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Mavraki E, Labrum R, Sergeant K, Alston CL, Woodward C, Smith C, Knowles CVY, Patel Y, Hodsdon P, Baines JP, Blakely EL, Polke J, Taylor RW, Fratter C. Genetic testing for mitochondrial disease: the United Kingdom best practice guidelines. Eur J Hum Genet 2023; 31:148-163. [PMID: 36513735 PMCID: PMC9905091 DOI: 10.1038/s41431-022-01249-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
Primary mitochondrial disease describes a diverse group of neuro-metabolic disorders characterised by impaired oxidative phosphorylation. Diagnosis is challenging; >350 genes, both nuclear and mitochondrial DNA (mtDNA) encoded, are known to cause mitochondrial disease, leading to all possible inheritance patterns and further complicated by heteroplasmy of the multicopy mitochondrial genome. Technological advances, particularly next-generation sequencing, have driven a shift in diagnostic practice from 'biopsy first' to genome-wide analyses of blood and/or urine DNA. This has led to the need for a reference framework for laboratories involved in mitochondrial genetic testing to facilitate a consistent high-quality service. In the United Kingdom, consensus guidelines have been prepared by a working group of Clinical Scientists from the NHS Highly Specialised Service followed by national laboratory consultation. These guidelines summarise current recommended technologies and methodologies for the analysis of mtDNA and nuclear-encoded genes in patients with suspected mitochondrial disease. Genetic testing strategies for diagnosis, family testing and reproductive options including prenatal diagnosis are outlined. Importantly, recommendations for the minimum levels of mtDNA testing for the most common referral reasons are included, as well as guidance on appropriate referrals and information on the minimal appropriate gene content of panels when analysing nuclear mitochondrial genes. Finally, variant interpretation and recommendations for reporting of results are discussed, focussing particularly on the challenges of interpreting and reporting mtDNA variants.
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Affiliation(s)
- Eleni Mavraki
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Robyn Labrum
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
| | - Kate Sergeant
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Charlotte L Alston
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Cathy Woodward
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
| | - Conrad Smith
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Charlotte V Y Knowles
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Yogen Patel
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
| | - Philip Hodsdon
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jack P Baines
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Emma L Blakely
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - James Polke
- Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London, UK
| | - Robert W Taylor
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Carl Fratter
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
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Li M, Foli Y, Liu Z, Wang G, Hu Y, Lu Q, Selvaraj S, Lam W, Paintsil E. High frequency of mitochondrial DNA mutations in HIV-infected treatment-experienced individuals. HIV Med 2016; 18:45-55. [PMID: 27328746 PMCID: PMC5132110 DOI: 10.1111/hiv.12390] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2016] [Indexed: 01/11/2023]
Abstract
OBJECTIVES We recently observed a decrease in deoxyribonucleotide (dNTP) pools in HIV-infected individuals on antiretroviral therapy (ART). Alterations in dNTPs result in mutations in mitochondrial DNA (mtDNA) in cell culture and animal models. Therefore, we investigated whether ART is associated with mitochondrial genome sequence variation in peripheral blood mononuclear cells (PBMCs) of HIV-infected treatment-experienced individuals. METHODS In this substudy of a case-control study, 71 participants were included: 22 'cases', who were HIV-infected treatment-experienced patients with mitochondrial toxicity, 25 HIV-infected treatment-experienced patients without mitochondrial toxicity, and 24 HIV-uninfected controls. Total DNA was extracted from PBMCs and purified polymerase chain reaction (PCR) products were subjected to third-generation sequencing using the PacBio Single Molecule Real-Time (SMRT) sequencing technology. The sequences were aligned against the revised Cambridge reference sequence for human mitochondrial DNA (NC_012920.1) for detection of variants. RESULTS We identified a total of 123 novel variants, 39 of them in the coding region. HIV-infected treatment-experienced patients with and without toxicity had significantly higher average numbers of mitochondrial variants per participant than HIV-uninfected controls. We observed a higher burden of mtDNA large-scale deletions in HIV-infected treatment-experienced patients with toxicity compared with HIV-uninfected controls (P = 0.02). The frequency of mtDNA molecules containing a common deletion (mt.δ4977) was higher in HIV-infected treatment-experienced patients with toxicity compared with HIV-uninfected controls (P = 0.06). There was no statistically significant difference in mtDNA variants between HIV-infected treatment-experienced patients with and without toxicity. CONCLUSIONS The frequency of mtDNA variants (mutations and large-scale deletions) was higher in HIV-infected treatment-experienced patients with or without ART-induced toxicity than in uninfected controls.
