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HelpTest ID CMITO Combined Mitochondrial Full Genome and Nuclear Gene Panel, Varies
Ordering Guidance
The diagnostic workup for a mitochondrial disorder may include testing to demonstrate elevations of the lactate-to-pyruvate ratio and an elevated growth differentiation factor 15 concentration. Consider LAPYP / Lactate Pyruvate Panel, Plasma and GDF15 / Growth Differentiation Factor 15, Plasma.
Customization of this panel and single gene analysis for any nuclear gene present on this panel are available. For more information see CGPH / Custom Gene Panel, Hereditary, Next-Generation Sequencing, Varies.
Targeted testing for familial variants (also called site-specific or known variants testing) is available for the nuclear genes on this panel. See FMTT / Familial Variant, Targeted Testing, Varies. Testing by a different methodology may be recommended for testing mitochondrial genome variants in family members. To obtain more information about this testing option, call 800-533-1710.
Shipping Instructions
Specimen Required
Patient Preparation: A previous hematopoietic stem cell transplant from an allogenic donor will interfere with testing. For information about testing patients who have received a hematopoietic stem cell transplant, call 800-533-1710.
Submit only 1 of the following specimens:
Specimen Type: Whole blood
Container/Tube: Lavender top (EDTA) or yellow top (ACD)
Specimen Volume: 3 mL
Collection Instructions:
1. Invert several times to mix blood.
2. Send whole blood specimen in original tube. Do not aliquot.
Specimen Stability Information: Ambient (preferred) 4 days/Refrigerated 4 days/Frozen 4 days
Additional Information:
1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.
2. To ensure minimum volume and concentration of DNA are met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.
Specimen Type: Cord blood
Container/Tube: Lavender top (EDTA) or yellow top (ACD)
Specimen Volume: 3 mL
Collection Instructions:
1. Invert several times to mix blood.
2. Send cord blood specimen in original tube. Do not aliquot.
Specimen Stability Information: Ambient (preferred) 4 days/Refrigerated 4 days/Frozen 4 days
Additional Information:
1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.
2. To ensure minimum volume and concentration of DNA are met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.
3. While a properly collected cord blood sample may not be at risk for maternal cell contamination, unanticipated complications may occur during collection. Therefore, maternal cell contamination studies are recommended to ensure the test results reflect that of the patient tested and are available at an additional charge. Order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen.
Specimen Type: Saliva
Patient Preparation: Patient should not eat, drink, smoke, or chew gum 30 minutes prior to collection.
Supplies: Saliva Swab Collection Kit (T786)
Specimen Volume: 2 Swabs
Collection Instructions: Collect and send specimen per kit instructions.
Specimen Stability Information: Ambient (preferred) 30 days/Refrigerated 30 days
Additional Information: Saliva specimens are acceptable but not recommended. Due to lower quantity/quality of DNA yielded from saliva, some aspects of the test may not perform as well as DNA extracted from a whole blood sample. When applicable, specific gene regions that were unable to be interrogated will be noted in the report. Alternatively, additional specimen may be required to complete testing.
Specimen Type: Blood spot
Supplies: Card-Blood Spot Collection (Filter Paper) (T493)
Container/Tube:
Preferred: Collection card (Whatman Protein Saver 903 Paper)
Acceptable: PerkinElmer 226 filter paper or blood spot collection card
Specimen Volume: 2 to 5 Blood spots
Collection Instructions:
1. An alternative blood collection option for a patient older than 1 year is a fingerstick. For detailed instructions, see How to Collect a Dried Blood Spot Sample.
2. Let blood dry on the filter paper at ambient temperature in a horizontal position for a minimum of 3 hours.
3. Do not expose specimen to heat or direct sunlight.
4. Do not stack wet specimens.
5. Keep specimen dry.
Specimen Stability Information: Ambient (preferred)/Refrigerated
Additional Information:
1. Blood spot specimens are acceptable but not recommended. Multiple extractions will be required to obtain sufficient yield for supplemental analysis, and there is significant risk for test failure due to insufficient DNA.
