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Zou W, Zong K, Zhang Z, Shen L, Wang X, Su X, Wang X, Yin T, Liang C, Liu Y, Liang D, Hu C, Cao Y, Ji D. Novel economical, accurate, sensitive, single-cell analytical method for mitochondrial DNA quantification in mtDNA mutation carriers. J Assist Reprod Genet 2023; 40:2197-2209. [PMID: 37462790 PMCID: PMC10440311 DOI: 10.1007/s10815-023-02878-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/20/2023] [Indexed: 08/22/2023] Open
Abstract
PURPOSE Although a variety of analytical methods have been developed to detect mitochondrial DNA (mtDNA) heteroplasmy, there are special requirements of mtDNA heteroplasmy quantification for women carrying mtDNA mutations receiving the preimplantation genetic diagnosis (PGD) and prenatal diagnosis (PD) in clinic. These special requirements include various sample types, large sample number, long-term follow-up, and the need for detection of single-cell from biopsied embryos. Therefore, developing an economical, accurate, high-sensitive, and single-cell analytical method for mtDNA heteroplasmy is necessary. METHODS In this study, we developed the Sanger sequencing combined droplet digital polymerase chain reaction (ddPCR) method for mtDNA quantification and compared the results to next-generation sequencing (NGS). A total of seventeen families with twelve mtDNA mutations were recruited in this study. RESULTS The results showed that both Sanger sequencing and ddPCR could be used to analyze the mtDNA heteroplasmy in single-cell samples. There was no statistically significant difference in heteroplasmy levels in common samples with high heteroplasmy (≥ 5%), low heteroplasmy (< 5%), and single-cell samples, either between Sanger sequencing and NGS methods, or between ddPCR and NGS methods (P > 0.05). However, Sanger sequencing was unable to detect extremely low heteroplasmy accurately. But even in samples with extremely low heteroplasmy (0.40% and 0.92%), ddPCR was always able to quantify them. Compared to NGS, Sanger sequencing combined ddPCR analytical methods greatly reduced the cost of sequencing. CONCLUSIONS In conclusion, this study successfully established an economical, accurate, sensitive, single-cell analytical method based on the Sanger sequencing combined ddPCR methods for mtDNA heteroplasmy quantification in a clinical setting.
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Affiliation(s)
- Weiwei Zou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Kai Zong
- Technical Center of Hefei Customs District, No. 329 Tunxi Road, Hefei, 230022, Anhui, China
| | - Zhikang Zhang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Lingchao Shen
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Xiaolei Wang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Xun Su
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Xin Wang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Tao Yin
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Chunmei Liang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Yajing Liu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Dan Liang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Chao Hu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China.
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China.
| | - Dongmei Ji
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China.
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China.
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2
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Jurkute N, Cancellieri F, Pohl L, Li CHZ, Heaton RA, Reurink J, Bellingham J, Quinodoz M, Yioti G, Stefaniotou M, Weener M, Zuleger T, Haack TB, Stingl K, Hoyng CB, Mahroo OA, Hargreaves I, Raymond FL, Michaelides M, Rivolta C, Kohl S, Roosing S, Webster AR, Arno G. Biallelic variants in coenzyme Q10 biosynthesis pathway genes cause a retinitis pigmentosa phenotype. NPJ Genom Med 2022; 7:60. [PMID: 36266294 PMCID: PMC9581764 DOI: 10.1038/s41525-022-00330-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/29/2022] [Indexed: 11/21/2022] Open
Abstract
The aim of this study was to investigate coenzyme Q10 (CoQ10) biosynthesis pathway defects in inherited retinal dystrophy. Individuals affected by inherited retinal dystrophy (IRD) underwent exome or genome sequencing for molecular diagnosis of their condition. Following negative IRD gene panel analysis, patients carrying biallelic variants in CoQ10 biosynthesis pathway genes were identified. Clinical data were collected from the medical records. Haplotypes harbouring the same missense variant were characterised from family genome sequencing (GS) data and direct Sanger sequencing. Candidate splice variants were characterised using Oxford Nanopore Technologies single molecule sequencing. The CoQ10 status of the human plasma was determined in some of the study patients. 13 individuals from 12 unrelated families harboured candidate pathogenic genotypes in the genes: PDSS1, COQ2, COQ4 and COQ5. The PDSS1 variant c.589 A > G was identified in three affected individuals from three unrelated families on a possible ancestral haplotype. Three variants (PDSS1 c.468-25 A > G, PDSS1 c.722-2 A > G, COQ5 c.682-7 T > G) were shown to lead to cryptic splicing. 6 affected individuals were diagnosed with non-syndromic retinitis pigmentosa and 7 had additional clinical findings. This study provides evidence of CoQ10 biosynthesis pathway gene defects leading to non-syndromic retinitis pigmentosa in some cases. Intronic variants outside of the canonical splice-sites represent an important cause of disease. RT-PCR nanopore sequencing is effective in characterising these splice defects.
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Affiliation(s)
- Neringa Jurkute
- Moorfields Eye Hospital NHS Foundation Trust, London, UK. .,Institute of Ophthalmology, University College London, London, UK.
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Lisa Pohl
- University Eye Hospital, Centre for Ophthalmology, University Hospital Tübingen, Tübingen, Germany
| | - Catherina H Z Li
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Robert A Heaton
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores, Liverpool, UK
| | - Janine Reurink
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - James Bellingham
- Institute of Ophthalmology, University College London, London, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Georgia Yioti
- University of Ioannina Medical School, Ioannina, Greece
| | | | | | - Theresia Zuleger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Katarina Stingl
- University Eye Hospital, Centre for Ophthalmology, University Hospital Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | | | - Carel B Hoyng
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Omar A Mahroo
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Iain Hargreaves
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores, Liverpool, UK
| | - F Lucy Raymond
- NIHR BioResource-Rare Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Michel Michaelides
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Susanne Roosing
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andrew R Webster
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Gavin Arno
- Moorfields Eye Hospital NHS Foundation Trust, London, UK. .,Institute of Ophthalmology, University College London, London, UK. .,North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children, London, UK.
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3
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Use of Next-Generation Sequencing for Identifying Mitochondrial Disorders. Curr Issues Mol Biol 2022; 44:1127-1148. [PMID: 35723297 PMCID: PMC8947152 DOI: 10.3390/cimb44030074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 12/06/2022] Open
Abstract
Mitochondria are major contributors to ATP synthesis, generating more than 90% of the total cellular energy production through oxidative phosphorylation (OXPHOS): metabolite oxidation, such as the β-oxidation of fatty acids, and the Krebs’s cycle. OXPHOS inadequacy due to large genetic lesions in mitochondrial as well as nuclear genes and homo- or heteroplasmic point mutations in mitochondrially encoded genes is a characteristic of heterogeneous, maternally inherited genetic disorders known as mitochondrial disorders that affect multisystemic tissues and organs with high energy requirements, resulting in various signs and symptoms. Several traditional diagnostic approaches, including magnetic resonance imaging of the brain, cardiac testing, biochemical screening, variable heteroplasmy genetic testing, identifying clinical features, and skeletal muscle biopsies, are associated with increased risks, high costs, a high degree of false-positive or false-negative results, or a lack of precision, which limits their diagnostic abilities for mitochondrial disorders. Variable heteroplasmy levels, mtDNA depletion, and the identification of pathogenic variants can be detected through genetic sequencing, including the gold standard Sanger sequencing. However, sequencing can be time consuming, and Sanger sequencing can result in the missed recognition of larger structural variations such as CNVs or copy-number variations. Although each sequencing method has its own limitations, genetic sequencing can be an alternative to traditional diagnostic methods. The ever-growing roster of possible mutations has led to the development of next-generation sequencing (NGS). The enhancement of NGS methods can offer a precise diagnosis of the mitochondrial disorder within a short period at a reasonable expense for both research and clinical applications.
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4
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García-Olivares V, Muñoz-Barrera A, Lorenzo-Salazar JM, Zaragoza-Trello C, Rubio-Rodríguez LA, Díaz-de Usera A, Jáspez D, Iñigo-Campos A, González-Montelongo R, Flores C. A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data. Sci Rep 2021; 11:20510. [PMID: 34654896 PMCID: PMC8519921 DOI: 10.1038/s41598-021-99895-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/28/2021] [Indexed: 12/18/2022] Open
Abstract
The mitochondrial genome (mtDNA) is of interest for a range of fields including evolutionary, forensic, and medical genetics. Human mitogenomes can be classified into evolutionary related haplogroups that provide ancestral information and pedigree relationships. Because of this and the advent of high-throughput sequencing (HTS) technology, there is a diversity of bioinformatic tools for haplogroup classification. We present a benchmarking of the 11 most salient tools for human mtDNA classification using empirical whole-genome (WGS) and whole-exome (WES) short-read sequencing data from 36 unrelated donors. We also assessed the best performing tool in third-generation long noisy read WGS data obtained with nanopore technology for a subset of the donors. We found that, for short-read WGS, most of the tools exhibit high accuracy for haplogroup classification irrespective of the input file used for the analysis. However, for short-read WES, Haplocheck and MixEmt were the most accurate tools. Based on the performance shown for WGS and WES, and the accompanying qualitative assessment, Haplocheck stands out as the most complete tool. For third-generation HTS data, we also showed that Haplocheck was able to accurately retrieve mtDNA haplogroups for all samples assessed, although only after following assembly-based approaches (either based on a referenced-based assembly or a hybrid de novo assembly). Taken together, our results provide guidance for researchers to select the most suitable tool to conduct the mtDNA analyses from HTS data.
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Affiliation(s)
- Víctor García-Olivares
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - José M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | | | - Luis A Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Antonio Iñigo-Campos
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
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5
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Verma RP. Evaluation and Risk Assessment of Congenital Anomalies in Neonates. CHILDREN (BASEL, SWITZERLAND) 2021; 8:862. [PMID: 34682127 PMCID: PMC8534483 DOI: 10.3390/children8100862] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/15/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022]
Abstract
Congenital anomalies (CA) are a large heterogeneous group of disorders of abnormal morphogenesis or biochemistry which present at birth and carry widely variable implications for morbidity and mortality. They are the leading cause of infant mortality in the USA, with an incidence of 3-4% of all births. CA are the fourth leading cause of neonatal mortality worldwide, with an estimated 295,000 deaths annually. The enormous variability in the clinical presentation in terms of severity, time of occurrence, course, complications, management, and outcomes makes the evaluation of CA complicated, highly specific, and individualized. The anomalies can impart tremendous physical, social, and emotional distress on the patient with massive emotional, social, financial, and medical implications for the family and society. The diagnosis may remain elusive despite rigorous, elaborate, and extensive investigations in many cases. While the enormous strides in genetic testing and gene modification therapy have an encouraging impact on the diagnosis and treatment, the risk assessment of recurrence in the family and population of CA remains obscure in most cases due to the lack of information and referable evidence.