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Affiliation(s)
- M Li
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Y Foli
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Z Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - G Wang
- Yale Center for Genome Analysis, Yale School of Medicine, West Haven, CT, USA
| | - Y Hu
- School of Public Health, Yale University, New Haven, CT, USA
| | - Q Lu
- School of Public Health, Yale University, New Haven, CT, USA
| | - S Selvaraj
- Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
| | - W Lam
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - E Paintsil
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA.,School of Public Health, Yale University, New Haven, CT, USA.,Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
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Fang H, Shi H, Li X, Sun D, Li F, Li B, Ding Y, Ma Y, Liu Y, Zhang Y, Shen L, Bai Y, Yang Y, Lu J. Exercise intolerance and developmental delay associated with a novel mitochondrial ND5 mutation. Sci Rep 2015; 5:10480. [PMID: 26014388 PMCID: PMC4444849 DOI: 10.1038/srep10480] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 04/15/2015] [Indexed: 11/22/2022] Open
Abstract
The aim of this study was to evaluate the contribution of mitochondrial DNA (mtDNA) mutations in oxidative phosphorylation (OXPHOS) deficiency. The complete mitochondrial genomes of 41 families with OXPHOS deficiency were screened for mutations. Mitochondrial functional analysis was then performed in primary and cybrid cells containing candidate mutations identified during the screening. A novel mitochondrial NADH dehydrogenase 5 (ND5) m.12955A > G mutation was identified in a patient with exercise intolerance and developmental delay. A biochemical analysis revealed deficiencies in the activity of complex I (NADH:quinone oxidoreductase) and IV (cytochrome c oxidase) of this patient. Defects in complexes I and IV were confirmed in transmitochondrial cybrid cells containing the m.12955A > G mutation, suggesting that this mutation impairs complex I assembly, resulting in reduced stability of complex IV. Further functional investigations revealed that mitochondria with the m.12955A > G mutation exhibited lower OXPHOS coupling respiration and adenosine triphosphate (ATP) generation. In addition, the cytotoxic effects, determined as reactive oxygen species (ROS) and lactate levels in the present study, increased in the cells carrying a higher m.12955A > G mutant load. In conclusion, we identified m.12955A > G as a mitochondrial disease-related mutation. Therefore, screening of m.12955A > G is advised for the diagnosis of patients with mitochondrial disease.
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Affiliation(s)
- Hezhi Fang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Hao Shi
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Xiyuan Li
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Dayan Sun
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Fengjie Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Bin Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Yuan Ding
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Yanyan Ma
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Yupeng Liu
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Yao Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Lijun Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
| | - Yidong Bai
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yanling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, China
| | - Jianxin Lu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, China
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Biological imprinting: Some genetic considerations. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2014. [DOI: 10.1016/j.ejmhg.2014.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Koh HR, Han KY, Jung J, Kim SK. Quantitative genotyping of single nucleotide polymorphism by single-molecule multi-color fluorescence resonance energy transfer. Chem Commun (Camb) 2011; 47:10362-4. [PMID: 21847490 DOI: 10.1039/c1cc12737c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We developed a new single nucleotide polymorphism (SNP) genotyping method based on single-molecule multi-color fluorescence resonance energy transfer (FRET). We demonstrated that this new method uses less than 1 fmol of sample and is also highly quantitative with a detection level of 1% or lower in the minor allele fraction.
