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Owusu R, Savarese M. Long-read sequencing improves diagnostic rate in neuromuscular disorders. ACTA MYOLOGICA : MYOPATHIES AND CARDIOMYOPATHIES : OFFICIAL JOURNAL OF THE MEDITERRANEAN SOCIETY OF MYOLOGY 2023; 42:123-128. [PMID: 38406378 PMCID: PMC10883326 DOI: 10.36185/2532-1900-394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 02/27/2024]
Abstract
Massive parallel sequencing methods, such as exome, genome, and targeted DNA sequencing, have aided molecular diagnosis of genetic diseases in the last 20 years. However, short-read sequencing methods still have several limitations, such inaccurate genome assembly, the inability to detect large structural variants, and variants located in hard-to-sequence regions like highly repetitive areas. The recently emerged PacBio single-molecule real-time (SMRT) and Oxford nanopore technology (ONT) long-read sequencing (LRS) methods have been shown to overcome most of these technical issues, leading to an increase in diagnostic rate. LRS methods are contributing to the detection of repeat expansions in novel disease-causing genes (e.g., ABCD3, NOTCH2NLC and RILPL1 causing an Oculopharyngodistal myopathy or PLIN4 causing a Myopathy with rimmed ubiquitin-positive autophagic vacuolation), of structural variants (e.g., in DMD), and of single nucleotide variants in repetitive regions (TTN and NEB). Moreover, these methods have simplified the characterization of the D4Z4 repeats in DUX4, facilitating the diagnosis of Facioscapulohumeral muscular dystrophy (FSHD). We review recent studies that have used either ONT or PacBio SMRT sequencing methods and discuss different types of variants that have been detected using these approaches in individuals with neuromuscular disorders.
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Affiliation(s)
| | - Marco Savarese
- Folkhälsan Research Center, Helsinki, Finland
- University of Helsinki, Faculty of Medicine, Helsinki, Finland
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2
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Akbar F, Saleem SM, Khalid E, Ibrahim S, Afroze B, Kirmani S, Khan S. The spectrum of hereditary neuromuscular disorders in the Pakistani population. Am J Med Genet A 2023; 191:2536-2550. [PMID: 37366078 DOI: 10.1002/ajmg.a.63332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/21/2023] [Accepted: 06/07/2023] [Indexed: 06/28/2023]
Abstract
Hereditary neuromuscular disorders (NMDs) are a broad group of clinically heterogeneous disorders with varying inheritance patterns, that are associated with over 500 implicated genes. In the context of a highly consanguineous Pakistani population, we expect that autosomal recessive NMDs may have a higher prevalence compared with patients of European descent. This is the first study to offer a detailed description of the spectrum of genes causing hereditary NMDs in the Pakistani population using NGS testing. To study the clinical and genetic profiles of patients presenting for evaluation of a hereditary neuromuscular disorder. This is a retrospective chart review of patients seen in the Neuromuscular Disorders Clinic and referred to the Genetics Clinic with a suspected hereditary neuromuscular disorder, between 2016 and 2020 at the Aga Khan University Hospital, Karachi and Mukhtiar A. Sheikh Hospital, Multan, Pakistan. The genetic testing for these patients included NGS-based single gene sequencing, NGS-based multi-gene panel and whole exome sequencing. In a total of 112 patients studied, 35 (31.3%) were female. The mean age of onset in all patients was 14.6 years (SD ±12.1 years), with the average age at presentation to the clinic of 22.4 years (SD ±14.10 years). Forty-seven (41.9%) patients had a positive genetic test result, 53 (47.3%) had one or more variants of uncertain significance (VUS), and 12 (10.7%) had a negative result. Upon further genotype-phenotype correlation and family segregation analysis, the diagnostic yield improved, with 59 (52.7%) patients reaching a diagnosis of a hereditary NMD. We also report probable founder variants in COL6A2, FKTN, GNE, and SGCB, previously reported in populations that have possible shared ancestry with the Pakistani population. Our findings reemphasizes that the rate of VUSs can be reduced by clinical correlation and family segregation studies.