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Affiliation(s)
- Rita P Verma
- Department of Pediatrics, Division of Neonatology, Nassau University Medical Center, East Meadow, NY 11554, USA
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6
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Mazzaccara C, Mirra B, Barretta F, Caiazza M, Lombardo B, Scudiero O, Tinto N, Limongelli G, Frisso G. Molecular Epidemiology of Mitochondrial Cardiomyopathy: A Search Among Mitochondrial and Nuclear Genes. Int J Mol Sci 2021; 22:ijms22115742. [PMID: 34072184 PMCID: PMC8197938 DOI: 10.3390/ijms22115742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/18/2021] [Accepted: 05/22/2021] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial Cardiomyopathy (MCM) is a common manifestation of multi-organ Mitochondrial Diseases (MDs), occasionally present in non-syndromic cases. Diagnosis of MCM is complex because of wide clinical and genetic heterogeneity and requires medical, laboratory, and neuroimaging investigations. Currently, the molecular screening for MCM is fundamental part of MDs management and allows achieving the definitive diagnosis. In this article, we review the current genetic knowledge associated with MDs, focusing on diagnosis of MCM and MDs showing cardiac involvement. We searched for publications on mitochondrial and nuclear genes involved in MCM, mainly focusing on genetic screening based on targeted gene panels for the molecular diagnosis of the MCM, by using Next Generation Sequencing. Here we report twelve case reports, four case-control studies, eleven retrospective studies, and two prospective studies, for a total of twenty-nine papers concerning the evaluation of cardiac manifestations in mitochondrial diseases. From the analysis of published causal mutations, we identified 130 genes to be associated with mitochondrial heart diseases. A large proportion of these genes (34.3%) encode for key proteins involved in the oxidative phosphorylation system (OXPHOS), either as directly OXPHOS subunits (22.8%), and as OXPHOS assembly factors (11.5%). Mutations in several mitochondrial tRNA genes have been also reported in multi-organ or isolated MCM (15.3%). This review highlights the main disease-genes, identified by extensive genetic analysis, which could be included as target genes in next generation panels for the molecular diagnosis of patients with clinical suspect of mitochondrial cardiomyopathies.
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Affiliation(s)
- Cristina Mazzaccara
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
- Correspondence: ; Tel.: +39-0817-462-422
| | - Bruno Mirra
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Ferdinando Barretta
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Martina Caiazza
- Monaldi Hospital, AO Colli, 80131 Naples, Italy; (M.C.); (G.L.)
- Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, 80134 Naples, Italy
| | - Barbara Lombardo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Olga Scudiero
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Nadia Tinto
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Giuseppe Limongelli
- Monaldi Hospital, AO Colli, 80131 Naples, Italy; (M.C.); (G.L.)
- Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, 80134 Naples, Italy
| | - Giulia Frisso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
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7
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Barp A, Mosca L, Sansone VA. Facilitations and Hurdles of Genetic Testing in Neuromuscular Disorders. Diagnostics (Basel) 2021; 11:diagnostics11040701. [PMID: 33919863 PMCID: PMC8070835 DOI: 10.3390/diagnostics11040701] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Neuromuscular disorders (NMDs) comprise a heterogeneous group of disorders that affect about one in every thousand individuals worldwide. The vast majority of NMDs has a genetic cause, with about 600 genes already identified. Application of genetic testing in NMDs can be useful for several reasons: correct diagnostic definition of a proband, extensive familial counselling to identify subjects at risk, and prenatal diagnosis to prevent the recurrence of the disease; furthermore, identification of specific genetic mutations still remains mandatory in some cases for clinical trial enrollment where new gene therapies are now approaching. Even though genetic analysis is catching on in the neuromuscular field, pitfalls and hurdles still remain and they should be taken into account by clinicians, as for example the use of next generation sequencing (NGS) where many single nucleotide variants of “unknown significance” can emerge, complicating the correct interpretation of genotype-phenotype relationship. Finally, when all efforts in terms of molecular analysis have been carried on, a portion of patients affected by NMDs still remain “not genetically defined”. In the present review we analyze the evolution of genetic techniques, from Sanger sequencing to NGS, and we discuss “facilitations and hurdles” of genetic testing which must always be balanced by clinicians, in order to ensure a correct diagnostic definition, but taking always into account the benefit that the patient could obtain especially in terms of “therapeutic offer”.
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Affiliation(s)
- Andrea Barp
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy;
- Correspondence:
| | - Lorena Mosca
- Medical Genetics Unit, ASST Grande Ospedale Metropolitano Niguarda, Piazza Ospedale Maggiore 3, 20162 Milano, Italy;
| | - Valeria Ada Sansone
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy;
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8
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Abstract
Neuromuscular disorders (NMDs) comprise a heterogeneous group of disorders that affect about one in every thousand individuals worldwide. The vast majority of NMDs has a genetic cause, with about 600 genes already identified. Application of genetic testing in NMDs can be useful for several reasons: correct diagnostic definition of a proband, extensive familial counselling to identify subjects at risk, and prenatal diagnosis to prevent the recurrence of the disease; furthermore, identification of specific genetic mutations still remains mandatory in some cases for clinical trial enrollment where new gene therapies are now approaching. Even though genetic analysis is catching on in the neuromuscular field, pitfalls and hurdles still remain and they should be taken into account by clinicians, as for example the use of next generation sequencing (NGS) where many single nucleotide variants of "unknown significance" can emerge, complicating the correct interpretation of genotype-phenotype relationship. Finally, when all efforts in terms of molecular analysis have been carried on, a portion of patients affected by NMDs still remain "not genetically defined". In the present review we analyze the evolution of genetic techniques, from Sanger sequencing to NGS, and we discuss "facilitations and hurdles" of genetic testing which must always be balanced by clinicians, in order to ensure a correct diagnostic definition, but taking always into account the benefit that the patient could obtain especially in terms of "therapeutic offer".
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Affiliation(s)
- Andrea Barp
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy
| | - Lorena Mosca
- Medical Genetics Unit, ASST Grande Ospedale Metropolitano Niguarda, Piazza Ospedale Maggiore 3, 20162 Milano, Italy
| | - Valeria Ada Sansone
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy
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9
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Gusic M, Prokisch H. Genetic basis of mitochondrial diseases. FEBS Lett 2021; 595:1132-1158. [PMID: 33655490 DOI: 10.1002/1873-3468.14068] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/13/2022]
Abstract
Mitochondrial disorders are monogenic disorders characterized by a defect in oxidative phosphorylation and caused by pathogenic variants in one of over 340 different genes. The implementation of whole-exome sequencing has led to a revolution in their diagnosis, duplicated the number of associated disease genes, and significantly increased the diagnosed fraction. However, the genetic etiology of a substantial fraction of patients exhibiting mitochondrial disorders remains unknown, highlighting limitations in variant detection and interpretation, which calls for improved computational and DNA sequencing methods, as well as the addition of OMICS tools. More intriguingly, this also suggests that some pathogenic variants lie outside of the protein-coding genes and that the mechanisms beyond the Mendelian inheritance and the mtDNA are of relevance. This review covers the current status of the genetic basis of mitochondrial diseases, discusses current challenges and perspectives, and explores the contribution of factors beyond the protein-coding regions and monogenic inheritance in the expansion of the genetic spectrum of disease.
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Affiliation(s)
- Mirjana Gusic
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Germany
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Germany
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10
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Next-generation Sequencing in Bone Marrow Failure Syndromes and Isolated Cytopenias: Experience of the Spanish Network on Bone Marrow Failure Syndromes. Hemasphere 2021; 5:e539. [PMID: 33718801 PMCID: PMC7951136 DOI: 10.1097/hs9.0000000000000539] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/11/2021] [Indexed: 11/26/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFSs) are a group of congenital rare diseases characterized by bone marrow failure, congenital anomalies, high genetic heterogeneity, and predisposition to cancer. Appropriate treatment and cancer surveillance ideally depend on the identification of the mutated gene. A next-generation sequencing (NGS) panel of genes could be 1 initial genetic screening test to be carried out in a comprehensive study of IBMFSs, allowing molecular detection in affected patients. We designed 2 NGS panels of IBMFS genes: version 1 included 129 genes and version 2 involved 145 genes. The cohort included a total of 204 patients with suspected IBMFSs without molecular diagnosis. Capture-based targeted sequencing covered > 99% of the target regions of 145 genes, with more than 20 independent reads. No differences were seen between the 2 versions of the panel. The NGS tool allowed a total of 91 patients to be diagnosed, with an overall molecular diagnostic rate of 44%. Among the 167 patients with classified IBMFSs, 81 patients (48%) were diagnosed. Unclassified IBMFSs involved a total of 37 patients, of whom 9 patients (24%) were diagnosed. The preexisting diagnosis of 6 clinically classified patients (6%) was amended, implying a change of therapy for some of them. Our NGS IBMFS gene panel assay is a useful tool in the molecular diagnosis of IBMFSs and a reasonable option as the first tier genetic test in these disorders.
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11
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Levy MA, Kerkhof J, Belmonte FR, Kaufman BA, Bhai P, Brady L, Bursztyn LLCD, Tarnopolsky M, Rupar T, Sadikovic B. Validation and clinical performance of a combined nuclear-mitochondrial next-generation sequencing and copy number variant analysis panel in a Canadian population. Am J Med Genet A 2020; 185:486-499. [PMID: 33300680 DOI: 10.1002/ajmg.a.61998] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/17/2022]
Abstract
Diagnosing mitochondrial disorders is a challenge due to the heterogeneous clinical presentation and large number of associated genes. A custom next generation sequencing (NGS) panel was developed incorporating the full mitochondrial genome (mtDNA) plus 19 nuclear genes involved in structural mitochondrial defects and mtDNA maintenance. This assay is capable of simultaneously detecting small gene sequence variations and larger copy number variants (CNVs) in both the nuclear and mitochondrial components along with heteroplasmy detection down to 5%. We describe technical validations of this panel and its implementation for clinical testing in a Canadian reference laboratory, and report its clinical performance in the initial 950 patients tested. Using this assay, we demonstrate a diagnostic yield of 18.1% of patients with known pathogenic variants. In addition to the common 5 kb mtDNA deletion, we describe significant contribution of pathogenic CNVs in both the mitochondrial genome and nuclear genes in this patient population.
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Affiliation(s)
- Michael A Levy
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Frances R Belmonte
- Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Brett A Kaufman
- Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Lauren Brady
- Division of Neuromuscular and Neurometabolic Disease, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | - Mark Tarnopolsky
- Division of Neuromuscular and Neurometabolic Disease, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Tony Rupar
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.,Departments of Biochemistry and Paediatrics, Schulich School of Medicine & Dentistry, Western University, and Biochemical Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
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12
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Abu Diab A, AlTalbishi A, Rosin B, Kanaan M, Kamal L, Swaroop A, Chowers I, Banin E, Sharon D, Khateb S. The combination of whole-exome sequencing and clinical analysis allows better diagnosis of rare syndromic retinal dystrophies. Acta Ophthalmol 2019; 97:e877-e886. [PMID: 30925032 DOI: 10.1111/aos.14095] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/03/2019] [Indexed: 01/05/2023]
Abstract
PURPOSE To identify the accurate clinical diagnosis of rare syndromic inherited retinal diseases (IRDs) based on the combination of clinical and genetic analyses. METHODS Four unrelated families with various autosomal recessive syndromic inherited retinal diseases were genetically investigated using whole-exome sequencing (WES). RESULTS Two affected subjects in family MOL0760 presented with a distinctive combination of short stature, developmental delay, congenital mental retardation, microcephaly, facial dysmorphism and retinitis pigmentosa (RP). Subjects were clinically diagnosed with suspected Kabuki syndrome. WES revealed a homozygous nonsense mutation (c.5492dup, p.Asn1831Lysfs*8) in VPS13B that is known to cause Cohen syndrome. The index case of family MOL1514 presented with both RP and liver dysfunction, suspected initially to be related. WES identified a homozygous frameshift mutation (c.1787_1788del, p.His596Argfs*47) in AGBL5, associated with nonsyndromic RP. The MOL1592 family included three affected subjects with crystalline retinopathy, skin ichthyosis, short stature and congenital adrenal hypoplasia, and were found to harbour a homozygous nonsense mutation (c.682C>T, p.Arg228Cys) in ALDH3A2, reported to cause Sjögren-Larsson syndrome (SLS). In the fourth family, SJ002, two siblings presented with hypotony, psychomotor delay, dysmorphic facial features, pathologic myopia, progressive external ophthalmoplegia and diffuse retinal atrophy. Probands were suspected to have atypical Kearns-Sayre syndrome, but were diagnosed with combined oxidative phosphorylation deficiency-20 due to a novel suspected missense variant (c.1691C>T, p.Ala564Val) in VARS2. CONCLUSION Our findings emphasize the important complement of WES and thorough clinical investigation in establishing precise clinical diagnosis. This approach constitutes the basis for personalized medicine in rare IRDs.