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Affiliation(s)
- Hye Ran Koh
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea
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Yang Y, Zhang P, He Q, Zhu Y, Yang X, Lv R, Chen J. A new strategy for the discrimination of mitochondrial DNA haplogroups in Han population. J Forensic Sci 2011; 56:586-90. [PMID: 21470221 DOI: 10.1111/j.1556-4029.2011.01711.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Mitochondrial DNA (mtDNA) haplogroup discrimination is interesting not only for phylogenetic and clinical but also for forensic studies. We discriminated the mtDNA haplogroups of 570 healthy unrelated Han people from Zhejiang Province, Southeast China, by comprehensive analysis mutations of the hypervariable segments-I sequence and diagnostic polymorphisms in mtDNA coding region using real-time polymerase chain reaction (RT-PCR), which was compared with the widely used PCR and restriction fragment length polymorphism (PCR-RFLP) method. The results showed that in superhaplogroup M, haplogroup D was the most common haplotype within this assay to 24.6%, and in the other superhaplotype N, haplogroup B and F were the most common groups. Samples re-identified by PCR-RFLP showed the consistent results that were got with RT-PCR. In conclusion, the RT-PCR strategy appears to be an accurate, reproducible, and sensitive technique for the discrimination of mtDNA haplogroups, especially for mass screenings quickly and economically.
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Affiliation(s)
- Yi Yang
- Kidney Disease Center, First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou 310003, China
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Tucker EJ, Compton AG, Thorburn DR. Recent advances in the genetics of mitochondrial encephalopathies. Curr Neurol Neurosci Rep 2010; 10:277-85. [PMID: 20446063 DOI: 10.1007/s11910-010-0112-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Mitochondrial encephalopathy, the most common neurometabolic disorder, may be caused by mutations in approximately 100 different genes and may present with various symptoms, such as seizures, ataxia, myopathy, cognitive impairment, blindness, and stroke. Fewer than 50% of patients with mitochondrial encephalopathy receive a molecular diagnosis, primarily because of the large degree of clinical and genetic heterogeneity among patients and the limited knowledge of the genes involved in mitochondrial function. Here we review the most recent discoveries of genes associated with mitochondrial disease with variable neuropathology. All these genes have been identified via homozygosity mapping or linkage analysis; however, advances in sequencing technology indicate that the future of genetic diagnosis and disease gene discovery likely lies in high-throughput sequencing.
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Affiliation(s)
- Elena J Tucker
- Murdoch Childrens Research Institute, The Royal Children's Hospital, 10th Floor, Flemington Road, Parkville, Victoria, 3052, Australia.
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Abstract
AbstractThe A3243G mutation in the mitochondrial tRNALeu (UUR) gene is one of the most common causes of mitochondrial DNA related disorders. Originally it was described in MELAS syndrome (Mitochondrial Encephalomyopathy, Lactic acidosis, Stroke-like episodes), later it had been found to be associated with various phenotypes. In our study the mutation frequency of the A3243G mtDNA mutation was investigated in patients with maternal sensoneural hearing loss, stroke-like episodes, ataxia and myopathy with undetermined etiology. We screened 631 Hungarian patients in North-East, South-West and Central Hungary between 1999 and 2008 for this mutation. The mtDNA analysis was performed from blood and/or muscle tissue. The A3243G substitution was present in 6 patients in heteroplasmic form. The segregation analysis detected 8 further cases. The frequency of the A3243G mutation was 2.22% in the investigated patients. The A3243G mutation frequency in Hungary does not differ significantly from other countries using similar patient selection criteria, however in Finland a higher mutation rate was found. In studies investigated the mutation frequency of this mutation in diabetes mellitus similarly wide variety was detected as well. We conclude that the study design has a huge impact on the result of the genetic epidemiological investigation analyzing the mutation frequency of the A3243G mutation due to the broad clinical phenotype and the different mutation load in different tissues.