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Affiliation(s)
- Fizza Akbar
- Division of Women and Child Health, The Aga Khan University, Karachi, Pakistan
| | | | | | - Shahnaz Ibrahim
- Department of Paediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Bushra Afroze
- Department of Paediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Salman Kirmani
- Division of Women and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Sara Khan
- Department of Neurology, The Aga Khan University, Karachi, Pakistan
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3
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Ortiz-Vitali JL, Wu J, Xu N, Shieh AW, Niknejad N, Takeuchi M, Paradas C, Lin C, Jafar-Nejad H, Haltiwanger RS, Wang SH, Darabi R. Disease modeling and gene correction of LGMDR21 iPSCs elucidates the role of POGLUT1 in skeletal muscle maintenance, regeneration, and the satellite cell niche. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:683-697. [PMID: 37650119 PMCID: PMC10462830 DOI: 10.1016/j.omtn.2023.07.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Autosomal recessive limb-girdle muscular dystrophy 21 (LGMDR21) is caused by pathogenic variants in protein O-glucosyltransferase 1 (POGLUT1), which is responsible for O-glucosylation of specific epidermal growth factor (EGF) repeats found in ∼50 mammalian proteins, including Notch receptors. Previous data from patient biopsies indicated that impaired Notch signaling, reduction of muscle stem cells, and accelerated differentiation are probably involved in disease etiopathology. Using patient induced pluripotent stem cells (iPSCs), their corrected isotypes, and control iPSCs, gene expression profiling indicated dysregulation of POGLUT1, NOTCH, muscle development, extracellular matrix (ECM), cell adhesion, and migration as involved pathways. They also exhibited reduced in vitro POGLUT1 enzymatic activity and NOTCH signaling as well as defective myogenesis, proliferation, migration and differentiation. Furthermore, in vivo studies demonstrated significant reductions in engraftment, muscle stem cell formation, PAX7 expression, and maintenance, along with an increased percentage of mislocalized PAX7+ cells in the interstitial space. Gene correction in patient iPSCs using CRISPR-Cas9 nickase led to the rescue of the main in vitro and in vivo phenotypes. These results demonstrate the efficacy of iPSCs and gene correction in disease modeling and rescue of the phenotypes and provide evidence of the involvement of muscle stem cell niche localization, PAX7 expression, and cell migration as possible mechanisms in LGMDR21.
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Affiliation(s)
- Jose L. Ortiz-Vitali
- Center for Stem Cell and Regenerative Medicine (CSCRM), University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jianbo Wu
- Center for Stem Cell and Regenerative Medicine (CSCRM), University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nasa Xu
- Center for Stem Cell and Regenerative Medicine (CSCRM), University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Annie W. Shieh
- Center for Human Genetics, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nima Niknejad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Megumi Takeuchi
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Carmen Paradas
- Neurology Department, Neuromuscular Disorders Unit, Instituto de Biomedicina de Sevilla, Hospital U. Virgen Del Rocío, CSIC, Universidad de Sevilla, Avd. Manuel Siurot s/n, 41013 Sevilla, Spain
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hamed Jafar-Nejad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert S. Haltiwanger
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Sidney H. Wang
- Center for Human Genetics, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Radbod Darabi
- Center for Stem Cell and Regenerative Medicine (CSCRM), University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Foltz SJ, Hartzell CH, Choo HJ. In vivo Electroporation of Skeletal Muscle Fibers in Mice. Bio Protoc 2023; 13:e4759. [PMID: 37456334 PMCID: PMC10339231 DOI: 10.21769/bioprotoc.4759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/21/2023] [Accepted: 05/29/2023] [Indexed: 07/18/2023] Open
Abstract
In vitro models are essential for investigating the molecular, biochemical, and cell-biological aspects of skeletal muscle. Still, models that utilize cell lines or embryonic cells do not fully recapitulate mature muscle fibers in vivo. Protein function is best studied in mature differentiated tissue, where biological context is maintained, but this is often difficult when reliable detection reagents, such as antibodies, are not commercially available. Exogenous expression of tagged proteins in vivo solves some of these problems, but this approach can be technically challenging because either a mouse must be engineered for each protein of interest or viral vectors are required for adequate levels of expression. While viral vectors can infect target cells following local administration, they carry the risk of genome integration that may interfere with downstream analyses. Plasmids are another accessible expression system, but they require ancillary means of cell penetration; electroporation is a simple physical method for this purpose that requires minimal training or specialized equipment. Here, we describe a method for in vivo plasmid expression in a foot muscle following electroporation.