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Affiliation(s)
- Alaa Abu Diab
- Department of Ophthalmology Hadassah‐Hebrew University Medical Center Jerusalem Israel
| | | | - Boris Rosin
- Department of Ophthalmology Hadassah‐Hebrew University Medical Center Jerusalem Israel
| | - Moien Kanaan
- Hereditary Research Lab Bethlehem University Jerusalem Israel
| | - Lara Kamal
- Hereditary Research Lab Bethlehem University Jerusalem Israel
| | - Anand Swaroop
- Neurobiology‐Neurodegeneration & Repair Laboratory National Eye Institute National Institutes of Health Bethesda Maryland USA
| | - Itay Chowers
- Department of Ophthalmology Hadassah‐Hebrew University Medical Center Jerusalem Israel
| | - Eyal Banin
- Department of Ophthalmology Hadassah‐Hebrew University Medical Center Jerusalem Israel
| | - Dror Sharon
- Department of Ophthalmology Hadassah‐Hebrew University Medical Center Jerusalem Israel
| | - Samer Khateb
- Department of Ophthalmology Hadassah‐Hebrew University Medical Center Jerusalem Israel
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13
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Garret P, Bris C, Procaccio V, Amati-Bonneau P, Vabres P, Houcinat N, Tisserant E, Feillet F, Bruel AL, Quéré V, Philippe C, Sorlin A, Tran Mau-Them F, Vitobello A, Costa JM, Boughalem A, Trost D, Faivre L, Thauvin-Robinet C, Duffourd Y. Deciphering exome sequencing data: Bringing mitochondrial DNA variants to light. Hum Mutat 2019; 40:2430-2443. [PMID: 31379041 DOI: 10.1002/humu.23885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 06/27/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022]
Abstract
The expanding use of exome sequencing (ES) in diagnosis generates a huge amount of data, including untargeted mitochondrial DNA (mtDNA) sequences. We developed a strategy to deeply study ES data, focusing on the mtDNA genome on a large unspecific cohort to increase diagnostic yield. A targeted bioinformatics pipeline assembled mitochondrial genome from ES data to detect pathogenic mtDNA variants in parallel with the "in-house" nuclear exome pipeline. mtDNA data coming from off-target sequences (indirect sequencing) were extracted from the BAM files in 928 individuals with developmental and/or neurological anomalies. The mtDNA variants were filtered out based on database information, cohort frequencies, haplogroups and protein consequences. Two homoplasmic pathogenic variants (m.9035T>C and m.11778G>A) were identified in 2 out of 928 unrelated individuals (0.2%): the m.9035T>C (MT-ATP6) variant in a female with ataxia and the m.11778G>A (MT-ND4) variant in a male with a complex mosaic disorder and a severe ophthalmological phenotype, uncovering undiagnosed Leber's hereditary optic neuropathy (LHON). Seven secondary findings were also found, predisposing to deafness or LHON, in 7 out of 928 individuals (0.75%). This study demonstrates the usefulness of including a targeted strategy in ES pipeline to detect mtDNA variants, improving results in diagnosis and research, without resampling patients and performing targeted mtDNA strategies.
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Affiliation(s)
- Philippine Garret
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Laboratoire CERBA, Saint-Ouen-l'Aumône, France
| | - Céline Bris
- Institut MITOVASC, UMR CNRS 6015-INSERM1083, University of Angers, Angers, France.,Centre de Référence maladies mitochondriales, CHU Angers, Angers, France
| | - Vincent Procaccio
- Institut MITOVASC, UMR CNRS 6015-INSERM1083, University of Angers, Angers, France.,Centre de Référence maladies mitochondriales, CHU Angers, Angers, France
| | - Patrizia Amati-Bonneau
- Institut MITOVASC, UMR CNRS 6015-INSERM1083, University of Angers, Angers, France.,Centre de Référence maladies mitochondriales, CHU Angers, Angers, France
| | - Pierre Vabres
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Centre de Référence Maladies Rares « Maladies Dermatologiques en Mosaïque », Service de dermatologie, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Service Dermatologie, CHU Dijon Bourgogne, Dijon, France
| | - Nada Houcinat
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de Référence Maladies Rares « déficience intellectuelle », Centre de Génétique, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Emilie Tisserant
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - François Feillet
- Service de Pédiatrie, Hôpital d'Enfants Brabois, CHRU Nancy, Vandoeuvre les Nancy, France.,INSERM-University of Lorraine-CHRU Nancy, UMRS 1256 NGERE, Nancy, France.,Centre de Références des maladies héréditaires du métabolisme, CHRU de Nancy, Nancy, France
| | - Ange-Line Bruel
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Virginie Quéré
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Centre de Référence Maladies Rares « Maladies Dermatologiques en Mosaïque », Service de dermatologie, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Christophe Philippe
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Arthur Sorlin
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de Référence Maladies Rares « Maladies Dermatologiques en Mosaïque », Service de dermatologie, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Frédéric Tran Mau-Them
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de Référence Maladies Rares « déficience intellectuelle », Centre de Génétique, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Antonio Vitobello
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | | | | | | | - Laurence Faivre
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de compétences des maladies mitochondriales, Dijon University Hospital, Dijon, France
| | - Christel Thauvin-Robinet
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de Référence Maladies Rares « déficience intellectuelle », Centre de Génétique, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Yannis Duffourd
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
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14
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Vázquez-Justes D, Carreño-Gago L, García-Arumi E, Traveset A, Montoya J, Ruiz-Pesini E, López R, Brieva L. Mitochondrial m.13513G>A Point Mutation in ND5 in a 16-Year-Old Man with Leber Hereditary Optic Neuropathy Detected by Next-Generation Sequencing. J Pediatr Genet 2019; 8:231-234. [PMID: 31687263 DOI: 10.1055/s-0039-1691812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 04/16/2019] [Indexed: 10/26/2022]
Abstract
This article reports a Leber hereditary optic neuropathy (LHON) case associated for the first time with mitochondrial m.13513G>A mutation. We present a 16-year-old man who complained of subacute, painless, visual loss. Ocular examination showed optic nerve atrophy, papillary pseudoedema, and optic disc pallor. Extraocular manifestations included hypertrophic myocardiopathy and myopathy. Initial genetic analysis excluded the three most common LHON mutations. Sanger sequencing of the whole mitochondrial deoxyribonucleic acid showed no mutation. Next-generation sequencing (NGS) revealed m.13513G>A mutation in the NADH dehydrogenase (ND5) subunit gene ( MT-ND5 ). The m.13513G>A mutation has never been associated with LHON phenotype without Leigh/mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes features. NGS techniques should be considered when this diagnosis is strongly suspected.
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Affiliation(s)
| | - Lidia Carreño-Gago
- Departament de Patología Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain
| | - Elena García-Arumi
- Departament de Patología Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain.,Àrea de Genètica Clínica i Molecular, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Alicia Traveset
- Department of Ophthalmology, Hospital Universitari Arnau de Vilanova, Lleida, Spain
| | - Julio Montoya
- Departamento de Bioquimica, Biologia Molecular y Celular, Universidad de Zaragoza, Centro de Investigaciones Biomédicas en Red de Enfermedades Raras, CIBERER, Instituto de Investigación Sanitaria de Aragón (IISAragón), Zaragoza, Spain
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquimica, Biologia Molecular y Celular, Universidad de Zaragoza, Centro de Investigaciones Biomédicas en Red de Enfermedades Raras, CIBERER, Instituto de Investigación Sanitaria de Aragón (IISAragón), Zaragoza, Spain
| | - Ricard López
- Unitat de Citogenètica, Laboratori Clínic ICS, Hospital Universitari Arnau de Vilanova, Lleida, Spain
| | - Luis Brieva
- Department of Neurology, Hospital Universitari Arnau de Vilanova, Lleida, Spain
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15
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Plutino M, Chaussenot A, Rouzier C, Ait-El-Mkadem S, Fragaki K, Paquis-Flucklinger V, Bannwarth S. Targeted next generation sequencing with an extended gene panel does not impact variant detection in mitochondrial diseases. BMC MEDICAL GENETICS 2018; 19:57. [PMID: 29625556 PMCID: PMC5889585 DOI: 10.1186/s12881-018-0568-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/21/2018] [Indexed: 12/29/2022]
Abstract
Background Since the advent of next generation sequencing (NGS), several studies have tried to evaluate the relevance of targeted gene panel sequencing and whole exome sequencing for molecular diagnosis of mitochondrial diseases. The comparison between these different strategies is extremely difficult. A recent study analysed a cohort of patients affected by a mitochondrial disease using a NGS approach based on a targeted gene panel including 132 genes. This strategy led to identify the causative mutations in 15.2% of cases. The number of novel genes responsible for respiratory chain deficiency increases very rapidly. Methods In order to determine the impact of larger panels used as a first screening strategy on molecular diagnosis success, we analysed a cohort of 80 patients affected by a mitochondrial disease with a first mitochondrial DNA (mtDNA) NGS screening and secondarily a targeted mitochondrial panel of 281 nuclear genes. Results Pathogenic mtDNA abnormalities were identified in 4.1% (1/24) of children and 25% (14/56) of adult patients. The remaining 65 patients were analysed with our targeted mitochondrial panel and this approach enabled us to achieve an identification rate of 21.7% (5/23) in children versus 7.1% (3/42) in adults. Conclusions Our results confirm that larger gene panels do not improve diagnostic yield of mitochondrial diseases due to (i) their very high genetic heterogeneity, (ii) the ongoing discovery of novel genes and (iii) mutations in genes apparently not related to mitochondrial function that lead to secondary respiratory chain deficiency. Electronic supplementary material The online version of this article (10.1186/s12881-018-0568-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Morgane Plutino
- Université Côte d'Azur, CHU de Nice, Inserm, CNRS, IRCAN, Nice, France
| | | | - Cécile Rouzier
- Université Côte d'Azur, CHU de Nice, Inserm, CNRS, IRCAN, Nice, France
| | | | | | | | - Sylvie Bannwarth
- Université Côte d'Azur, CHU de Nice, Inserm, CNRS, IRCAN, Nice, France. .,IRCAN UMR CNRS 7284/INSERM U1081, Medicine School, 28 av de Valombrose, 06107, Nice cedex 2, France.
