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McCormick EM, Lott MT, Dulik MC, Shen L, Attimonelli M, Vitale O, Karaa A, Bai R, Pineda-Alvarez DE, Singh LN, Stanley CM, Wong S, Bhardwaj A, Merkurjev D, Mao R, Sondheimer N, Zhang S, Procaccio V, Wallace DC, Gai X, Falk MJ. Specifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretation. Hum Mutat 2020; 41:2028-2057. [PMID: 32906214 DOI: 10.1002/humu.24107] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 08/20/2020] [Accepted: 08/28/2020] [Indexed: 12/12/2022]
Abstract
Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently, there are insufficient standardized criteria for mtDNA variant assessment, which leads to inconsistencies in clinical variant pathogenicity reporting. An international working group of mtDNA experts was assembled within the Mitochondrial Disease Sequence Data Resource Consortium and obtained Expert Panel status from ClinGen. This group reviewed the 2015 American College of Medical Genetics and Association of Molecular Pathology standards and guidelines that are widely used for clinical interpretation of DNA sequence variants and provided further specifications for additional and specific guidance related to mtDNA variant classification. These Expert Panel consensus specifications allow for consistent consideration of the unique aspects of the mtDNA genome that directly influence variant assessment, including addressing mtDNA genome composition and structure, haplogroups and phylogeny, maternal inheritance, heteroplasmy, and functional analyses unique to mtDNA, as well as specifications for utilization of mtDNA genomic databases and computational algorithms.
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Affiliation(s)
- Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew C Dulik
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Ornella Vitale
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Amel Karaa
- Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christine M Stanley
- Variantyx, Inc, Framingham, Massachusetts, USA.,QNA Diagnostics, Cambridge, Massachusetts, USA
| | | | - Anshu Bhardwaj
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Daria Merkurjev
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Rong Mao
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Neal Sondheimer
- Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Vincent Procaccio
- Department of Biochemistry and Genetics, MitoVasc Institute, UMR CNRS 6015- INSERM U1083, CHU Angers, Angers, France
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA.,Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Marni J Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Martín-Navarro A, Gaudioso-Simón A, Álvarez-Jarreta J, Montoya J, Mayordomo E, Ruiz-Pesini E. Machine learning classifier for identification of damaging missense mutations exclusive to human mitochondrial DNA-encoded polypeptides. BMC Bioinformatics 2017; 18:158. [PMID: 28270093 PMCID: PMC5341421 DOI: 10.1186/s12859-017-1562-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/24/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several methods have been developed to predict the pathogenicity of missense mutations but none has been specifically designed for classification of variants in mtDNA-encoded polypeptides. Moreover, there is not available curated dataset of neutral and damaging mtDNA missense variants to test the accuracy of predictors. Because mtDNA sequencing of patients suffering mitochondrial diseases is revealing many missense mutations, it is needed to prioritize candidate substitutions for further confirmation. Predictors can be useful as screening tools but their performance must be improved. RESULTS We have developed a SVM classifier (Mitoclass.1) specific for mtDNA missense variants. Training and validation of the model was executed with 2,835 mtDNA damaging and neutral amino acid substitutions, previously curated by a set of rigorous pathogenicity criteria with high specificity. Each instance is described by a set of three attributes based on evolutionary conservation in Eukaryota of wildtype and mutant amino acids as well as coevolution and a novel evolutionary analysis of specific substitutions belonging to the same domain of mitochondrial polypeptides. Our classifier has performed better than other web-available tested predictors. We checked performance of three broadly used predictors with the total mutations of our curated dataset. PolyPhen-2 showed the best results for a screening proposal with a good sensitivity. Nevertheless, the number of false positive predictions was too high. Our method has an improved sensitivity and better specificity in relation to PolyPhen-2. We also publish predictions for the complete set of 24,201 possible missense variants in the 13 human mtDNA-encoded polypeptides. CONCLUSIONS Mitoclass.1 allows a better selection of candidate damaging missense variants from mtDNA. A careful search of discriminatory attributes and a training step based on a curated dataset of amino acid substitutions belonging exclusively to human mtDNA genes allows an improved performance. Mitoclass.1 accuracy could be improved in the future when more mtDNA missense substitutions will be available for updating the attributes and retraining the model.
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Affiliation(s)
- Antonio Martín-Navarro
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet 177, Zaragoza, 50013, Spain.,Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, C/ María de Luna 1, Zaragoza, 50018, Spain
| | - Andrés Gaudioso-Simón
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet 177, Zaragoza, 50013, Spain
| | - Jorge Álvarez-Jarreta
- Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, C/ María de Luna 1, Zaragoza, 50018, Spain.,Instituto de Investigación en Ingeniería de Aragón (I3A), Universidad de Zaragoza, Zaragoza, Spain
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet 177, Zaragoza, 50013, Spain.,Instituto de Investigación Sanitaria de Aragón (IISA), Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Universidad de Zaragoza, Zaragoza, Spain
| | - Elvira Mayordomo
- Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, C/ María de Luna 1, Zaragoza, 50018, Spain. .,Instituto de Investigación en Ingeniería de Aragón (I3A), Universidad de Zaragoza, Zaragoza, Spain.
