test.- Molecular Genetics
- DDeletion/duplication analysis
- Next-Generation (NGS)/Massively parallel sequencing (MPS)
- Illumina MiSeq/NextSeq
- CSequence analysis of the entire coding region
- Next-Generation (NGS)/Massively parallel sequencing (MPS)
- Illumina MiSeq/NextSeq
- TTargeted variant analysis
- RT-qPCR
- Roche LightCycler 480
Establish or confirm diagnosis
- Primary Mitochondrial Disorders Overview - PubMed ID: 20301403
- https://www.ncbi.nlm.nih.gov/books/NBK1224
Guidance for management
- Primary Mitochondrial Disorders Overview - PubMed ID: 20301403
- https://www.ncbi.nlm.nih.gov/books/NBK1224
Guidance for selecting a drug therapy and/or dose
- Primary Mitochondrial Disorders Overview - PubMed ID: 20301403
- https://www.ncbi.nlm.nih.gov/books/NBK1224
Reproductive decision-making
- Primary Mitochondrial Disorders Overview - PubMed ID: 20301403
- https://www.ncbi.nlm.nih.gov/books/NBK1224
Clinical validity
HelpHow consistently and accurately the test detects or predicts the intermediate or final outcomes of interest. Lab-provided.Not provided
Testing strategy
HelpThe lab's suggested sequence of ordering tests based on clinical scenarios. It may include information on: reflex testing including each test component, and scenarios which prompt additional components of testing; whether lab communicates interim results or automatically proceeds to further analyses; and if any components are performed in another laboratory.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)
Test services
HelpLaboratory's order or catalog code for the test (used in the order requisition form).IMPORTANT NOTE: NIH does not independently verify information submitted to the GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in the 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.