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16
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Recent Advances in Detecting Mitochondrial DNA Heteroplasmic Variations. Molecules 2018; 23:molecules23020323. [PMID: 29401641 PMCID: PMC6017848 DOI: 10.3390/molecules23020323] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 01/27/2018] [Accepted: 01/31/2018] [Indexed: 12/31/2022] Open
Abstract
The co-existence of wild-type and mutated mitochondrial DNA (mtDNA) molecules termed heteroplasmy becomes a research hot point of mitochondria. In this review, we listed several methods of mtDNA heteroplasmy research, including the enrichment of mtDNA and the way of calling heteroplasmic variations. At the present, while calling the novel ultra-low level heteroplasmy, high-throughput sequencing method is dominant while the detection limit of recorded mutations is accurate to 0.01% using the other quantitative approaches. In the future, the studies of mtDNA heteroplasmy may pay more attention to the single-cell level and focus on the linkage of mutations.
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17
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The clinical and genetic characteristics in children with mitochondrial disease in China. SCIENCE CHINA-LIFE SCIENCES 2017. [PMID: 28639102 DOI: 10.1007/s11427-017-9080-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Mitochondrial disease was a clinically and genetically heterogeneous group of diseases, thus the diagnosis was very difficult to clinicians. Our objective was to analyze clinical and genetic characteristics of children with mitochondrial disease in China. We tested 141 candidate patients who have been suspected of mitochondrial disorders by using targeted next-generation sequencing (NGS), and summarized the clinical and genetic data of gene confirmed cases from Neurology Department, Beijing Children's Hospital, Capital Medical University from October 2012 to January 2015. In our study, 40 cases of gene confirmed mitochondrial disease including eight kinds of mitochondrial disease, among which Leigh syndrome was identified to be the most common type, followed by mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS). The age-of-onset varies among mitochondrial disease, but early onset was common. All of 40 cases were gene confirmed, among which 25 cases (62.5%) with mitochondrial DNA (mtDNA) mutation, and 15 cases (37.5%) with nuclear DNA (nDNA) mutation. M.3243A>G (n=7) accounts for a large proportion of mtDNA mutation. The nDNA mutations include SURF1 (n=7), PDHA1 (n=2), and NDUFV1, NDUFAF6, SUCLA2, SUCLG1, RRM2B, and C12orf65, respectively.
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18
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Sofronova JK, Ilinsky YY, Orishchenko KE, Chupakhin EG, Lunev EA, Mazunin IO. Detection of Mutations in Mitochondrial DNA by Droplet Digital PCR. BIOCHEMISTRY (MOSCOW) 2017; 81:1031-1037. [PMID: 27908228 DOI: 10.1134/s0006297916100011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mutations in mitochondrial DNA (mtDNA) may result in various pathological processes. Detection of mutant mtDNAs is a problem for diagnostic practice that is complicated by heteroplasmy - a phenomenon of the inferring presence of at least two allelic variants of the mitochondrial genome. Also, the level of heteroplasmy largely determines the profile and severity of clinical manifestations. Here we discuss detection of mutations in heteroplasmic mtDNA using up-to-date methods that have not yet been introduced as routine clinical assays. These methods can be used for detecting mutations in mtDNA to verify diagnosis of "mitochondrial disease", studying dynamics of mutant mtDNA in body tissues of patients, as well as investigating structural features of mtDNAs. Original data on allele-specific discrimination of m.11778G>A mutation by droplet digital PCR are presented, which demonstrate an opportunity for simultaneous detection and quantitative assessment of mutations in mtDNAs.
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Affiliation(s)
- J K Sofronova
- Immanuil Kant Baltic Federal University, Institute of Chemistry and Biology, Kaliningrad, 236038, Russia.
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19
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Pronicka E, Piekutowska-Abramczuk D, Ciara E, Trubicka J, Rokicki D, Karkucińska-Więckowska A, Pajdowska M, Jurkiewicz E, Halat P, Kosińska J, Pollak A, Rydzanicz M, Stawinski P, Pronicki M, Krajewska-Walasek M, Płoski R. New perspective in diagnostics of mitochondrial disorders: two years' experience with whole-exome sequencing at a national paediatric centre. J Transl Med 2016; 14:174. [PMID: 27290639 PMCID: PMC4903158 DOI: 10.1186/s12967-016-0930-9] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/31/2016] [Indexed: 12/30/2022] Open
Abstract
Background Whole-exome sequencing (WES) has led to an exponential increase in identification of causative variants in mitochondrial disorders (MD). Methods We performed WES in 113 MD suspected patients from Polish paediatric reference centre, in whom routine testing failed to identify a molecular defect. WES was performed using TruSeqExome enrichment, followed by variant prioritization, validation by Sanger sequencing, and segregation with the disease phenotype in the family. Results Likely causative mutations were identified in 67 (59.3 %) patients; these included variants in mtDNA (6 patients) and nDNA: X-linked (9 patients), autosomal dominant (5 patients), and autosomal recessive (47 patients, 11 homozygotes). Novel variants accounted for 50.5 % (50/99) of all detected changes. In 47 patients, changes in 31 MD-related genes (ACAD9, ADCK3, AIFM1, CLPB, COX10, DLD, EARS2, FBXL4, MTATP6, MTFMT, MTND1, MTND3, MTND5, NAXE, NDUFS6, NDUFS7, NDUFV1, OPA1, PARS2, PC, PDHA1, POLG, RARS2, RRM2B, SCO2, SERAC1, SLC19A3, SLC25A12, TAZ, TMEM126B, VARS2) were identified. The ACAD9, CLPB, FBXL4, PDHA1 genes recurred more than twice suggesting higher general/ethnic prevalence. In 19 cases, variants in 18 non-MD related genes (ADAR, CACNA1A, CDKL5, CLN3, CPS1, DMD, DYSF, GBE1, GFAP, HSD17B4, MECP2, MYBPC3, PEX5, PGAP2, PIGN, PRF1, SBDS, SCN2A) were found. The percentage of positive WES results rose gradually with increasing probability of MD according to the Mitochondrial Disease Criteria (MDC) scale (from 36 to 90 % for low and high probability, respectively). The percentage of detected MD-related genes compared with non MD-related genes also grew with the increasing MD likelihood (from 20 to 97 %). Molecular diagnosis was established in 30/47 (63.8 %) neonates and in 17/28 (60.7 %) patients with basal ganglia involvement. Mutations in CLPB, SERAC1, TAZ genes were identified in neonates with 3-methylglutaconic aciduria (3-MGA) as a discriminative feature. New MD-related candidate gene (NDUFB8) is under verification. Conclusions We suggest WES rather than targeted NGS as the method of choice in diagnostics of MD in children, including neonates with 3-MGA aciduria, who died without determination of disease cause and with limited availability of laboratory data. There is a strong correlation between the degree of MD diagnosis by WES and MD likelihood expressed by the MDC scale. Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-0930-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ewa Pronicka
- Department of Medical Genetics, The Children's Memorial Health Institute, 04-730, Warsaw, Poland. .,Department of Paediatrics, Nutrition and Metabolic Diseases,, The Children's Memorial Health Institute, Warsaw, Poland.
| | | | - Elżbieta Ciara
- Department of Medical Genetics, The Children's Memorial Health Institute, 04-730, Warsaw, Poland
| | - Joanna Trubicka
- Department of Medical Genetics, The Children's Memorial Health Institute, 04-730, Warsaw, Poland
| | - Dariusz Rokicki
- Department of Paediatrics, Nutrition and Metabolic Diseases,, The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Magdalena Pajdowska
- Department of Biochemistry and Experimental Medicine, The Children's Memorial Health Institute, Warsaw, Poland
| | - Elżbieta Jurkiewicz
- Department of Radiology, The Children's Memorial Health Institute, Warsaw, Poland
| | - Paulina Halat
- Department of Medical Genetics, The Children's Memorial Health Institute, 04-730, Warsaw, Poland
| | - Joanna Kosińska
- Department of Medical Genetics, Warsaw Medical University, Pawińskiego str, 02-106, Warsaw, Poland
| | - Agnieszka Pollak
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Nadarzyn, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Warsaw Medical University, Pawińskiego str, 02-106, Warsaw, Poland
| | - Piotr Stawinski
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Nadarzyn, Poland
| | - Maciej Pronicki
- Department of Pathology, The Children's Memorial Health Institute, Warsaw, Poland
| | | | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Pawińskiego str, 02-106, Warsaw, Poland.
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Montero R, Yubero D, Villarroya J, Henares D, Jou C, Rodríguez MA, Ramos F, Nascimento A, Ortez CI, Campistol J, Perez-Dueñas B, O'Callaghan M, Pineda M, Garcia-Cazorla A, Oferil JC, Montoya J, Ruiz-Pesini E, Emperador S, Meznaric M, Campderros L, Kalko SG, Villarroya F, Artuch R, Jimenez-Mallebrera C. GDF-15 Is Elevated in Children with Mitochondrial Diseases and Is Induced by Mitochondrial Dysfunction. PLoS One 2016; 11:e0148709. [PMID: 26867126 PMCID: PMC4750949 DOI: 10.1371/journal.pone.0148709] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/20/2016] [Indexed: 02/04/2023] Open
Abstract
Background We previously described increased levels of growth and differentiation factor 15 (GDF-15) in skeletal muscle and serum of patients with mitochondrial diseases. Here we evaluated GDF-15 as a biomarker for mitochondrial diseases affecting children and compared it to fibroblast-growth factor 21 (FGF-21). To investigate the mechanism of GDF-15 induction in these pathologies we measured its expression and secretion in response to mitochondrial dysfunction. Methods We analysed 59 serum samples from 48 children with mitochondrial disease, 19 samples from children with other neuromuscular diseases and 33 samples from aged-matched healthy children. GDF-15 and FGF-21 circulating levels were determined by ELISA. Results Our results showed that in children with mitochondrial diseases GDF-15 levels were on average increased by 11-fold (mean 4046pg/ml, 1492 SEM) relative to healthy (350, 21) and myopathic (350, 32) controls. The area under the curve for the receiver-operating-characteristic curve for GDF-15 was 0.82 indicating that it has a good discriminatory power. The overall sensitivity and specificity of GDF-15 for a cut-off value of 550pg/mL was 67.8% (54.4%-79.4%) and 92.3% (81.5%-97.9%), respectively. We found that elevated levels of GDF-15 and or FGF-21 correctly identified a larger proportion of patients than elevated levels of GDF-15 or FGF-21 alone. GDF-15, as well as FGF-21, mRNA expression and protein secretion, were significantly induced after treatment of myotubes with oligomycin and that levels of expression of both factors significantly correlated. Conclusions Our data indicate that GDF-15 is a valuable serum quantitative biomarker for the diagnosis of mitochondrial diseases in children and that measurement of both GDF-15 and FGF-21 improves the disease detection ability of either factor separately. Finally, we demonstrate for the first time that GDF-15 is produced by skeletal muscle cells in response to mitochondrial dysfunction and that its levels correlate in vitro with FGF-21 levels.