2. Due to lower concentration of DNA yielded from blood spot, some aspects of the test may not perform as well as DNA extracted from a whole blood sample. When applicable, specific gene regions that were unable to be interrogated will be noted in the report. Alternatively, additional specimen may be required to complete testing.
3. For collection instructions, see Blood Spot Collection Instructions
4. For collection instructions in Spanish, see Blood Spot Collection Card-Spanish Instructions (T777) 5. For collection instructions in Chinese, see Blood Spot Collection Card-Chinese Instructions (T800)
Specimen Type: Tissue biopsy
Supplies: Hank's Solution (T132)
Container/Tube: Sterile container with sterile Hank's balanced salt solution, Ringer's solution, or normal saline
Specimen Volume: 0.5 to 3 cm(3) or larger
Specimen Stability Information: Ambient (preferred) <24 hours/Refrigerated <24 hours
Additional Information:
1. Specimens are preferred to be received within 24 hours of collection. Culture and extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.
2. A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing. An additional 3 to 4 weeks are required to culture fibroblasts before genetic testing can occur
Specimen Type: Skin biopsy
Supplies: Fibroblast Biopsy Transport Media (T115)
Container/Tube: Sterile container with any standard cell culture media (eg, minimal essential media, RPMI 1640). The solution should be supplemented with 1% penicillin and streptomycin.
Specimen Volume: 4-mm Punch
Specimen Stability Information: Ambient (preferred) <24 hours/Refrigerated <24 hours
Additional Information:
1. Specimens are preferred to be received within 24 hours of collection. Culture and extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.
2. A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing. An additional 3 to 4 weeks are required to culture fibroblasts before genetic testing can occur.
Specimen Type: Cultured fibroblasts
Source: Skin
Container/Tube: T-25 flask
Specimen Volume: 2 Flasks
Collection Instructions: Submit confluent cultured fibroblast cells from a skin biopsy.
Specimen Stability Information: Ambient (preferred) <24 hours/Refrigerated <24 hours
Additional Information:
1. Specimens are preferred to be received within 24 hours of collection. Culture and extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.
2. A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing. An additional 3 to 4 weeks are required to culture fibroblasts before genetic testing can occur.
Specimen Type: Extracted DNA
Container/Tube:
Preferred: Screw Cap Micro Tube, 2 mL with skirted conical base
Acceptable: Matrix tube, 1 mL
Collection Instructions:
1. The preferred volume is at least 100 mcL at a concentration of 75 ng/mcL.
2. Include concentration and volume on tube.
Specimen Stability Information: Frozen (preferred) 1 year/Ambient/Refrigerated
Additional Information: DNA must be extracted in a CLIA-certified laboratory or equivalent and must be extracted from a specimen type listed as acceptable for this test (including applicable anticoagulants). Our laboratory has experience with Chemagic, Puregene, Autopure, MagnaPure, and EZ1 extraction platforms and cannot guarantee that all extraction methods are compatible with this test. If testing fails, one repeat will be attempted, and if unsuccessful, the test will be reported as failed and a charge will be applied. If applicable, specific gene regions that were unable to be interrogated due to DNA quality will be noted in the report.
PRENATAL SPECIMENS
Due to its complexity, consultation with the laboratory is required for all prenatal testing; call 800-533-1710 to speak to a genetic counselor.
Specimen Type: Amniotic fluid
Container/Tube: Amniotic fluid container
Specimen Volume: 20 mL
Specimen Stability Information: Ambient (preferred) <24 hours/Refrigerated <24 hours
Additional Information: Specimen will only be tested after culture.
1. Specimens are preferred to be received within 24 hours of collection. Culture and extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.
2. A separate culture charge will be assessed under CULAF / Culture for Genetic Testing, Amniotic Fluid. An additional 2 to 3 weeks are required to culture amniotic fluid before genetic testing can occur.
3. All prenatal specimens must be accompanied by a maternal blood specimen; order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen.
Specimen Type: Confluent cultured amniocytes
Container/Tube: T-25 flask
Specimen Volume: 2 Flasks
Collection Instructions: Submit confluent cultured amniocytes from another laboratory
Specimen Stability Information: Ambient (preferred) <24 hours/Refrigerated <24 hours
Additional Information:
1. Specimens are preferred to be received within 24 hours of collection. Culture and extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.