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Vasta V, Ng SB, Turner EH, Shendure J, Hahn SH. Next generation sequence analysis for mitochondrial disorders. Genome Med 2009; 1:100. [PMID: 19852779 PMCID: PMC2784303 DOI: 10.1186/gm100] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 09/04/2009] [Accepted: 10/23/2009] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Mitochondrial disorders can originate from mutations in one of many nuclear genes controlling the organelle function or in the mitochondrial genome (mitochondrial DNA (mtDNA)). The large numbers of potential culprit genes, together with the little guidance offered by most clinical phenotypes as to which gene may be causative, are a great challenge for the molecular diagnosis of these disorders. METHODS We developed a novel targeted resequencing assay for mitochondrial disorders relying on microarray-based hybrid capture coupled to next-generation sequencing. Specifically, we subjected the entire mtDNA genome and the exons and intron-exon boundary regions of 362 known or candidate causative nuclear genes to targeted capture and resequencing. We here provide proof-of-concept data by testing one HapMap DNA sample and two positive control samples. RESULTS Over 94% of the targeted regions were captured and sequenced with appropriate coverage and quality, allowing reliable variant calling. Pathogenic mutations blindly tested in patients' samples were 100% concordant with previous Sanger sequencing results: a known mutation in Pyruvate dehydrogenase alpha 1 subunit (PDHA1), a novel splicing and a known coding mutation in Hydroxyacyl-CoA dehydrogenase alpha subunit (HADHA) were correctly identified. Of the additional variants recognized, 90 to 94% were present in dbSNP while 6 to 10% represented new alterations. The novel nonsynonymous variants were all in heterozygote state and mostly predicted to be benign. The depth of sequencing coverage of mtDNA was extremely high, suggesting that it may be feasible to detect pathogenic mtDNA mutations confounded by low level heteroplasmy. Only one sequencing lane of an eight lane flow cell was utilized for each sample, indicating that a cost-effective clinical test can be achieved. CONCLUSIONS Our study indicates that the use of next generation sequencing technology holds great promise as a tool for screening mitochondrial disorders. The availability of a comprehensive molecular diagnostic tool will increase the capacity for early and rapid identification of mitochondrial disorders. In addition, the proposed approach has the potential to identify new mutations in candidate genes, expanding and redefining the spectrum of causative genes responsible for mitochondrial disorders.
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Affiliation(s)
- Valeria Vasta
- Seattle Children's Research Institute, 1900 9th Ave, Seattle, WA 98101, USA.
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Nogueira C, Nunes J, Evangelista T, Fattori F, Tessa A, Pereira C, Santorelli FM, Vilarinho L. A new mtDNA-tRNA(Glu) mutation (14728T>C) presenting a late-onset mitochondrial encephalomyopathy. Mitochondrion 2007; 7:396-8. [PMID: 17897888 DOI: 10.1016/j.mito.2007.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Revised: 06/26/2007] [Accepted: 08/09/2007] [Indexed: 11/18/2022]
Abstract
We identified a new mutation in the mtDNA-encoded transfer RNA glutamate gene (tRNAGlu) in a patient presenting with late-onset myopathy. The mutation was nearly homoplasmic in muscle but hardly detectable in peripheral blood. Adding to the list of disease-related mtDNA variants, our findings propose to consider screening of tRNAGlu in cases of late-onset neuromuscular disorders.
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Affiliation(s)
- Célia Nogueira
- Instituto de Genética Médica, Jacinto de Magalhães, Praça Pedro Nunes, 88, 4099-028 Porto, Portugal
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Pereira C, Nogueira C, Barbot C, Tessa A, Soares C, Fattori F, Guimarães A, Santorelli FM, Vilarinho L. Identification of a new mtDNA mutation (14724G>A) associated with mitochondrial leukoencephalopathy. Biochem Biophys Res Commun 2007; 354:937-41. [PMID: 17266923 DOI: 10.1016/j.bbrc.2007.01.068] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Accepted: 01/15/2007] [Indexed: 10/23/2022]
Abstract
We report a novel 14724G>A mutation in the mitochondrial tRNA glutamic acid gene in a 4-year-old boy with myopathy and leukoencephalopathy. A muscle biopsy showed cytochrome c oxidase-negative ragged-red fibers and biochemical analysis of the respiratory chain enzymes in muscle homogenate revealed partial complex I and complex IV deficiencies. The mutation, which affects the dihydrouridine arm at a conserved site, was nearly homoplasmic in muscle and heteroplasmic in blood DNA of the proband, but it was absent in peripheral leukocytes from the asymptomatic mother, sister, and two maternal aunts, suggesting that it arose de novo. This report proposes to look for variants in the mitochondrial genome when dealing with otherwise undetermined leukodystrophies of childhood.