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Affiliation(s)
- Raquel Montero
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain, Instituto de Salud Carlos III, Madrid, Spain
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
| | - Delia Yubero
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain, Instituto de Salud Carlos III, Madrid, Spain
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
| | - Joan Villarroya
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
- Biochemistry and Molecular Biology Department, Biomedical Institute University of Barcelona (IBUB), Center for Biomedical Research on Obesity and Nutrition (CIBEROBN), Madrid, Spain
| | - Desiree Henares
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, Fundacion Sant Joan de Deu, Barcelona, Spain
| | - Cristina Jou
- Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain, Instituto de Salud Carlos III, Madrid, Spain
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
- Pathology Department, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Maria Angeles Rodríguez
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, Fundacion Sant Joan de Deu, Barcelona, Spain
| | - Federico Ramos
- Neuropaediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Andrés Nascimento
- Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain, Instituto de Salud Carlos III, Madrid, Spain
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, Fundacion Sant Joan de Deu, Barcelona, Spain
| | - Carlos Ignacio Ortez
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, Fundacion Sant Joan de Deu, Barcelona, Spain
| | - Jaume Campistol
- Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain, Instituto de Salud Carlos III, Madrid, Spain
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
- Neuropaediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Belen Perez-Dueñas
- Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain, Instituto de Salud Carlos III, Madrid, Spain
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
- Neuropaediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Mar O'Callaghan
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
- Neuropaediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Mercedes Pineda
- Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain, Instituto de Salud Carlos III, Madrid, Spain
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
| | - Angeles Garcia-Cazorla
- Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain, Instituto de Salud Carlos III, Madrid, Spain
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
- Neuropaediatrics Department, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Jaume Colomer Oferil
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, Fundacion Sant Joan de Deu, Barcelona, Spain
| | - Julio Montoya
- Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain, Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Molecular Biology Department, University of Zaragoza, Zaragoza, Spain
| | - Eduardo Ruiz-Pesini
- Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain, Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Molecular Biology Department, University of Zaragoza, Zaragoza, Spain
- Fundación ARAID, Universidad de Zaragoza, Zaragoza, Spain
| | - Sonia Emperador
- Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain, Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Molecular Biology Department, University of Zaragoza, Zaragoza, Spain
| | - Marija Meznaric
- Institute of Anatomy, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Laura Campderros
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
- Biochemistry and Molecular Biology Department, Biomedical Institute University of Barcelona (IBUB), Center for Biomedical Research on Obesity and Nutrition (CIBEROBN), Madrid, Spain
| | - Susana G. Kalko
- Bioinformatics Core Facility, IDIBAPS, Hospital Clinic, Barcelona, Spain
| | - Francesc Villarroya
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
- Biochemistry and Molecular Biology Department, Biomedical Institute University of Barcelona (IBUB), Center for Biomedical Research on Obesity and Nutrition (CIBEROBN), Madrid, Spain
| | - Rafael Artuch
- Clinical Biochemistry Department, Hospital Sant Joan de Déu, Barcelona, Spain
- Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain, Instituto de Salud Carlos III, Madrid, Spain
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
| | - Cecilia Jimenez-Mallebrera
- Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain, Instituto de Salud Carlos III, Madrid, Spain
- Institute of Pediatric Research Sant Joan de Déu, Barcelona, Spain
- Neuromuscular Unit, Neuropaediatrics Department, Hospital Sant Joan de Déu, Fundacion Sant Joan de Deu, Barcelona, Spain
- * E-mail:
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Pena JA, Lotze T, Yang Y, Umana L, Walkiewicz M, Hunter JV, Scaglia F. Methionyl-tRNA Formyltransferase (MTFMT) Deficiency Mimicking Acquired Demyelinating Disease. J Child Neurol 2016; 31:215-9. [PMID: 26060307 DOI: 10.1177/0883073815587946] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 04/28/2015] [Indexed: 11/17/2022]
Abstract
Disease-related mutations in the mitochondrial methionyl-tRNA formyltransferase (MTFMT) gene encoding a critical enzyme for mitochondrial translation have been rarely reported and are described in association with Leigh syndrome and combined oxidative phosphorylation deficiency. Symptoms include developmental delay, followed by ataxia and spasticity manifesting at later stages. A man had a clinical picture suggestive of an acquired demyelinating disease. Brain magnetic resonance imaging (MRI) demonstrated extensive involvement of the optic nerves, cerebral white matter, brain stem, and spinal cord. Whole-exome sequencing detected a pathologic homozygous c.626C>T mutation in the MTFMT gene. These findings expand the clinical features and neuroimaging spectrum associated with MTFMT mutations to include a relapsing-remitting phenotype.
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Affiliation(s)
- Joaquin A Pena
- Division of Pediatric Neurology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Timothy Lotze
- Division of Pediatric Neurology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Luis Umana
- Department of Pediatric Genetics and Metabolism, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, TX, USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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22
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Shamseldin HE, Smith LL, Kentab A, Alkhalidi H, Summers B, Alsedairy H, Xiong Y, Gupta VA, Alkuraya FS. Mutation of the mitochondrial carrier SLC25A42 causes a novel form of mitochondrial myopathy in humans. Hum Genet 2015; 135:21-30. [PMID: 26541337 DOI: 10.1007/s00439-015-1608-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 10/24/2015] [Indexed: 01/08/2023]
Abstract
Myopathies are heterogeneous disorders characterized clinically by weakness and hypotonia, usually in the absence of gross dystrophic changes. Mitochondrial dysfunction is a frequent cause of myopathy. We report a simplex case born to consanguineous parents who presented with muscle weakness, lactic acidosis, and muscle changes suggestive of mitochondrial dysfunction. Combined autozygome and exome analysis revealed a missense variant in the SLC25A42 gene, which encodes an inner mitochondrial membrane protein that imports coenzyme A into the mitochondrial matrix. Zebrafish slc25a42 knockdown morphants display severe muscle disorganization and weakness. Importantly, these features are rescued by normal human SLC25A42 RNA, but not by RNA harboring the patient's variant. Our data support a potentially causal link between SLC25A42 mutation and mitochondrial myopathy in humans.
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Affiliation(s)
- Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Laura L Smith
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amal Kentab
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Hisham Alkhalidi
- Department of Pathology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Brady Summers
- Department of Molecular Biophysics & Biochemistry 260 Whitney Avenue P.O. Box 208114. New Haven, CT, USA
| | - Haifa Alsedairy
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Yong Xiong
- Department of Molecular Biophysics & Biochemistry 260 Whitney Avenue P.O. Box 208114. New Haven, CT, USA
| | - Vandana A Gupta
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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23
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Macciotta N, Gaspa G, Bomba L, Vicario D, Dimauro C, Cellesi M, Ajmone-Marsan P. Genome-wide association analysis in Italian Simmental cows for lactation curve traits using a low-density (7K) SNP panel. J Dairy Sci 2015; 98:8175-85. [DOI: 10.3168/jds.2015-9500] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 06/22/2015] [Indexed: 01/15/2023]
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24
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Ghemlas I, Li H, Zlateska B, Klaassen R, Fernandez CV, Yanofsky RA, Wu J, Pastore Y, Silva M, Lipton JH, Brossard J, Michon B, Abish S, Steele M, Sinha R, Belletrutti M, Breakey VR, Jardine L, Goodyear L, Sung L, Dhanraj S, Reble E, Wagner A, Beyene J, Ray P, Meyn S, Cada M, Dror Y. Improving diagnostic precision, care and syndrome definitions using comprehensive next-generation sequencing for the inherited bone marrow failure syndromes. J Med Genet 2015; 52:575-84. [PMID: 26136524 DOI: 10.1136/jmedgenet-2015-103270] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/07/2015] [Indexed: 11/04/2022]
Abstract
BACKGROUND Phenotypic overlap among the inherited bone marrow failure syndromes (IBMFSs) frequently limits the ability to establish a diagnosis based solely on clinical features. >70 IBMFS genes have been identified, which often renders genetic testing prolonged and costly. Since correct diagnosis, treatment and cancer surveillance often depend on identifying the mutated gene, strategies that enable timely genotyping are essential. METHODS To overcome these challenges, we developed a next-generation sequencing assay to analyse a panel of 72 known IBMFS genes. Cases fulfilling the clinical diagnostic criteria of an IBMFS but without identified causal genotypes were included. RESULTS The assay was validated by detecting 52 variants previously found by Sanger sequencing. A total of 158 patients with unknown mutations were studied. Of 75 patients with known IBMFS categories (eg, Fanconi anaemia), 59% had causal mutations. Among 83 patients with unclassified IBMFSs, we found causal mutations and established the diagnosis in 18% of the patients. The assay detected mutant genes that had not previously been reported to be associated with the patient phenotypes. In other cases, the assay led to amendments of diagnoses. In 20% of genotype cases, the results indicated a cancer surveillance programme. CONCLUSIONS The novel assay is efficient, accurate and has a major impact on patient care.
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Affiliation(s)
- Ibrahim Ghemlas
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hongbing Li
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada
| | - Bozana Zlateska
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada
| | - Robert Klaassen
- Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | | | - John Wu
- British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | | | | | - Jeff H Lipton
- Princess Margaret Hospital, Toronto, Ontario, Canada
| | - Josee Brossard
- Centre hospitalier universitaire, Sherbrooke, Quebec, Canada
| | - Bruno Michon
- Centre Hospital University Quebec-Pav CHUL, Sainte-Foy, Quebec, Canada
| | - Sharon Abish
- Montreal Children's Hospital, Montreal, Québec, Canada
| | | | - Roona Sinha
- University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Mark Belletrutti
- Stollery Children's Hospital, University of Alberta, Edmonton, Alberta, Canada
| | - Vicky R Breakey
- McMaster Children's Hospital, McMaster University, Hamilton, Ontario, Canada
| | - Lawrence Jardine
- Children's Hospital at London Health Sciences Centre, London, Ontario, Canada
| | - Lisa Goodyear
- Janeway Child Health Centre, St. John's, Newfoundland, Canada
| | - Lillian Sung
- Population Health Sciences, Research Institute, The Hospital For Sick Children, Toronto, Ontario, Canada
| | - Santhosh Dhanraj
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada Faculty of Medicine, Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Emma Reble
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada
| | - Amanda Wagner
- Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Joseph Beyene
- Program in Population Genomics, Department of Clinical Epidemiology & Biostatistics, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Peter Ray
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada Molecular Genetic Laboratory, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stephen Meyn
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada
| | - Michaela Cada
- Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yigal Dror
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada Faculty of Medicine, Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
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Coughlin CR, Scharer GH, Friederich MW, Yu HC, Geiger EA, Creadon-Swindell G, Collins AE, Vanlander AV, Coster RV, Powell CA, Swanson MA, Minczuk M, Van Hove JLK, Shaikh TH. Mutations in the mitochondrial cysteinyl-tRNA synthase gene, CARS2, lead to a severe epileptic encephalopathy and complex movement disorder. J Med Genet 2015; 52:532-40. [PMID: 25787132 DOI: 10.1136/jmedgenet-2015-103049] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/26/2015] [Indexed: 11/03/2022]
Abstract
BACKGROUND Mitochondrial disease is often suspected in cases of severe epileptic encephalopathy especially when a complex movement disorder, liver involvement and progressive developmental regression are present. Although mutations in either mitochondrial DNA or POLG are often present, other nuclear defects in mitochondrial DNA replication and protein translation have been associated with a severe epileptic encephalopathy. METHODS AND RESULTS We identified a proband with an epileptic encephalopathy, complex movement disorder and a combined mitochondrial respiratory chain enzyme deficiency. The child presented with neurological regression, complex movement disorder and intractable seizures. A combined deficiency of mitochondrial complexes I, III and IV was noted in liver tissue, along with increased mitochondrial DNA content in skeletal muscle. Incomplete assembly of complex V, using blue native polyacrylamide gel electrophoretic analysis and complex I, using western blotting, suggested a disorder of mitochondrial transcription or translation. Exome sequencing identified compound heterozygous mutations in CARS2, a mitochondrial aminoacyl-tRNA synthetase. Both mutations affect highly conserved amino acids located within the functional ligase domain of the cysteinyl-tRNA synthase. A specific decrease in the amount of charged mt-tRNA(Cys) was detected in patient fibroblasts compared with controls. Retroviral transfection of the wild-type CARS2 into patient skin fibroblasts led to the correction of the incomplete assembly of complex V, providing functional evidence for the role of CARS2 mutations in disease aetiology. CONCLUSIONS Our findings indicate that mutations in CARS2 result in a mitochondrial translational defect as seen in individuals with mitochondrial epileptic encephalopathy.
