Mitochondrial Full Genome Analysis - Clinical Genetic Test - GTR

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Mitochondrial Full Genome Analysis

Clinical Genetic Test

offered by

Mayo Clinic Laboratories

View lab's test page

GTR Test Accession: GTR000593325.1

CAP

INHERITED DISEASEMITOCHONDRIAL DISEASEMETABOLIC DISEASE ... View more

Registered in GTR: 2021-06-08

Last annual review date for the lab: 2024-05-28

At a Glance

Test purpose:

Diagnosis

Conditions (29):

Mitochondrial disease; Adult-onset chronic progressive external ophthalmoplegia with mitochondrial myopathy; Congenital cataract-progressive muscular hypotonia-hearing loss-developmental delay syndrome more...

Genes (37):

MT-ATP6 (); MT-ATP8 (); MT-CO1 (); MT-CO2 (); MT-CO3 () more...

Methods (1):

Molecular Genetics - Sequence analysis of the entire coding region: Next-Generation (NGS)/Massively parallel sequencing (MPS)

Target population:

Individuals with clinical features of mitochondrial disease

Clinical validity:

Not provided

Clinical utility:

Not provided

Ordering Information

Offered by:

Mayo Clinic Laboratories
View lab's website
View lab's test page

Test short name:

MITOP

Specimen Source:

Dried blood spot (DBS) card
Fibroblasts
Frozen tissue
Peripheral (whole) blood
Skin
View specimen requirements

Who can order:

Genetic Counselor
Health Care Provider
Licensed Dentist
Licensed Physician
Nurse Practitioner
Physician Assistant
Public Health Mandate
Registered Nurse

Test Order Code:

MITOP
View other test codes

LOINC codes:

**LOINC codes notice

Lab contact:

Elizabeth Selner, MS, CGC, Certified Genetic counselor, CGC, Genetic Counselor
gcmolgen@mayo.edu
800-533-1710

Contact Policy:

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:

https://www.mayocliniclabs.com/test-catalog/Specimen/62510
Order URL

Test development:

Test developed by laboratory (no manufacturer test name)

Informed consent required:

Based on applicable state law

Pre-test genetic counseling required:

Post-test genetic counseling required:

Recommended fields not provided:

Test strategy

Conditions

Total conditions: 29

Condition/Phenotype	Identifier

Test Targets

Genes

Total genes: 37

Gene	Associated Condition	Germline or Somatic	Allele (Lab-provided)	Variant in NCBI

Methodology

Total methods: 1

Method Category

Test method

Instrument

Sequence analysis of the entire coding region

Next-Generation (NGS)/Massively parallel sequencing (MPS)

Illumina MiSeq

Clinical Information

Test purpose:

Diagnosis

Target population:

Individuals with clinical features of mitochondrial disease

View citations (1)

Molecular genetics of mitochondrial disorders. Wong LJ, et al. Dev Disabil Res Rev. 2010;16(2):154-62. doi:10.1002/ddrr.104. PMID: 20818730.

Variant Interpretation:

What is the protocol for interpreting a variation as a VUS?
All detected variants are evaluated according to the most recent American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) recommendations. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.

Are family members with defined clinical status recruited to assess significance of VUS without charge?
Decline to answer. Contact lab for details

Will the lab re-contact the ordering physician if variant interpretation changes?
No. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time.

Research:

Is research allowed on the sample after clinical testing is complete?
Research testing is only performed under IRB approved protocol with an opt-out policy in place.

Recommended fields not provided:

Clinical validity, Clinical utility, Sample negative report, Sample positive report

Technical Information

Test Procedure:

Next-generation sequencing (NGS) is used to test for the presence of variants within the mitochondrial genome (includes 13 protein coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes) and to determine the mitochondrial haplogroup of the patient. Large deletions within the mitochondrial genome are first detected by gel … View more

Test Confirmation:

Positive results are confirmed when appropriate.

Availability:

Tests performed
Entire test performed in-house

Analytical Validity:

Analytical sensitivity, specificity, and accuracy are ≥ 99%

Assay limitations:

Clinical Correlations: A small percentage of individuals who have mitochondrial genome involvement may have a variant that is not identified by the methods performed. The absence of a variant, therefore, does not eliminate the possibility of a mitochondrial disease due to variant in the mitochondrial genome. Variants in mitochondrial genes … Clinical Correlations: A small percentage of individuals who have mitochondrial genome involvement may have a variant that is not identified by the methods performed. The absence of a variant, therefore, does not eliminate the possibility of a mitochondrial disease due to variant in the mitochondrial genome. Variants in mitochondrial genes encoded by the nuclear genome will not be detected with this assay. For predictive testing of asymptomatic individuals, it is important to first document the presence of a gene variant in an affected family member. Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete. Technical Limitations: In some cases, DNA variants of undetermined significance may be identified. Rare alterations exist that could lead to false-negative or false-positive results. If results obtained do not match the clinical findings, additional testing should be considered. Evaluation Tools: Multiple in-silico evaluation tools were used to assist in the interpretation of these results. These tools are updated regularly; therefore, changes to these algorithms may result in different predictions for a given alteration. Additionally, the predictability of these tools for the determination of pathogenicity is currently unvalidated. Unless reported or predicted to cause disease, alterations in protein coding genes that do not result in an amino acid substitution are not reported. The mitochondrial haplogroup classification of the patient will be reported, but the individual nucleotide changes that define the haplogroup will not be reported. These and common alterations identified for this patient are available upon request. Reclassification of Variants-Policy: At this time, it is not standard practice for the laboratory to systematically review likely deleterious alterations or variants of uncertain significance that are detected and reported. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time. View more

Proficiency testing (PT):

Is proficiency testing performed for this test?
Yes

Method used for proficiency testing:
Formal PT program

PT Provider:
American College of Medical Genetics / College of American Pathologists, ACMG/CAP

VUS:

Software used to interpret novel variations
Variants may be analyzed using any combination of the following: Alamut, REVEL, Polyphen-2, SIFT, AGVGD, MutationTaster, SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, gene-specific online databases, ISCA, UCSC Genome Browser

Laboratory's policy on reporting novel variations
All novel variants and copy number variants are evaluated for potential pathogenicity and included in the written report, accordingly.

Recommended fields not provided:

Citations to support assay limitations, Description of internal test validation method, Citations for Analytical validity, Description of PT method, Major CAP category, CAP category, CAP test list

Regulatory Approval

FDA Review:

Category: FDA exercises enforcement discretion

Additional Information

Reviews:

Genereviews

PubMed Clinical Queries

Clinical resources:

Molecular resources:

View MT-TC variations in ClinVar

View MT-ND1 variations in ClinVar

View MT-ND4 variations in ClinVar

View MT-ND5 variations in ClinVar

View MT-ND6 variations in ClinVar

View MT-TA variations in ClinVar

View MT-TD variations in ClinVar

View MT-TF variations in ClinVar

View MT-TH variations in ClinVar

View MT-TK variations in ClinVar

View MT-TL1 variations in ClinVar

View MT-TL2 variations in ClinVar

View MT-TM variations in ClinVar

View MT-TQ variations in ClinVar

View MT-TR variations in ClinVar

View MT-TS1 variations in ClinVar

View MT-TS2 variations in ClinVar

View MT-TT variations in ClinVar

View MT-TV variations in ClinVar

View MT-TW variations in ClinVar

View MT-TY variations in ClinVar

Consumer resources:

Genetic Alliance

MedlinePlus

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.