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet 177, Zaragoza, 50013, Spain. .,Instituto de Investigación Sanitaria de Aragón (IISA), Universidad de Zaragoza, Zaragoza, Spain. .,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Universidad de Zaragoza, Zaragoza, Spain. .,Fundación ARAID, Universidad de Zaragoza, Zaragoza, Spain.
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3
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Hagen CM, Aidt FH, Havndrup O, Hedley PL, Jensen MK, Kanters JK, Pham TT, Bundgaard H, Christiansen M. Private mitochondrial DNA variants in danish patients with hypertrophic cardiomyopathy. PLoS One 2015; 10:e0124540. [PMID: 25923817 PMCID: PMC4414448 DOI: 10.1371/journal.pone.0124540] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/19/2015] [Indexed: 02/02/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a genetic cardiac disease primarily caused by mutations in genes coding for sarcomeric proteins. A molecular-genetic etiology can be established in ~60% of cases. Evolutionarily conserved mitochondrial DNA (mtDNA) haplogroups are susceptibility factors for HCM. Several polymorphic mtDNA variants are associated with a variety of late-onset degenerative diseases and affect mitochondrial function. We examined the role of private, non-haplogroup associated, mitochondrial variants in the etiology of HCM. In 87 Danish HCM patients, full mtDNA sequencing revealed 446 variants. After elimination of 312 (69.9%) non-coding and synonymous variants, a further 109 (24.4%) with a global prevalence > 0.1%, three (0.7%) haplogroup associated and 19 (2.0%) variants with a low predicted in silico likelihood of pathogenicity, three variants: MT-TC: m.5772G>A, MT-TF: m.644A>G, and MT-CYB: m.15024G>A, p.C93Y remained. A detailed analysis of these variants indicated that none of them are likely to cause HCM. In conclusion, private mtDNA mutations are frequent, but they are rarely, if ever, associated with HCM.
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Affiliation(s)
- Christian M. Hagen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frederik H. Aidt
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Ole Havndrup
- Department of Cardiology, Roskilde Hospital, Roskilde, Denmark
| | - Paula L. Hedley
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Morten K. Jensen
- Department of Medicine B, The Heart Center, Rigshospitalet, Copenhagen, Denmark
| | - Jørgen K. Kanters
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tam T. Pham
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Henning Bundgaard
- Department of Medicine B, The Heart Center, Rigshospitalet, Copenhagen, Denmark
| | - Michael Christiansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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4
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Blakely EL, Yarham JW, Alston CL, Craig K, Poulton J, Brierley C, Park SM, Dean A, Xuereb JH, Anderson KN, Compston A, Allen C, Sharif S, Enevoldson P, Wilson M, Hammans SR, Turnbull DM, McFarland R, Taylor RW. Pathogenic mitochondrial tRNA point mutations: nine novel mutations affirm their importance as a cause of mitochondrial disease. Hum Mutat 2014; 34:1260-8. [PMID: 23696415 PMCID: PMC3884772 DOI: 10.1002/humu.22358] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/10/2013] [Indexed: 11/26/2022]
Abstract
Mutations in the mitochondrial genome, and in particular the mt-tRNAs, are an important cause of human disease. Accurate classification of the pathogenicity of novel variants is vital to allow accurate genetic counseling for patients and their families. The use of weighted criteria based on functional studies—outlined in a validated pathogenicity scoring system—is therefore invaluable in determining whether novel or rare mt-tRNA variants are pathogenic. Here, we describe the identification of nine novel mt-tRNA variants in nine families, in which the probands presented with a diverse range of clinical phenotypes including mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes, isolated progressive external ophthalmoplegia, epilepsy, deafness and diabetes. Each of the variants identified (m.4289T>C, MT-TI; m.5541C>T, MT-TW; m.5690A>G, MT-TN; m.7451A>T, MT-TS1; m.7554G>A, MT-TD; m.8304G>A, MT-TK; m.12206C>T, MT-TH; m.12317T>C, MT-TL2; m.16023G>A, MT-TP) was present in a different tRNA, with evidence in support of pathogenicity, and where possible, details of mutation transmission documented. Through the application of the pathogenicity scoring system, we have classified six of these variants as “definitely pathogenic” mutations (m.5541C>T, m.5690A>G, m.7451A>T, m.12206C>T, m.12317T>C, and m.16023G>A), whereas the remaining three currently lack sufficient evidence and are therefore classed as ‘possibly pathogenic’ (m.4289T>C, m.7554G>A, and m.8304G>A).