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Affiliation(s)
- Curtis R Coughlin
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Gunter H Scharer
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA Intellectual and Developmental Disabilities Research Center, University of Colorado School of Medicine, Aurora, Colorado, USA Department of Pediatrics, Section of Clinical Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Marisa W Friederich
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Hung-Chun Yu
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Elizabeth A Geiger
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Geralyn Creadon-Swindell
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Abigail E Collins
- Department of Pediatrics, Section of Neurology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Arnaud V Vanlander
- Department of Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Rudy Van Coster
- Department of Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | | | - Michael A Swanson
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - Johan L K Van Hove
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Tamim H Shaikh
- Department of Pediatrics, Section of Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA Intellectual and Developmental Disabilities Research Center, University of Colorado School of Medicine, Aurora, Colorado, USA
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Kettwig M, Schubach M, Zimmermann FA, Klinge L, Mayr JA, Biskup S, Sperl W, Gärtner J, Huppke P. From ventriculomegaly to severe muscular atrophy: Expansion of the clinical spectrum related to mutations in AIFM1. Mitochondrion 2015; 21:12-8. [DOI: 10.1016/j.mito.2015.01.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 09/02/2014] [Accepted: 01/05/2015] [Indexed: 12/20/2022]
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27
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Chae JH, Vasta V, Cho A, Lim BC, Zhang Q, Eun SH, Hahn SH. Utility of next generation sequencing in genetic diagnosis of early onset neuromuscular disorders. J Med Genet 2015; 52:208-16. [DOI: 10.1136/jmedgenet-2014-102819] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Whole-mitochondrial genome sequencing in primary open-angle glaucoma using massively parallel sequencing identifies novel and known pathogenic variants. Genet Med 2014; 17:279-84. [PMID: 25232845 DOI: 10.1038/gim.2014.121] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 08/07/2014] [Indexed: 02/03/2023] Open
Abstract
PURPOSE The aim of this study was to determine whether mutations in mitochondrial DNA play a role in high-pressure primary open-angle glaucoma (OMIM 137760) by analyzing new data from massively parallel sequencing of mitochondrial DNA. METHODS Glaucoma patients with high-tension primary open-angle glaucoma and ethnically matched and age-matched control subjects without glaucoma were recruited. The entire human mitochondrial genome was amplified in two overlapping fragments by long-range polymerase chain reaction and used as a template for massively parallel sequencing on an Ion Torrent Personal Genome Machine. All variants were confirmed by conventional Sanger sequencing. RESULTS Whole-mitochondrial genome sequencing was performed in 32 patients with primary open-angle glaucoma from India (n = 16) and Ireland (n = 16). In 16 of the 32 patients with primary open-angle glaucoma (50% of cases), there were 22 mitochondrial DNA mutations consisting of 7 novel mutations and 8 previously reported disease-associated sequence variants. Eight of 22 (36.4%) of the mitochondrial DNA mutations were in complex I mitochondrial genes. CONCLUSION Massively parallel sequencing using the Ion Torrent Personal Genome Machine with confirmation by Sanger sequencing detected a pathogenic mitochondrial DNA mutation in 50% of the primary open-angle glaucoma cohort. Our findings support the emerging concept that mitochondrial dysfunction results in the development of glaucoma and, more specifically, that complex I defects play a significant role in primary open-angle glaucoma pathogenesis.
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Ye F, Samuels DC, Clark T, Guo Y. High-throughput sequencing in mitochondrial DNA research. Mitochondrion 2014; 17:157-63. [PMID: 24859348 PMCID: PMC4149223 DOI: 10.1016/j.mito.2014.05.004] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 04/04/2014] [Accepted: 05/13/2014] [Indexed: 12/14/2022]
Abstract
Next-generation sequencing, also known as high-throughput sequencing, has greatly enhanced researchers' ability to conduct biomedical research on all levels. Mitochondrial research has also benefitted greatly from high-throughput sequencing; sequencing technology now allows for screening of all 16,569 base pairs of the mitochondrial genome simultaneously for SNPs and low level heteroplasmy and, in some cases, the estimation of mitochondrial DNA copy number. It is important to realize the full potential of high-throughput sequencing for the advancement of mitochondrial research. To this end, we review how high-throughput sequencing has impacted mitochondrial research in the categories of SNPs, low level heteroplasmy, copy number, and structural variants. We also discuss the different types of mitochondrial DNA sequencing and their pros and cons. Based on previous studies conducted by various groups, we provide strategies for processing mitochondrial DNA sequencing data, including assembly, variant calling, and quality control.
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Affiliation(s)
- Fei Ye
- Department of Biostatistics, Vanderbilt University, Nashville, TN 37232, USA
| | - David C Samuels
- Center for Human Genetics, Vanderbilt University, Nashville, TN 37232, USA
| | - Travis Clark
- Vanderbilt Technology for Advanced Genomics, Vanderbilt University, Nashville, TN 37232, USA
| | - Yan Guo
- Department of Cancer Biology, Vanderbilt University, Nashville, TN 37232, USA
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Nogueira C, Almeida LS, Nesti C, Pezzini I, Videira A, Vilarinho L, Santorelli FM. Syndromes associated with mitochondrial DNA depletion. Ital J Pediatr 2014; 40:34. [PMID: 24708634 PMCID: PMC3985578 DOI: 10.1186/1824-7288-40-34] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 03/28/2014] [Indexed: 01/21/2023] Open
Abstract
Mitochondrial dysfunction accounts for a large group of inherited metabolic disorders most of which are due to a dysfunctional mitochondrial respiratory chain (MRC) and, consequently, deficient energy production. MRC function depends on the coordinated expression of both nuclear (nDNA) and mitochondrial (mtDNA) genomes. Thus, mitochondrial diseases can be caused by genetic defects in either the mitochondrial or the nuclear genome, or in the cross-talk between the two. This impaired cross-talk gives rise to so-called nuclear-mitochondrial intergenomic communication disorders, which result in loss or instability of the mitochondrial genome and, in turn, impaired maintenance of qualitative and quantitative mtDNA integrity. In children, most MRC disorders are associated with nuclear gene defects rather than alterations in the mtDNA itself. The mitochondrial DNA depletion syndromes (MDSs) are a clinically heterogeneous group of disorders with an autosomal recessive pattern of transmission that have onset in infancy or early childhood and are characterized by a reduced number of copies of mtDNA in affected tissues and organs. The MDSs can be divided into least four clinical presentations: hepatocerebral, myopathic, encephalomyopathic and neurogastrointestinal. The focus of this review is to offer an overview of these syndromes, listing the clinical phenotypes, together with their relative frequency, mutational spectrum, and possible insights for improving diagnostic strategies.
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Affiliation(s)
| | | | | | | | | | - Laura Vilarinho
- National Institute of Health, Genetics Department, Research and Development Unit, Porto, Portugal.
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Coates BS. Assembly and annotation of full mitochondrial genomes for the corn rootworm species, Diabrotica virgifera virgifera and Diabrotica barberi (Insecta: Coleoptera: Chrysomelidae), using Next Generation Sequence data. Gene 2014; 542:190-7. [PMID: 24657060 DOI: 10.1016/j.gene.2014.03.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 03/13/2014] [Accepted: 03/18/2014] [Indexed: 01/08/2023]
Abstract
Complete mitochondrial genomes for two corn rootworm species, Diabrotica virgifera virgifera (16,747 bp) and Diabrotica barberi (16,632; Insecta: Coleoptera: Chrysomelidae), were assembled from Illumina HiSeq2000 read data. Annotation indicated that the order and orientation of 13 protein coding genes (PCGs), and 22 tRNA and 2 rRNA sequences were in typical of insect mitochondrial genomes. Non-standard nad4 and cox3 stop codons were composed of single T nucleotides and likely completed by adenylation, and atypical TTT start codons was predicted for both D. v. virgifera and D. barberinad1 genes. The D. v. virgifera and D. barberi haplotypes showed 819 variable nucleotide positions within PCG regions (7.36% divergence), which suggest that speciation may have occurred ~3.68 million years ago assuming a linear rate of short-term substitution. Phylogenetic analyses of Coleopteran MtD genome show clustering based on family level, and may have the capacity to resolve the evolutionary history within this Order of insects.
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Affiliation(s)
- Brad S Coates
- United States Department of Agriculture, Agricultural Research Service, Corn Insects & Crop Genetics Research Unit, Iowa State University, Ames, IA, 50011, USA; Iowa State University Department of Entomology, Ames, IA, 50011, USA.
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From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes. BMC Genomics 2014; 15:68. [PMID: 24460871 PMCID: PMC3922791 DOI: 10.1186/1471-2164-15-68] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 01/17/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better appreciation of their importance in answering biological questions, there remain significant obstacles to the successful implementation of NGS-based projects, especially for new users. RESULTS Here we present an 'A to Z' protocol for obtaining complete human mitochondrial (mtDNA) genomes - from DNA extraction to consensus sequence. Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling). CONCLUSIONS All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. The molecular steps are scalable to large numbers (hundreds) of individuals and all steps post-DNA extraction can be carried out in 96-well plate format. Also, the protocol has been assembled so that individual 'modules' can be swapped out to suit available resources.
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Capturing protein-coding genes across highly divergent species. Biotechniques 2014; 54:321-6. [PMID: 23758502 DOI: 10.2144/000114039] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/25/2013] [Indexed: 11/23/2022] Open
Abstract
DNA hybridization capture combined with next generation sequencing can be used to determine the sequences of hundreds of target genes across hundreds of individuals in a single experiment. However, the approach has thus far only been successfully applied to capture targets that are highly similar in sequence to the bait molecules. Here we introduce modifications that extend the reach of the method to allow efficient capture of highly divergent homologous target sequences using a single set of baits. These modifications have important implications for comparative biology.