2. A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing.
3. All prenatal specimens must be accompanied by a maternal blood specimen; order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen.
Specimen Type: Chorionic villi
Container/Tube: 15-mL tube containing 15 mL of transport media
Specimen Volume: 20 mg
Specimen Stability Information: Ambient (preferred) <24 hours/Refrigerated <24 hours
Additional Information: Specimen will only be tested after culture.
1. Specimens are preferred to be received within 24 hours of collection. Culture and extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.
2. A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing. An additional 3 to 4 weeks are required to culture fibroblasts before genetic testing can occur.
3. All prenatal specimens must be accompanied by a maternal blood specimen; order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen.
Specimen Type: Cultured chorionic villi
Container/Tube: T-25 flasks
Specimen Volume: 2 Full flasks
Collection Instructions: Submit confluent cultured cells from another laboratory
Specimen Stability Information: Ambient (preferred) <24 hours/Refrigerated <24 hours
Additional Information:
1. Specimens are preferred to be received within 24 hours of collection. Culture and extraction will be attempted for specimens received after 24 hours and will be evaluated to determine if testing may proceed.
2. A separate culture charge will be assessed under CULFB / Fibroblast Culture for Biochemical or Molecular Testing.
3. All prenatal specimens must be accompanied by a maternal blood specimen; order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen.
Forms
1. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file. The following documents are available:
-Informed Consent for Genetic Testing (T576)
-Informed Consent for Genetic Testing (Spanish) (T826)
2. Molecular Genetics: Biochemical Disorders Patient Information (T527)
3. If not ordering electronically, complete, print, and send 1 of the following forms with the specimen:
Useful For
Diagnosing mitochondrial disease that results from variants in either nuclear-encoded genes or the mitochondrial genome
A second-tier test for patients in whom previous targeted gene variant analyses for specific mitochondrial disease-related genes were negative
Identifying variants known to be associated with mitochondrial disease, allowing for predictive testing of at-risk family members
Genetics Test Information
This test utilizes next-generation sequencing to detect single nucleotide and copy number variants in 221 nuclear genes and amplification of the entire mitochondrial genome by long-range polymerase chain reaction: AARS2, ABAT, ABCB7, ACACA, ACAD9, ACO2, AFG3L2, AGK, AIFM1, ALDH3A2, APOPT1 (COA8), APTX, ATP5F1A, ATP5F1E, ATPAF2, AUH, BCS1L, BOLA3, C12orf65 (MTRFR), CA5A, CARS2, CHAT, CHCHD10, CLPP, COA5, COA6, COA8 (APOPT1), COASY, COQ2, COQ4, COQ6, COQ7, COQ8A, COQ8B, COQ9, COX10, COX14, COX15, COX20, COX4I1, COX4I2, COX6A1, COX6A2, COX6B1, COX7B, COX8A, CPT1C, CYC1, D2HGDH, DARS2, DGUOK, DLAT, DLD, DNA2, DNAJC19, DNM1L, EARS2, ELAC2, ETFA, ETFB, ETFDH, ETHE1, FARS2, FASTKD2, FBXL4, FDX2, FDXR, FH, FOXRED1, FXN, GAMT, GARS1, GCDH, GDAP1, GFER, GFM1, GFM2, GLYCTK, GPT2, GTPBP3, HARS2, HIBCH, HK1, HSPD1, IARS2, IBA57, IDH2, INF2, ISCU, L2HGDH, LARS2, LIAS, LRPPRC, LYRM4, LYRM7, MARS2, MFF, MGME1, MICU1, MPC1, MPV17, MRPL3, MRPL44, MRPS16, MRPS2, MRPS22, MRPS7, MSTO1, MTFMT, MTO1, MTPAP, MTRFR (C12orf65), NARS2, NBAS, NDUFA1, NDUFA10, NDUFA11, NDUFA12, NDUFA13, NDUFA2, NDUFA4, NDUFA9, NDUFAF1, NDUFAF2, NDUFAF3, NDUFAF4, NDUFAF5, NDUFAF6, NDUFB3, NDUFB9, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NFU1, NR2F1, NUBPL, OGDH, OPA1, OPA3, OXCT1, PANK2, PARS2, PC, PCK2, PDHA1, PDHB, PDHX, PDP1, PDSS1, PDSS2, PET100, PNKD, PNPT1, POLG, POLG2, PTRH2, PUS1, QARS1, RARS1, RARS2, RMND1, RNASEH1, RRM2B, RTN4IP1, SACS, SARS2, SCO1, SCO2, SDHAF1, SERAC1, SFXN4, SLC19A3, SLC25A1, SLC25A12, SLC25A19, SLC25A22, SLC25A26, SLC25A3, SLC25A4, SLC25A42, SLC25A46, SLC52A2, SLC9A6, SOD1, SPG7, SUCLA2, SUCLG1, SUGCT, SURF1, TACO1, TAFAZZIN (TAZ), TARS2, TAZ (TAFAZZIN), TFAM, TIMM8A, TK2, TMEM126A, TMEM126B, TMEM70, TOP3A, TPK1, TRIT1, TRMT10C, TRMU, TRNT1, TSFM, TTC19, TUFM, TWNK, TYMP, UQCC2, UQCRB, UQCRC2, UQCRQ, VARS2, WDR45, XPNPEP3, and YARS2.
See Targeted Genes and Methodology Details for Combined Mitochondrial Full Genome and Nuclear Gene Panel, Varies and Method Description for additional details.
Identification of a disease-causing variant may assist with diagnosis, prognosis, clinical management, familial screening, and genetic counseling for mitochondrial disease.
Reflex Tests
| Test ID | Reporting Name | Available Separately | Always Performed |
|---|---|---|---|
| CULFB | Fibroblast Culture for Genetic Test | Yes | No |
| CULAF | Amniotic Fluid Culture/Genetic Test | Yes | No |
| MATCC | Maternal Cell Contamination, B | Yes | No |
Testing Algorithm
Skin biopsy:
If skin biopsy is received, fibroblast culture will be added at an additional charge. If viable cells are not obtained, the client will be notified.
Prenatal specimens:
If an amniotic fluid specimen is received, an amniotic fluid culture will be performed at an additional charge.
If chorionic villi, cultured chorionic villi, or cultured amniocyte specimen is received, a fibroblast culture will be performed at an additional charge.
For any prenatal specimen that is received, maternal cell contamination testing will be performed at an additional charge.
Cord blood:
For cord blood specimens that have an accompanying maternal blood specimen, maternal cell contamination studies will be performed at an additional charge.
For more information see:
-Epilepsy: Unexplained Refractory and/or Familial Testing Algorithm
Method Name
Nuclear Genes: Sequence Capture and Targeted Next-Generation Sequencing (NGS) followed by Polymerase Chain Reaction (PCR) and Sanger Sequencing
Mitochondrial Genome: Long-Range Polymerase Chain Reaction (LR-PCR) followed by Next-Generation Sequencing (NGS) and Droplet Digital Polymerase Chain Reaction (ddPCR) as needed
Reporting Name
Combined mtDNA+Nuclear Gene PanelSpecimen Type
VariesSpecimen Minimum Volume
See Specimen Required
Specimen Stability Information
| Specimen Type | Temperature | Time |
|---|---|---|
| Varies | Varies | |
Reject Due To
All specimens will be evaluated at Mayo Clinic Laboratories for test suitability.Clinical Information
The mitochondrion occupies a unique position in eukaryotic biology. It is the site of energy metabolism, and it is the sole subcellular organelle composed of proteins derived from 2 genomes, mitochondrial and nuclear. A group of hereditary disorders due to variants in either the mitochondrial genome or nuclear mitochondrial genes have been well characterized.