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Affiliation(s)
- Steven J. Foltz
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Criss H. Hartzell
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Hyojung J. Choo
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
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5
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Introduction. Neuromuscul Disord 2022. [DOI: 10.1016/b978-0-323-71317-7.00001-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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François-Heude MC, Walther-Louvier U, Espil-Taris C, Beze-Beyrie P, Rivier F, Baudou E, Uro-Coste E, Rigau V, Martin Negrier ML, Rendu J, Morales RJ, Pégeot H, Thèze C, Lacourt D, Coville AC, Cossée M, Cances C. Evaluating next-generation sequencing in neuromuscular diseases with neonatal respiratory distress. Eur J Paediatr Neurol 2021; 31:78-87. [PMID: 33667896 DOI: 10.1016/j.ejpn.2021.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/18/2020] [Accepted: 01/19/2021] [Indexed: 02/09/2023]
Abstract
With the exception of infantile spinal muscular atrophy (SMA) and congenital myotonic dystrophy 1 (DM1), congenital myopathies and muscular dystrophies with neonatal respiratory distress pose diagnostic challenges. Next-generation sequencing (NGS) provides hope for the diagnosis of these rare diseases. We evaluated the efficiency of next-generation sequencing (NGS) in ventilated newborns with peripheral hypotonia. We compared the results of our previous study in a cohort of 19 patients analysed by Sanger sequencing from 2007 to 2012, with a diagnostic yield of 26% (5/19), and those of a new retrospective study in 28 patients from 2007 to 2018 diagnosed using MyoPanel, a neuromuscular disease panel, with a diagnostic yield of 43% (12/28 patients). Pathogenic variants were found in five genes: ACTA1 (n = 4 patients), RYR1 (n = 2), CACNA1S (n = 1), NEB (n = 3), and MTM1 (n = 2). Myopanel increased the diagnosis of congenital neuromuscular diseases, but more than half the patients remained undiagnosed. Whole exome sequencing did not seem to fully respond to this diagnostic limitation. Therefore, explorations with whole genome sequencing will be the next step.
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Affiliation(s)
- Marie-Céline François-Heude
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Toulouse University Hospital, Toulouse, France
| | - Ulrike Walther-Louvier
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Montpellier University Hospital, Montpellier, France
| | - Caroline Espil-Taris
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Bordeaux University Hospital, Aquitaine, France
| | | | - François Rivier
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Montpellier University Hospital, Montpellier, France
| | - Eloise Baudou
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Toulouse University Hospital, Toulouse, France
| | - Emmanuelle Uro-Coste
- Department of Pathology, Toulouse University Hospital, Toulouse, France; INSERM U1037, Cancer Research Centre of Toulouse (CRCT), Toulouse, France
| | - Valérie Rigau
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Aquitaine, France; Department of Pathology, Centre Hospitalier Universitaire Montpellier, Montpellier, France
| | | | - John Rendu
- INSERM U1216, Grenoble Alpes University Hospital, University of Grenoble Alpes, Grenoble, France
| | - Raul Juntas Morales
- Laboratory of Rare Genetic Diseases (LGMR), University of Montpellier, Montpellier, France
| | - Henri Pégeot
- Molecular Genetics Laboratory, Montpellier University Hospital Centre, Montpellier, France
| | - Corinne Thèze
- Molecular Genetics Laboratory, Montpellier University Hospital Centre, Montpellier, France
| | - Delphine Lacourt
- Molecular Genetics Laboratory, Montpellier University Hospital Centre, Montpellier, France
| | - Anne Cécile Coville
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Toulouse University Hospital, Toulouse, France
| | - Mireille Cossée
- Laboratory of Rare Genetic Diseases (LGMR), University of Montpellier, Montpellier, France; Molecular Genetics Laboratory, Montpellier University Hospital Centre, Montpellier, France
| | - Claude Cances
- AOC (Atlantique-Occitanie-Caraïbe) Reference Centre for Neuromuscular Disorders, Neuropaediatric Department, Toulouse University Hospital, Toulouse, France.