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Affiliation(s)
- Cristina Pereira
- Instituto de Genética Médica Jacinto de Magalhães, Praça Pedro Nunes, 88, 4099-028 Porto, Portugal
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Abu-Amero KK, Ozand PT, Al-Dhalaan H. Novel mitochondrial DNA transversion mutation in transfer ribonucleic acid for leucine 2 (CUN) in a patient with the clinical features of MELAS. J Child Neurol 2006; 21:971-2. [PMID: 17092464 DOI: 10.1177/08830738060210110601] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We describe an 11-year-old Saudi boy who had an encephalopathy suggestive of mitochondrial encephalomyopathy with lactic acidosis and strokelike episodes (MELAS). We screened his entire mitochondrial DNA coding region and detected one novel transversion point mutation at nt-12299 A > C in the transfer ribonucleic acid for leucine 2 (CUN) that is located in the anticodon loop. We believe that this mutation is the cause of his disease condition.
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Affiliation(s)
- Khaled K Abu-Amero
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
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Parr RL, Maki J, Reguly B, Dakubo GD, Aguirre A, Wittock R, Robinson K, Jakupciak JP, Thayer RE. The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation. BMC Genomics 2006; 7:185. [PMID: 16859552 PMCID: PMC1538596 DOI: 10.1186/1471-2164-7-185] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Accepted: 07/21/2006] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Nuclear mitochondrial pseudogenes (numts) are a potential source of contamination during mitochondrial DNA PCR amplification. This possibility warrants careful experimental design and cautious interpretation of heteroplasmic results. RESULTS Here we report the cloning and sequencing of numts loci, amplified from human tissue and rho-zero (rho0) cells (control) with primers known to amplify the mitochondrial genome. This paper is the first to fully sequence 46 paralogous nuclear DNA fragments that represent the entire mitochondrial genome. This is a surprisingly small number due primarily to the primer sets used in this study, because prior to this, BLAST searches have suggested that nuclear DNA harbors between 400 to 1,500 paralogous mitochondrial DNA fragments. Our results indicate that multiple numts were amplified simultaneously with the mitochondrial genome and increased the load of pseudogene signal in PCR reactions. Further, the entire mitochondrial genome was represented by multiple copies of paralogous nuclear sequences. CONCLUSION These findings suggest that mitochondrial genome disease-associated biomarkers must be rigorously authenticated to preclude any affiliation with paralogous nuclear pseudogenes. Importantly, the common perception that mitochondrial template "swamps" numts loci precluding detectable amplification, depends on the region of the mitochondrial genome targeted by the PCR reaction and the number of pseudogene loci that may co-amplify. Cloning and relevant sequencing data will facilitate the correct interpretation. This is the first complete, wet-lab characterization of numts that represent the entire mitochondrial genome.