The diagnosis of mitochondrial disease can be particularly challenging as the presentation can occur at any age, involve virtually any organ system, and be associated with widely varying severities. Due to the considerable overlap in the clinical phenotypes of various mitochondrial disorders, it is often difficult to distinguish these specific inherited disorders without genetic testing. This test utilizes massively parallel sequencing, also termed next-generation sequencing (NGS), to analyze 221 nuclear-encoded genes implicated in mitochondrial disease and to determine the exact sequence of the entire 16,569 base-pair mitochondrial genome.
The utility of this test is to assist in the diagnosis of mitochondrial diseases that result from variants in both nuclear encoded genes and in the mitochondrial genome. Those diseases involving nuclear genes include disorders of mitochondrial protein synthesis, coenzyme Q10 biosynthesis, respiratory chain complexes, and mitochondrial DNA (mtDNA) maintenance (ie, mtDNA depletion disorders). Disorders of the mitochondrial genome include those caused by single nucleotide variants, such as mitochondrial encephalomyopathy, lactic acidosis, stroke-like episodes (MELAS), myoclonic epilepsy with ragged red fibers (MERRF), mitochondrial myopathy (MM), neurogenic muscle weakness, ataxia, and retinitis pigmentosa (NARP), Leigh syndrome, Leber hereditary optic neuropathy (LHON), and chronic progressive external ophthalmoplegia (CPEO). In addition to the detection of single base changes with these disorders, large deletions, such as those associated with Kearns-Sayre or Pearson syndromes, are also detected. In contrast to variants in nuclear genes, which are present in either 0, 1, or 2 copies, mitochondrial variants can be present in any fraction of the total organelles, a phenomenon known as heteroplasmy. Typically, the severity of disease presentation is a function of the degree of heteroplasmy. Individuals with a higher fraction of altered mitochondria present with more severe disease than those with lower percentages of altered alleles. The sensitivity for the detection of altered alleles in a background of wild-type (or normal) mitochondrial sequences by NGS is approximately 10%.
Reference Values
An interpretive report will be provided.
Interpretation
All detected variants are evaluated according to American College of Medical Genetics and Genomics recommendations.(1-2) Other gene-specific guidelines may also be considered. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance. For variants identified in the mitochondrial genome, the degree of heteroplasmy of each single nucleotide or delin (deletion-insertion) variant, defined as the ratio (percentage) of variant sequence reads to the total number of reads, will also be reported. Variants detected at or above 95% will be reported as homoplasmic. Heteroplasmy for large deletions will be reported and is determined by droplet digital polymerase chain reaction. Variants classified as benign or likely benign are not reported.
Cautions
Clinical Correlations:
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.
If testing was performed because of a clinically significant family history, it is often useful to first test an affected family member. Detection of a reportable variant in an affected family member would allow for more informative testing of at-risk individuals.
To discuss the availability of additional testing options or for assistance in the interpretation of these results, contact the Mayo Clinic Laboratories genetic counselors at 800-533-1710.
Technical Limitations:
Next-generation sequencing may not detect all types of genomic variants. In rare cases, false-negative or false-positive results may occur. The depth of coverage may be variable for some target regions; assay performance below the minimum acceptable criteria or for failed regions will be noted. Given these limitations, negative results do not rule out the diagnosis of a genetic disorder. If a specific clinical disorder is suspected, evaluation by alternative methods can be considered.
There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. Confirmation of select reportable variants will be performed by alternate methodologies based on internal laboratory criteria.
This test is validated to detect 95% of deletions up to 75 base pairs (bp) and insertions up to 47 bp. Deletions-insertions (delins) of 40 or more bp, including mobile element insertions, may be less reliably detected than smaller delins.
This analysis targets single and multi-exon deletions/duplications; however, in some instances single exon resolution cannot be achieved due to isolated reduction in sequence coverage or inherent genomic complexity. Balanced structural rearrangements (such as translocations and inversions) may not be detected.
This test is not designed to detect low levels of mosaicism or to differentiate between somatic mutations and germline variants. If there is a possibility that any detected variant is somatic, additional testing may be necessary to clarify the significance of results.
Genes may be added or removed based on updated clinical relevance. For detailed information regarding gene-specific performance and technical limitations, see Method Description or contact a laboratory genetic counselor.