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7
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Savarese M, Johari M, Johnson K, Arumilli M, Torella A, Töpf A, Rubegni A, Kuhn M, Giugliano T, Gläser D, Fattori F, Thompson R, Penttilä S, Lehtinen S, Gibertini S, Ruggieri A, Mora M, Maver A, Peterlin B, Mankodi A, Lochmüller H, Santorelli FM, Schoser B, Fajkusová L, Straub V, Nigro V, Hackman P, Udd B. Improved Criteria for the Classification of Titin Variants in Inherited Skeletal Myopathies. J Neuromuscul Dis 2020; 7:153-166. [PMID: 32039858 DOI: 10.3233/jnd-190423] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Extensive genetic screening results in the identification of thousands of rare variants that are difficult to interpret. Because of its sheer size, rare variants in the titin gene (TTN) are detected frequently in any individual. Unambiguous interpretation of molecular findings is almost impossible in many patients with myopathies or cardiomyopathies. OBJECTIVE To refine the current classification framework for TTN-associated skeletal muscle disorders and standardize the interpretation of TTN variants. METHODS We used the guidelines issued by the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) to re-analyze TTN genetic findings from our patient cohort. RESULTS We identified in the classification guidelines three rules that are not applicable to titin-related skeletal muscle disorders; six rules that require disease-/gene-specific adjustments and four rules requiring quantitative thresholds for a proper use. In three cases, the rule strength need to be modified. CONCLUSIONS We suggest adjustments are made to the guidelines. We provide frequency thresholds to facilitate filtering of candidate causative variants and guidance for the use and interpretation of functional data and co-segregation evidence. We expect that the variant classification framework for TTN-related skeletal muscle disorders will be further improved along with a better understanding of these diseases.
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Affiliation(s)
- Marco Savarese
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Mridul Johari
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Katherine Johnson
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Meharji Arumilli
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Annalaura Torella
- Dipartimento di Medicina di Precisione, Universitá degli Studi della Campania "Luigi Vanvitelli", Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Ana Töpf
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Teresa Giugliano
- Dipartimento di Medicina di Precisione, Universitá degli Studi della Campania "Luigi Vanvitelli", Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | | | - Fabiana Fattori
- Unit for Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Hospital, Rome, Italy
| | - Rachel Thompson
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Sini Penttilä
- Neuromuscular Research Center, Department of Genetics, Fimlab Laboratories, Tampere, Finland
| | - Sara Lehtinen
- Neuromuscular Research Center, Department of Genetics, Fimlab Laboratories, Tampere, Finland
| | - Sara Gibertini
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Alessandra Ruggieri
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy.,Department of Molecular and Translation Medicine, Unit of Biology and Genetics, University of Brescia, Brescia, Italy
| | - Marina Mora
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Ales Maver
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Ami Mankodi
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, Unites States
| | - Hanns Lochmüller
- Department of Neuropediatrics and Muscle Disorders, Medical Center - University of Freiburg, Faculty of Medicine, Freiburg, Germany.,Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
| | | | - Benedikt Schoser
- Friedrich-Baur-Institut, Neurologische Klinik Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lenka Fajkusová
- Centre of Molecular Biology and Gene Therapy, University Hospital Brno and Masaryk University Brno, Brno, Czech Republic
| | - Volker Straub
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Vincenzo Nigro
- Dipartimento di Medicina di Precisione, Universitá degli Studi della Campania "Luigi Vanvitelli", Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Peter Hackman
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Bjarne Udd