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Affiliation(s)
- Ryan L Parr
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
| | - Jennifer Maki
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
| | - Brian Reguly
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
| | - Gabriel D Dakubo
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
| | - Andrea Aguirre
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
| | - Roy Wittock
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
| | - Kerry Robinson
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
| | - John P Jakupciak
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Robert E Thayer
- Genesis Genomics Inc, 1294 Balmoral Street, Thunder Bay, Ontario, P7B 5Z5, Canada
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Cassandrini D, Calevo MG, Tessa A, Manfredi G, Fattori F, Meschini MC, Carrozzo R, Tonoli E, Pedemonte M, Minetti C, Zara F, Santorelli FM, Bruno C. A new method for analysis of mitochondrial DNA point mutations and assess levels of heteroplasmy. Biochem Biophys Res Commun 2006; 342:387-93. [PMID: 16483543 DOI: 10.1016/j.bbrc.2006.01.152] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Accepted: 01/23/2006] [Indexed: 11/26/2022]
Abstract
Determination of mitochondrial DNA (mtDNA) heteroplasmy for the diagnosis of patients with mitochondrial disorders is a difficult task due to the coexistence of wild-type and mutant genomes. We have developed a new method for genotyping and quantification of heteroplasmic point mutations in mtDNA based on the SNaPshot technology. We compared the data of this method with the widely used "last hot-cycle" PCR-RFLP method by studying 15 patients carrying mtDNA mutations. We showed that SNaPshot is an accurate, reproducible, and sensitive technique for the determination of heteroplasmic mtDNA mutations in different tissues from patients, and it is a promising system to be used in prenatal and postnatal diagnosis of mtDNA-associated disorders.
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Affiliation(s)
- Denise Cassandrini
- Unit of Muscular and Neurodegenerative Diseases, University of Genoa, Genoa, Italy
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Wilding CS, Cadwell K, Tawn EJ, Relton CL, Taylor GA, Chinnery PF, Turnbull DM. Mitochondrial DNA mutations in individuals occupationally exposed to ionizing radiation. Radiat Res 2006; 165:202-7. [PMID: 16435918 DOI: 10.1667/rr3494.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Mutations in a 443-bp amplicon of the hypervariable region HVR1 of the D-loop of mitochondrial DNA (mtDNA) were quantified in DNA extracted from peripheral blood samples of 10 retired radiation workers who had accumulated external radiation doses of >0.9 Sv over the course of their working life and were compared to the levels of mutations in 10 control individuals matched for age and smoking status. The mutation rate in the 10 exposed individuals was 9.92 x 10(-5) mutations/ nucleotide, and for the controls it was 8.65 x 10(-5) mutations/ nucleotide, with a procedural error rate of 2.65 x 10(-5) mutations/nucleotide. No increase in mtDNA mutations due to radiation exposure was detectable (P = 0.640). In contrast, chromosomal translocation frequencies, a validated radiobiological technique for retrospective dosimetric purposes, were significantly elevated in the exposed individuals. This suggests that mutations identified through sequencing of mtDNA in peripheral blood lymphocytes do not represent a promising genetic marker of DNA damage after low-dose or low-dose-rate exposures to ionizing radiation. There was an increase in singleton mutations above that attributable to procedural error in both exposed and control groups that is likely to reflect age-related somatic mutation.
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Affiliation(s)
- Craig S Wilding
- Genetics Department, Westlakes Research Institute, Moor Row, Cumbria, CA24 3JY, United Kingdom.
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17
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Abstract
The mammalian mitochondrial genome encodes for 37 genes which are involved in a broad range of cellular functions. The mitochondrial DNA (mtDNA) molecule is commonly assumed to be inherited through oocyte cytoplasm in a clonal manner, and apparently species-specific mechanisms have evolved to eliminate the contribution of sperm mitochondria after natural fertilization. However, recent evidence for paternal mtDNA inheritance in embryos and offspring questions the general validity of this model, particularly in the context of assisted reproduction and embryo biotechnology. In addition to normal mt DNA haplotype variation, oocytes and spermatozoa show remarkable differences in mtDNA content and may be affected by inherited or acquired mtDNA aberrations. All these parameters have been correlated with gamete quality and reproductive success rates. Nuclear transfer (NT) technology provides experimental models for studying interactions between nuclear and mitochondrial genomes. Recent studies demonstrated (i) a significant effect of mtDNA haplotype or other maternal cytoplasmic factors on the efficiency of NT; (ii) phenotypic differences between transmitochondrial clones pointing to functionally relevant nuclear-cytoplasmic interactions; and (iii) neutral or non-neutral selection of mtDNA haplotypes in heteroplasmic conditions. Mitochondria form a dynamic reticulum, enabling complementation of mitochondrial components and possibly mixing of different mtDNA populations in heteroplasmic individuals. Future directions of research on mtDNA in the context of reproductive biotechnology range from the elimination of adverse effects of artificial heteroplasmy, e.g. created by ooplasm transfer, to engineering of optimized constellations of nuclear and cytoplasmic genes for the production of superior livestock.