If the patient has had an allogeneic hematopoietic stem cell transplant or a recent non-leukocyte reduced blood transfusion, results may be inaccurate due to the presence of donor DNA. Call Mayo Clinic Laboratories for instructions for testing patients who have received an allogeneic hematopoietic stem cell transplant.
Reclassification of Variants:
Currently, it is not standard practice for the laboratory to systematically review previously classified variants on a regular basis. The laboratory encourages healthcare professionals to contact the laboratory at any time to learn how the classification of a particular variant may have changed over time. Due to broadening genetic knowledge, it is possible that the laboratory may discover new information of relevance to the patient. Should that occur, the laboratory may issue an amended report.
Variant Evaluation:
Evaluation and categorization of variants are performed using published American College of Medical Genetics and Genomics and the Association for Molecular Pathology recommendations as a guideline.(1) Other gene-specific guidelines may also be considered. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance. For variants identified in the mitochondrial genome, the degree of heteroplasmy of each single nucleotide or delin variant, defined as the ratio (percentage) of variant sequence reads to the total number of reads, will also be reported. Variants detected at or above 95% will be reported as homoplasmic. Heteroplasmy for large deletions will be reported and is determined by droplet digital polymerase chain reaction. Variants classified as benign or likely benign are not reported.
Multiple in silico evaluation tools may be used to assist in the interpretation of these results. The accuracy of predictions made by in silico evaluation tools is highly dependent upon the data available for a given gene, and periodic updates to these tools may cause predictions to change over time. Results from in silico evaluation tools should be interpreted with caution and professional clinical judgment.
Rarely, incidental or secondary findings may implicate another predisposition or presence of active disease. These findings will be carefully reviewed to determine whether they will be reported.
Clinical Reference
1. Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405-424
2. McCormick EM, Lott MT, Dulik MC, et al. Specifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretation. Hum Mutat. 2020;41(12):2028-2057
3. Munnich A, Rotig A, Cormier-Daire V, Rustin P. Clinical presentation of respiratory chain deficiency. In: Valle D, Antonarakis S, Ballabio A, Beaudet AL, Mitchell GA, eds. The Online Metabolic and Molecular Basis of Inherited Disease. McGraw-Hill; 2019. Accessed June 13, 2025. Available at https://ommbid.mhmedical.com/content.aspx?bookid=2709§ionid=225086827
4. Wallace DC, Lott MT, Brown MD, Kerstann K. Mitochondria and neuro-ophthalmologic diseases. In: Valle D, Antonarakis S, Ballabio A, Beaudet AL, Mitchell GA, eds. The Online Metabolic and Molecular Basis of Inherited Disease. McGraw-Hill; 2019. Accessed June 13, 2024. Available at https://ommbid.mhmedical.com/content.aspx?bookid=2709§ionid=225088522
5. Wong LJ. Molecular genetics of mitochondrial disorders. Dev Disabil Res Rev. 2010;16(2):154-162
6. Barca E, Long Y, Cooley V, et al. Mitochondrial disease in North America: An analysis of the NAMDC Registry. Neurol Genet. 2020;6(2):e402
Method Description
Next-generation sequencing (NGS) and/or Sanger sequencing are performed to test for the presence of variants in coding regions and intron/exon boundaries of the genes analyzed, as well as some other regions that have known disease-causing variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At least 99% of the bases are covered at a read depth over 30X. Sensitivity is estimated to be over 99% for single nucleotide variants, over 94% for deletions-insertions (delins) less than 40 base pairs (bp), and over 95% for deletions up to 75 bp and insertions up to 47 bp. NGS and/or a polymerase chain reaction (PCR)-based quantitative method is performed to test for the presence of deletions and duplications in the genes analyzed.
There may be regions of genes that cannot be effectively evaluated by sequencing or deletion and duplication analysis as a result of technical limitations of the assay, including regions of homology, high guanine-cytosine (GC) content, and repetitive sequences. See Targeted Genes and Methodology Details for Combined Mitochondrial Full Genome and Nuclear Gene Panel, Varies for details regarding the targeted genes analyzed for each test and specific gene regions not routinely covered.(Unpublished Mayo method)
Confirmation of select reportable variants may be performed by alternate methodologies based on internal laboratory criteria.