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Gurses C, Azakli H, Alptekin A, Cakiris A, Abaci N, Arikan M, Kursun O, Gokyigit A, Ustek D. Mitochondrial DNA profiling via genomic analysis in mesial temporal lobe epilepsy patients with hippocampal sclerosis. Gene 2014; 538:323-7. [PMID: 24440288 DOI: 10.1016/j.gene.2014.01.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 12/28/2013] [Accepted: 01/10/2014] [Indexed: 11/25/2022]
Abstract
INTRODUCTION Mitochondria have an essential role in neuronal excitability and neuronal survival. In addition to energy production, mitochondria also play a crucial role in the maintenance of intracellular calcium homeostasis, generation of reactive oxygen species and mechanisms of cell death. There is a relative paucity of data about the role of mitochondria in epilepsy. Mitochondrial genome analysis is rarely carried out in the investigation of some diseases. In mesial temporal lobe epilepsies (MTLE) cases, genome analysis has never been used previously. The aim of this study is to show mitochondrial dysfunctions using genome analysis in patients with MTLE-hippocampal sclerosis (HS). METHODS 44 patients with MTLE-HS and 86 matched healthy unrelated controls were included in this study. The patients were divided into four groups according to their clinical presentation as the following: Group 1 consists of patients with intractable epilepsy who refused operation; Group 2 of operated seizure free patients; Group 3 of operated patients with seizures; and Group 4 unoperated seizure free patients with or without antiepileptic drugs. Blood samples were used to isolate DNA. Parallel tagged sequencing was employed to allow pyrosequencing of 130 samples. Complete mtDNA is amplified in two overlapping fragments (11 and 9 kb). The PCR amplicons were pooled in equimolar ratios. Titanium kits were used to produce shotgun libraries according to the manufacturer's protocol. RESULTS The average coverage in total was 130 ± 30 and an average of 2365127 bases and 337 bp fragment length was received from all samples. The mean mtDNA heteroplasmy in patients was 26.35 ± 12.3 and in controls 25.03 ± 9.34. Three mutations had prominently high significance in patient samples. The most significantly associated variation was located in the MT-ATP-8 gene (8502 A>T, Asn46Ile) whereas the other two were in the MT-ND4 (11994 C>T, Thr412Ile) and MT-ND5 (13231 A>C, Lys299Gln) genes. CONCLUSIONS We have observed that three mutations were significantly related to the presence of epilepsy. These mutations were found at the 8502, 11994, and 13,231 bp of mtDNA, which resulted in amino acid changes at the MT-ATP-8, MT-ND4 and MT-ND5 genes. Finding mutations can lead us to knowing more about the pathophysiology of the MTLE disease.
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Affiliation(s)
- Candan Gurses
- Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey.
| | - Hulya Azakli
- Genetics, Institute for Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Ahmet Alptekin
- Computer Engineering, Istanbul University, Istanbul, Turkey
| | - Aris Cakiris
- Genetics, Institute for Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Neslihan Abaci
- Genetics, Institute for Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Muzaffer Arikan
- Genetics, Institute for Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Olcay Kursun
- Computer Engineering, Istanbul University, Istanbul, Turkey
| | - Aysen Gokyigit
- Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Duran Ustek
- Genetics, Institute for Experimental Medicine, Istanbul University, Istanbul, Turkey.
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Zhang W, Li X, Shang X, Zhao Q, Hu Y, Xu X, He R, Duan L, Zhang F. Gene expression analysis in response to osmotic stimuli in the intervertebral disc with DNA microarray. Eur J Med Res 2013; 18:62. [PMID: 24369767 PMCID: PMC3911967 DOI: 10.1186/2047-783x-18-62] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 12/06/2013] [Indexed: 12/02/2022] Open
Abstract
Background Intervertebral disc (IVD) cells experience a broad range of physicochemical stimuli under physiologic conditions, including alterations in their osmotic environment. At present, the molecular mechanisms underlying osmotic regulation in IVD cells are poorly understood. This study aims to screen genes affected by changes in osmotic pressure in cells of subjects aged 29 to 63 years old, with top-scoring pair (TSP) method. Methods Gene expression data set GSE1648 was downloaded from Gene Expression Omnibus database, including four hyper-osmotic stimuli samples, four iso-osmotic stimuli samples, and three hypo-osmotic stimuli samples. A novel, simple method, referred to as the TSP, was used in this study. Through this method, there was no need to perform data normalization and transformation before data analysis. Results A total of five pairs of genes ((CYP2A6, FNTB), (PRPF8, TARDBP), (RPS5, OAZ1), (SLC25A3, NPM1) and (CBX3, SRSF9)) were selected based on the TSP method. We inferred that all these genes might play important roles in response to osmotic stimuli and age in IVD cells. Additionally, hyper-osmotic and iso-osmotic stimuli conditions were adverse factors for IVD cells. Conclusions We anticipate that our results will provide new thoughts and methods for the study of IVD disease.
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Affiliation(s)
| | - Xu Li
- Department of Orthopaedics, Anhui Provincial Hospital, No, 17, Road Lujiang, Hefei 230001, China.
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DaRe JT, Vasta V, Penn J, Tran NTB, Hahn SH. Targeted exome sequencing for mitochondrial disorders reveals high genetic heterogeneity. BMC MEDICAL GENETICS 2013; 14:118. [PMID: 24215330 PMCID: PMC3827825 DOI: 10.1186/1471-2350-14-118] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 11/06/2013] [Indexed: 12/11/2022]
Abstract
Background Mitochondrial disorders are difficult to diagnose due to extreme genetic and phenotypic heterogeneities. Methods We explored the utility of targeted next-generation sequencing for the diagnosis of mitochondrial disorders in 148 patients submitted for clinical testing. A panel of 447 nuclear genes encoding mitochondrial respiratory chain complexes, and other genes inducing secondary mitochondrial dysfunction or that cause diseases which mimic mitochondrial disorders were tested. Results We identified variants considered to be possibly disease-causing based on family segregation data and/or variants already known to cause disease in twelve genes in thirteen patients. Rare or novel variants of unknown significance were identified in 45 additional genes for various metabolic, genetic or neurogenetic disorders. Conclusions Primary mitochondrial defects were confirmed only in four patients indicating that majority of patients with suspected mitochondrial disorders are presumably not the result of direct impairment of energy production. Our results support that clinical and routine laboratory ascertainment for mitochondrial disorders are challenging due to significant overlapping non-specific clinical symptoms and lack of specific biomarkers. While next-generation sequencing shows promise for diagnosing suspected mitochondrial disorders, the challenges remain as the underlying genetic heterogeneity may be greater than suspected and it is further confounded by the similarity of symptoms with other conditions as we report here.
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Affiliation(s)
| | | | | | | | - Si Houn Hahn
- Seattle Children's Hospital Research Institute, 1900 9th Ave, Seattle, WA 98101, USA.
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Gemmell NJ, Jalilzadeh A, Didham RK, Soboleva T, Tompkins DM. The Trojan female technique: a novel, effective and humane approach for pest population control. Proc Biol Sci 2013; 280:20132549. [PMID: 24174117 DOI: 10.1098/rspb.2013.2549] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Humankind's ongoing battle with pest species spans millennia. Pests cause or carry disease, damage or consume food crops and other resources, and drive global environmental change. Conventional approaches to pest management usually involve lethal control, but such approaches are costly, of varying efficiency and often have ethical issues. Thus, pest management via control of reproductive output is increasingly considered an optimal solution. One of the most successful such 'fertility control' strategies developed to date is the sterile male technique (SMT), in which large numbers of sterile males are released into a population each generation. However, this approach is time-consuming, labour-intensive and costly. We use mathematical models to test a new twist on the SMT, using maternally inherited mitochondrial (mtDNA) mutations that affect male, but not female reproductive fitness. 'Trojan females' carrying such mutations, and their female descendants, produce 'sterile-male'-equivalents under natural conditions over multiple generations. We find that the Trojan female technique (TFT) has the potential to be a novel humane approach for pest control. Single large releases and relatively few small repeat releases of Trojan females both provided effective and persistent control within relatively few generations. Although greatest efficacy was predicted for high-turnover species, the additive nature of multiple releases made the TFT applicable to the full range of life histories modelled. The extensive conservation of mtDNA among eukaryotes suggests this approach could have broad utility for pest control.
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Affiliation(s)
- Neil J Gemmell
- Centre for Reproduction and Genomics and Allan Wilson Centre for Molecular Ecology and Evolution, Department of Anatomy, University of Otago, , Dunedin, New Zealand, Department of Mathematics and Statistics, University of Otago, , Dunedin, New Zealand, School of Animal Biology, University of Western Australia and CSIRO Ecosystem Sciences, , Perth, Western Australia 6009, Australia, Science and Risk Assessment Directorate, Ministry for Primary Industries, , PO Box 2526, Wellington, New Zealand, Landcare Research, , Private Bag 1930, Dunedin, New Zealand
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Valsesia A, Macé A, Jacquemont S, Beckmann JS, Kutalik Z. The Growing Importance of CNVs: New Insights for Detection and Clinical Interpretation. Front Genet 2013; 4:92. [PMID: 23750167 PMCID: PMC3667386 DOI: 10.3389/fgene.2013.00092] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Accepted: 05/04/2013] [Indexed: 02/03/2023] Open
Abstract
Differences between genomes can be due to single nucleotide variants, translocations, inversions, and copy number variants (CNVs, gain or loss of DNA). The latter can range from sub-microscopic events to complete chromosomal aneuploidies. Small CNVs are often benign but those larger than 500 kb are strongly associated with morbid consequences such as developmental disorders and cancer. Detecting CNVs within and between populations is essential to better understand the plasticity of our genome and to elucidate its possible contribution to disease. Hence there is a need for better-tailored and more robust tools for the detection and genome-wide analyses of CNVs. While a link between a given CNV and a disease may have often been established, the relative CNV contribution to disease progression and impact on drug response is not necessarily understood. In this review we discuss the progress, challenges, and limitations that occur at different stages of CNV analysis from the detection (using DNA microarrays and next-generation sequencing) and identification of recurrent CNVs to the association with phenotypes. We emphasize the importance of germline CNVs and propose strategies to aid clinicians to better interpret structural variations and assess their clinical implications.
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Affiliation(s)
- Armand Valsesia
- Genetics Core, Nestlé Institute of Health Sciences Lausanne, Switzerland
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Dames S, Chou LS, Xiao Y, Wayman T, Stocks J, Singleton M, Eilbeck K, Mao R. The development of next-generation sequencing assays for the mitochondrial genome and 108 nuclear genes associated with mitochondrial disorders. J Mol Diagn 2013; 15:526-34. [PMID: 23665194 DOI: 10.1016/j.jmoldx.2013.03.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 03/08/2013] [Accepted: 03/15/2013] [Indexed: 01/25/2023] Open
Abstract
Sanger sequencing of multigenic disorders can be technically challenging, time consuming, and prohibitively expensive. High-throughput next-generation sequencing (NGS) can provide a cost-effective method for sequencing targeted genes associated with multigenic disorders. We have developed a NGS clinical targeted gene assay for the mitochondrial genome and for 108 selected nuclear genes associated with mitochondrial disorders. Mitochondrial disorders have a reported incidence of 1 in 5000 live births, encompass a broad range of phenotypes, and are attributed to mutations in the mitochondrial and nuclear genomes. Approximately 20% of mitochondrial disorders result from mutations in mtDNA, with the remaining 80% found in nuclear genes that affect mtDNA levels or mitochondrion protein assembly. In our NGS approach, the 16,569-bp mtDNA is enriched by long-range PCR and the 108 nuclear genes (which represent 1301 amplicons and 680 kb) are enriched by RainDance emulsion PCR. Sequencing is performed on Illumina HiSeq 2000 or MiSeq platforms, and bioinformatics analysis is performed using commercial and in-house developed bioinformatics pipelines. A total of 16 validation and 13 clinical samples were examined. All previously reported variants associated with mitochondrial disorders were found in validation samples, and 5 of the 13 clinical samples were found to have mutations associated with mitochondrial disorders in either the mitochondrial genome or the 108 nuclear genes. All variants were confirmed by Sanger sequencing.
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Affiliation(s)
- Shale Dames
- Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, UT 84108, USA.