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Affiliation(s)
- Emma L Blakely
- Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, UK
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5
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Tang S, Wang J, Zhang VW, Li FY, Landsverk M, Cui H, Truong CK, Wang G, Chen LC, Graham B, Scaglia F, Schmitt ES, Craigen WJ, Wong LJC. Transition to next generation analysis of the whole mitochondrial genome: a summary of molecular defects. Hum Mutat 2013; 34:882-93. [PMID: 23463613 DOI: 10.1002/humu.22307] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 02/15/2013] [Indexed: 01/06/2023]
Abstract
The diagnosis of mitochondrial disorders is challenging because of the clinical variability and genetic heterogeneity. Conventional analysis of the mitochondrial genome often starts with a screening panel for common mitochondrial DNA (mtDNA) point mutations and large deletions (mtScreen). If negative, it has been traditionally followed by Sanger sequencing of the entire mitochondrial genome (mtWGS). The recently developed "Next-Generation Sequencing" (NGS) technology offers a robust high-throughput platform for comprehensive mtDNA analysis. Here, we summarize the results of the past 6 years of clinical practice using the mtScreen and mtWGS tests on 9,261 and 2,851 unrelated patients, respectively. A total of 344 patients (3.7%) had mutations identified by mtScreen and 99 (3.5%) had mtDNA mutations identified by mtWGS. The combinatorial analyses of mtDNA and POLG revealed a diagnostic yield of 6.7% in patients with suspected mitochondrial disorders but no recognizable syndromes. From the initial mtWGS-NGS cohort of 391 patients, 21 mutation-positive cases (5.4%) have been identified. The mtWGS-NGS provides a one-step approach to detect common and uncommon point mutations, as well as deletions. Additionally, NGS provides accurate, sensitive heteroplasmy measurement, and the ability to map deletion breakpoints. A new era of more efficient molecular diagnosis of mtDNA mutations has arrived.
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Affiliation(s)
- Sha Tang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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6
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Sobrido MJ, Cacheiro P, Carracedo A, Bertram L. Databases for neurogenetics: introduction, overview, and challenges. Hum Mutat 2012; 33:1311-4. [PMID: 22890789 DOI: 10.1002/humu.22164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The importance for research and clinical utility of mutation databases, as well as the issues and difficulties entailed in their construction, is discussed within the Human Variome Project. While general principles and standards can apply to most human diseases, some specific questions arise when dealing with the nature of genetic neurological disorders. So far, publically accessible mutation databases exist for only about half of the genes causing neurogenetic disorders; and a considerable work is clearly still needed to optimize their content. The current landscape, main challenges, some potential solutions, and future perspectives on genetic databases for disorders of the nervous system are reviewed in this special issue of Human Mutation on neurogenetics.
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Affiliation(s)
- María-Jesús Sobrido
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Santiago de Compostela, Galicia, Spain.
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7
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Bates MGD, Bourke JP, Giordano C, d'Amati G, Turnbull DM, Taylor RW. Cardiac involvement in mitochondrial DNA disease: clinical spectrum, diagnosis, and management. Eur Heart J 2012; 33:3023-33. [PMID: 22936362 PMCID: PMC3530901 DOI: 10.1093/eurheartj/ehs275] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 07/16/2012] [Accepted: 08/07/2012] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial disease refers to a heterogenous group of genetic disorders that result from dysfunction of the final common pathway of energy metabolism. Mitochondrial DNA mutations affect key components of the respiratory chain and account for the majority of mitochondrial disease in adults. Owing to critical dependence of the heart on oxidative metabolism, cardiac involvement in mitochondrial disease is common and may occur as the principal clinical manifestation or part of multisystem disease. Recent advances in our understanding of the clinical spectrum and genetic aetiology of cardiac involvement in mitochondrial DNA disease have important implications for cardiologists in terms of the investigation and multi-disciplinary management of patients.
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Affiliation(s)
- Matthew G. D. Bates
- Wellcome Trust Centre for Mitochondrial
Research, Institute for Ageing and Health, The Medical School,
Newcastle University, Newcastle upon Tyne NE2 4HH,
UK
- Newcastle upon Tyne Hospitals NHS Foundation
Trust, Newcastle upon Tyne NE7 7DN,
UK
| | - John P. Bourke
- Newcastle upon Tyne Hospitals NHS Foundation
Trust, Newcastle upon Tyne NE7 7DN,
UK
| | - Carla Giordano
- Department of Radiology, Oncology and
Pathology, Sapienza University,
Rome, Italy
| | - Giulia d'Amati
- Department of Radiology, Oncology and
Pathology, Sapienza University,
Rome, Italy
| | - Douglass M. Turnbull
- Wellcome Trust Centre for Mitochondrial
Research, Institute for Ageing and Health, The Medical School,
Newcastle University, Newcastle upon Tyne NE2 4HH,
UK
- Newcastle upon Tyne Hospitals NHS Foundation
Trust, Newcastle upon Tyne NE7 7DN,
UK
| | - Robert W. Taylor
- Wellcome Trust Centre for Mitochondrial
Research, Institute for Ageing and Health, The Medical School,
Newcastle University, Newcastle upon Tyne NE2 4HH,
UK
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