NGS is also 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 electrophoresis (as size-shifted polymerase chain reaction bands), and the locations of the deletions in the mitochondrial DNA are then determined from the NGS data. Droplet digital PCR (ddPCR) is utilized to confirm the presence of large deletions and determine heteroplasmy level.(Unpublished Mayo method)
The haplogroup is computed using the software package HaploGrep and PhyloTree.(Weissensteiner H, Pacher D, Kloss-Brandstatter A, et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 2016;44[W1]:W58-W63. doi:10.1093/nar/gkw233; van Oven M, Kayser M. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat. 2009;30[2]:E386-E394. doi:10.1002/humu.20921. Available at www.phylotree.org)
Genes analyzed: AARS2, ABAT, ABCB7, ACACA, ACAD9, ACO2, AFG3L2, AGK, AIFM1, ALDH3A2, APOPT1 (COA8), APTX, ATP5F1A, ATP5F1E, ATPAF2, AUH, BCS1L, BOLA3, C12orf65 (MTRFR), CA5A, CARS2, CHAT, CHCHD10, CLPP, COA5, COA6, COA8 (APOPT1), COASY, COQ2, COQ4, COQ6, COQ7, COQ8A, COQ8B, COQ9, COX10, COX14, COX15, COX20, COX4I1, COX4I2, COX6A1, COX6A2, COX6B1, COX7B, COX8A, CPT1C, CYC1, D2HGDH, DARS2, DGUOK, DLAT, DLD, DNA2, DNAJC19, DNM1L, EARS2, ELAC2, ETFA, ETFB, ETFDH, ETHE1, FARS2, FASTKD2, FBXL4, FDX2, FDXR, FH, FOXRED1, FXN, GAMT, GARS1, GCDH, GDAP1, GFER, GFM1, GFM2, GLYCTK, GPT2, GTPBP3, HARS2, HIBCH, HK1, HSPD1, IARS2, IBA57, IDH2, INF2, ISCU, L2HGDH, LARS2, LIAS, LRPPRC, LYRM4, LYRM7, MARS2, MFF, MGME1, MICU1, MPC1, MPV17, MRPL3, MRPL44, MRPS16, MRPS2, MRPS22, MRPS7, MSTO1, MTFMT, MTO1, MTPAP, MTRFR (C12orf65), NARS2, NBAS, NDUFA1, NDUFA10, NDUFA11, NDUFA12, NDUFA13, NDUFA2, NDUFA4, NDUFA9, NDUFAF1, NDUFAF2, NDUFAF3, NDUFAF4, NDUFAF5, NDUFAF6, NDUFB3, NDUFB9, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NFU1, NR2F1, NUBPL, OGDH, OPA1, OPA3, OXCT1, PANK2, PARS2, PC, PCK2, PDHA1, PDHB, PDHX, PDP1, PDSS1, PDSS2, PET100, PNKD, PNPT1, POLG, POLG2, PTRH2, PUS1, QARS1, RARS1, RARS2, RMND1, RNASEH1, RRM2B, RTN4IP1, SACS, SARS2, SCO1, SCO2, SDHAF1, SERAC1, SFXN4, SLC19A3, SLC25A1, SLC25A12, SLC25A19, SLC25A22, SLC25A26, SLC25A3, SLC25A4, SLC25A42, SLC25A46, SLC52A2, SLC9A6, SOD1, SPG7, SUCLA2, SUCLG1, SUGCT, SURF1, TACO1, TAFAZZIN (TAZ), TARS2, TAZ (TAFAZZIN), TFAM, TIMM8A, TK2, TMEM126A, TMEM126B, TMEM70, TOP3A, TPK1, TRIT1, TRMT10C, TRMU, TRNT1, TSFM, TTC19, TUFM, TWNK, TYMP, UQCC2, UQCRB, UQCRC2, UQCRQ, VARS2, WDR45, XPNPEP3, and YARS2 and mitochondrial genome
Day(s) Performed
Varies
Report Available
28 to 42 daysTest Classification
This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.CPT Code Information
81460
81440
81465