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Affiliation(s)
- S Hiendleder
- Institut für Molekulare Tierzucht und Biotechnologie, Genzentrum der Ludwig-Maximilians-Universität München, Germany.
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18
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Lynn S, Borthwick GM, Charnley RM, Walker M, Turnbull DM. Heteroplasmic ratio of the A3243G mitochondrial DNA mutation in single pancreatic beta cells. Diabetologia 2003; 46:296-9. [PMID: 12627331 DOI: 10.1007/s00125-002-1018-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2002] [Accepted: 08/23/2002] [Indexed: 11/27/2022]
Abstract
AIMS/HYPOTHESIS To examine whether there is a high content of mutated mitochondrial DNA in individual pancreatic beta cells from a patient with the A3243G mitochondrial DNA mutation. METHODS Tissues were available from a patient with diabetes and the A3243G mutation including pancreatic tissue. We quantified the amount of mutated mitochondrial DNA in tissue homogenates and single pancreatic beta cells using hot last cycle PCR. RESULTS The percentage ratio of mutated to wild-type mtDNA was high in tissues such as muscle and brain (>60%), but surprisingly low in both pancreatic islets and in individual beta cells from these islets. The islets were smaller in the patient than in control subjects in keeping with a decreased beta-cell mass. CONCLUSIONS/INTERPRETATION These observations suggest that either the beta cells show increased sensitivity to the effects mtDNA mutations on respiratory chain function, and/or cells with a high mutant load are preferentially removed leading to a progressive decrease in the islet beta-cell mass.
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Affiliation(s)
- S Lynn
- Department of Medicine, The Medical School, University of Newcastle upon Tyne, Framlington Place, NE2 4HH Newcastle upon Tyne, United Kingdom
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19
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Taylor RW, Taylor GA, Durham SE, Turnbull DM. The determination of complete human mitochondrial DNA sequences in single cells: implications for the study of somatic mitochondrial DNA point mutations. Nucleic Acids Res 2001; 29:E74-4. [PMID: 11470889 PMCID: PMC55839 DOI: 10.1093/nar/29.15.e74] [Citation(s) in RCA: 135] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Studies of single cells have previously shown intracellular clonal expansion of mitochondrial DNA (mtDNA) mutations to levels that can cause a focal cytochrome c oxidase (COX) defect. Whilst techniques are available to study mtDNA rearrangements at the level of the single cell, recent interest has focused on the possible role of somatic mtDNA point mutations in ageing, neurodegenerative disease and cancer. We have therefore developed a method that permits the reliable determination of the entire mtDNA sequence from single cells without amplifying contaminating, nuclear-embedded pseudogenes. Sequencing and PCR-RFLP analyses of individual COX-negative muscle fibres from a patient with a previously described heteroplasmic COX II (T7587C) mutation indicate that mutant loads as low as 30% can be reliably detected by sequencing. This technique will be particularly useful in identifying the mtDNA mutational spectra in age-related COX-negative cells and will increase our understanding of the pathogenetic mechanisms by which they occur.
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Affiliation(s)
- R W Taylor
- Department of Neurology, The Medical School, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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20
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Abstract
Pseudogenes are commonly encountered during investigation of the genomes of a wide range of life forms. This review concentrates on vertebrate, and in particular mammalian, pseudogenes and describes their origin and subsequent evolution. Consideration is also given to pseudogenes that are transcribed and to the unusual group of genes that exist at the interface between functional genes and non-functional pseudogenes. As the sequences of different genomes are characterised, the recognition and interpretation of pseudogene sequences will become more important and have a greater impact in the field of molecular genetics.
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Affiliation(s)
- A J Mighell
- Molecular Medicine Unit, The University of Leeds, Clinical Sciences Building, St. James's University Hospital, Leeds, UK.
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