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Lieber DS, Calvo SE, Shanahan K, Slate NG, Liu S, Hershman SG, Gold NB, Chapman BA, Thorburn DR, Berry GT, Schmahmann JD, Borowsky ML, Mueller DM, Sims KB, Mootha VK. Targeted exome sequencing of suspected mitochondrial disorders. Neurology 2013; 80:1762-70. [PMID: 23596069 DOI: 10.1212/wnl.0b013e3182918c40] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVE To evaluate the utility of targeted exome sequencing for the molecular diagnosis of mitochondrial disorders, which exhibit marked phenotypic and genetic heterogeneity. METHODS We considered a diverse set of 102 patients with suspected mitochondrial disorders based on clinical, biochemical, and/or molecular findings, and whose disease ranged from mild to severe, with varying age at onset. We sequenced the mitochondrial genome (mtDNA) and the exons of 1,598 nuclear-encoded genes implicated in mitochondrial biology, mitochondrial disease, or monogenic disorders with phenotypic overlap. We prioritized variants likely to underlie disease and established molecular diagnoses in accordance with current clinical genetic guidelines. RESULTS Targeted exome sequencing yielded molecular diagnoses in established disease loci in 22% of cases, including 17 of 18 (94%) with prior molecular diagnoses and 5 of 84 (6%) without. The 5 new diagnoses implicated 2 genes associated with canonical mitochondrial disorders (NDUFV1, POLG2), and 3 genes known to underlie other neurologic disorders (DPYD, KARS, WFS1), underscoring the phenotypic and biochemical overlap with other inborn errors. We prioritized variants in an additional 26 patients, including recessive, X-linked, and mtDNA variants that were enriched 2-fold over background and await further support of pathogenicity. In one case, we modeled patient mutations in yeast to provide evidence that recessive mutations in ATP5A1 can underlie combined respiratory chain deficiency. CONCLUSION The results demonstrate that targeted exome sequencing is an effective alternative to the sequential testing of mtDNA and individual nuclear genes as part of the investigation of mitochondrial disease. Our study underscores the ongoing challenge of variant interpretation in the clinical setting.
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Affiliation(s)
- Daniel S Lieber
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
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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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Vasta V, Merritt JL, Saneto RP, Hahn SH. Next-generation sequencing for mitochondrial diseases: a wide diagnostic spectrum. Pediatr Int 2012; 54:585-601. [PMID: 22494076 DOI: 10.1111/j.1442-200x.2012.03644.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND The current diagnostic approach for mitochondrial disorders requires invasive procedures such as muscle biopsy and multiple biochemical testing but the results are often inconclusive. Clinical sequencing tests are available only for a limited number of genes. Recently, massively parallel sequencing has become a powerful tool for testing genetically heterogeneous conditions such as mitochondrial disorders. METHODS Targeted next-generation sequencing was performed on 26 patients with known or suspected mitochondrial disorders using in-solution capture for the exons of 908 known and candidate nuclear genes and an Illumina genome analyzer. RESULTS None of the 18 patients with various abnormal respiratory chain complex (RCC) activities had molecular defects in either subunits or assembly factors of mitochondrial RCC enzymes except a reference control sample with known mutations in SURF1. Instead, several variants in known pathogenic genes including CPT2, POLG, PDSS1, UBE3A, SDHD, and a few potentially pathogenic variants in candidate genes such as MTO1 or SCL7A13 were identified. CONCLUSIONS Sequencing only nuclear genes for RCC subunits and assembly factors may not provide the diagnostic answers for suspected patients with mitochondrial disorders. The present findings indicate that the diagnostic spectrum of mitochondrial disorders is much broader than previously thought, which could potentially lead to misdiagnosis and/or inappropriate treatment. Overall analytic sensitivity and precision appear acceptable for clinical testing. Despite the limitations in finding mutations in all patients, the present findings underscore the considerable clinical benefits of targeted next-generation sequencing and serve as a prototype for extending the clinical evaluation in this clinically heterogeneous patient group.
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Affiliation(s)
- Valeria Vasta
- University of Washington School of Medicine, Seattle Children's Research Institute, C9S, 1900 9th Avenue, Seattle, WA 98101, USA
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Calvo SE, Compton AG, Hershman SG, Lim SC, Lieber DS, Tucker EJ, Laskowski A, Garone C, Liu S, Jaffe DB, Christodoulou J, Fletcher JM, Bruno DL, Goldblatt J, Dimauro S, Thorburn DR, Mootha VK. Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing. Sci Transl Med 2012; 4:118ra10. [PMID: 22277967 DOI: 10.1126/scitranslmed.3003310] [Citation(s) in RCA: 338] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Advances in next-generation sequencing (NGS) promise to facilitate diagnosis of inherited disorders. Although in research settings NGS has pinpointed causal alleles using segregation in large families, the key challenge for clinical diagnosis is application to single individuals. To explore its diagnostic use, we performed targeted NGS in 42 unrelated infants with clinical and biochemical evidence of mitochondrial oxidative phosphorylation disease. These devastating mitochondrial disorders are characterized by phenotypic and genetic heterogeneity, with more than 100 causal genes identified to date. We performed "MitoExome" sequencing of the mitochondrial DNA (mtDNA) and exons of ~1000 nuclear genes encoding mitochondrial proteins and prioritized rare mutations predicted to disrupt function. Because patients and healthy control individuals harbored a comparable number of such heterozygous alleles, we could not prioritize dominant-acting genes. However, patients showed a fivefold enrichment of genes with two such mutations that could underlie recessive disease. In total, 23 of 42 (55%) patients harbored such recessive genes or pathogenic mtDNA variants. Firm diagnoses were enabled in 10 patients (24%) who had mutations in genes previously linked to disease. Thirteen patients (31%) had mutations in nuclear genes not previously linked to disease. The pathogenicity of two such genes, NDUFB3 and AGK, was supported by complementation studies and evidence from multiple patients, respectively. The results underscore the potential and challenges of deploying NGS in clinical settings.
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Affiliation(s)
- Sarah E Calvo
- Center for Human Genetic Research and Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Sixth Floor, Boston, MA 02114, USA
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Hoefs SJ, Rodenburg RJ, Smeitink JA, van den Heuvel LP. Molecular base of biochemical complex I deficiency. Mitochondrion 2012; 12:520-32. [DOI: 10.1016/j.mito.2012.07.106] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 07/06/2012] [Accepted: 07/10/2012] [Indexed: 12/21/2022]
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Newborn screening and renal disease: where we have been; where we are now; where we are going. Pediatr Nephrol 2012; 27:1453-64. [PMID: 21947256 DOI: 10.1007/s00467-011-1995-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 07/22/2011] [Accepted: 08/12/2011] [Indexed: 10/17/2022]
Abstract
Newborn screening (NBS) has rapidly changed since its origins in the 1960s. Beginning with a single condition, then a handful in the 1990 s, NBS has expanded in the past decade to allow the detection of many disorders of amino-acid, organic-acid, and fatty-acid metabolism. These conditions often present with recurrent acute attacks of metabolic acidosis, hypoglycemia, liver failure, and hyperammonemia that may be prevented with initiation of early treatment. Renal disease is an important component of these disorders and is a frequent source of morbidity. Hemodialysis is often required for hyperammonemia in the organic acidemias and urea-cycle disorders. Rhabdomyolysis with renal failure is a frequent complication in fatty-acid oxidation disorders. Newer screening methods are under investigation to detect lysosomal storage diseases, primary immunodeficiencies, and primary renal disorders. These advances will present many challenges to nephrologists and pediatricians with respect to closely monitoring and caring for children with such disorders.
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Coonrod EM, Durtschi JD, Margraf RL, Voelkerding KV. Developing genome and exome sequencing for candidate gene identification in inherited disorders: an integrated technical and bioinformatics approach. Arch Pathol Lab Med 2012; 137:415-33. [PMID: 22770468 DOI: 10.5858/arpa.2012-0107-ra] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Advances in sequencing technology with the commercialization of next-generation sequencing (NGS) has substantially increased the feasibility of sequencing human genomes and exomes. Next-generation sequencing has been successfully applied to the discovery of disease-causing genes in rare, inherited disorders. By necessity, the advent of NGS has fostered the concurrent development of bioinformatics approaches to expeditiously analyze the large data sets generated. Next-generation sequencing has been used for important discoveries in the research setting and is now being implemented into the clinical diagnostic arena. OBJECTIVE To review the current literature on technical and bioinformatics approaches for exome and genome sequencing and highlight examples of successful disease gene discovery in inherited disorders. To discuss the challenges for implementing NGS in the clinical research and diagnostic arenas. DATA SOURCES Literature review and authors' experience. CONCLUSIONS Next-generation sequencing approaches are powerful and require an investment in infrastructure and personnel expertise for effective use; however, the potential for improvement of patient care through faster and more accurate molecular diagnoses is high.
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Affiliation(s)
- Emily M Coonrod
- Research and Development, ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84108, USA
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Abstract
Next-generation sequencing has become a powerful tool for testing genetically and clinically heterogeneous conditions such as mitochondrial disorders. A recent study published in Science Translational Medicine underscores the considerable clinical benefits of targeted next-generation sequencing for the diagnosis of mitochondrial disorders. The findings also suggest that the genetic heterogeneity that can result in mitochondrial disease appears much broader than previously thought.
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Affiliation(s)
- Si Houn Hahn
- Department of Pediatrics, Division of Genetic Medicine, University of Washington School of Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
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Pagniez-Mammeri H, Rak M, Legrand A, Bénit P, Rustin P, Slama A. Mitochondrial complex I deficiency of nuclear origin II. Non-structural genes. Mol Genet Metab 2012; 105:173-9. [PMID: 22099533 DOI: 10.1016/j.ymgme.2011.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Revised: 10/07/2011] [Accepted: 10/07/2011] [Indexed: 12/01/2022]
Abstract
Complex I deficiency is the most frequent cause of respiratory chain diseases. This large multiprotein complex is composed in human of 45 structural subunits, of which 7 are mitochondrial-encoded and 38 are nuclear-encoded. Most of the pathological mutations responsible for complex I deficiencies have been identified to date in complex I structural subunits. Numerous studies from last decade gave some insight into the biogenesis of this huge multi subunit complex of double genetic origin. A sequential incorporation of the structural subunits as well as ten complex I assembly factors has been described. Here, we present a short overview of the human complex I biogenesis and we review the pathological mutations identified to date in eight of the ten known complex I assembly factors.
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Affiliation(s)
- Hélène Pagniez-Mammeri
- Laboratoire de Biochimie, APHP Hôpital de Bicêtre, 78 rue du Général Leclerc, 94275 Le Kremlin Bicêtre cedex, France
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Pagniez-Mammeri H, Loublier S, Legrand A, Bénit P, Rustin P, Slama A. Mitochondrial complex I deficiency of nuclear origin I. Structural genes. Mol Genet Metab 2012; 105:163-72. [PMID: 22142868 DOI: 10.1016/j.ymgme.2011.11.188] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Revised: 11/09/2011] [Accepted: 11/09/2011] [Indexed: 10/15/2022]
Abstract
Complex I (or NADH-ubiquinone oxidoreductase), is by far the largest respiratory chain complex with 38 subunits nuclearly encoded and 7 subunits encoded by the mitochondrial genome. Its deficiency is the most frequently encountered in mitochondrial disorders. Here, we summarize recent data obtained on architecture of complex I, and review the pathogenic mutations identified to date in nuclear structural complex I genes. The structural NDUFS1, NDUFS2, NDUFV1, and NDUFS4 genes are mutational hot spot genes for isolated complex I deficiency. The majority of the pathogenic mutations are private and the genotype-phenotype correlation is inconsistent in the rare recurrent mutations.
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Affiliation(s)
- Hélène Pagniez-Mammeri
- Laboratoire de Biochimie, APHP Hôpital de Bicêtre, 78 rue du Général Leclerc, 94275 Le Kremlin Bicêtre cedex, France
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