- Folkhälsan Research Center, Helsinki, Finland.,Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland.,Department of Neurology, Vaasa Central Hospital, Vaasa, Finland.,Neuromuscular Research Center, Tampere University and University Hospital, Tampere, Finland
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8
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Beecroft SJ, Lamont PJ, Edwards S, Goullée H, Davis MR, Laing NG, Ravenscroft G. The Impact of Next-Generation Sequencing on the Diagnosis, Treatment, and Prevention of Hereditary Neuromuscular Disorders. Mol Diagn Ther 2020; 24:641-652. [PMID: 32997275 DOI: 10.1007/s40291-020-00495-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2020] [Indexed: 12/13/2022]
Abstract
The impact of high-throughput sequencing in genetic neuromuscular disorders cannot be overstated. The ability to rapidly and affordably sequence multiple genes simultaneously has enabled a second golden age of Mendelian disease gene discovery, with flow-on impacts for rapid genetic diagnosis, evidence-based treatment, tailored therapy development, carrier-screening, and prevention of disease recurrence in families. However, there are likely many more neuromuscular disease genes and mechanisms to be discovered. Many patients and families remain without a molecular diagnosis following targeted panel sequencing, clinical exome sequencing, or even genome sequencing. Here we review how massively parallel, or next-generation, sequencing has changed the field of genetic neuromuscular disorders, and anticipate future benefits of recent technological innovations such as RNA-seq implementation and detection of tandem repeat expansions from short-read sequencing.
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Affiliation(s)
- Sarah J Beecroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | | | - Samantha Edwards
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Hayley Goullée
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Mark R Davis
- Neurogenetic Unit, Department of Diagnostic Genomics, PP Block, QEII Medical Centre, Nedlands, WA, Australia
| | - Nigel G Laing
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia.,Neurogenetic Clinic, Royal Perth Hospital, Perth, Australia
| | - Gianina Ravenscroft
- Neurogenetic Diseases Group, Centre for Medical Research, QEII Medical Centre, University of Western Australia, 6 Verdun St, Nedlands, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, 6009, Australia.
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9
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Winder TL, Tan CA, Klemm S, White H, Westbrook JM, Wang JZ, Entezam A, Truty R, Nussbaum RL, McNally EM, Aradhya S. Clinical utility of multigene analysis in over 25,000 patients with neuromuscular disorders. NEUROLOGY-GENETICS 2020; 6:e412. [PMID: 32337338 PMCID: PMC7164976 DOI: 10.1212/nxg.0000000000000412] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 12/30/2019] [Indexed: 11/29/2022]
Abstract
Objective Molecular genetic testing for hereditary neuromuscular disorders is increasingly used to identify disease subtypes, determine prevalence, and inform management and prognosis, and although many small disease-specific studies have demonstrated the utility of genetic testing, comprehensive data sets are better positioned to assess the complexity of genetic analysis. Methods Using high depth-of-coverage next-generation sequencing (NGS) with simultaneous detection of sequence variants and copy number variants (CNVs), we tested 25,356 unrelated individuals for subsets of 266 genes. Results A definitive molecular diagnosis was obtained in 20% of this cohort, with yields ranging from 4% among individuals with congenital myasthenic syndrome to 33% among those with a muscular dystrophy. CNVs accounted for as much as 39% of all clinically significant variants, with 10% of them occurring as rare, private pathogenic variants. Multigene testing successfully addressed differential diagnoses in at least 6% of individuals with positive results. Even for classic disorders like Duchenne muscular dystrophy, at least 49% of clinically significant results were identified through gene panels intended for differential diagnoses rather than through single-gene analysis. Variants of uncertain significance (VUS) were observed in 53% of individuals. Only 0.7% of these variants were later reclassified as clinically significant, most commonly in RYR1, GDAP1, SPAST, and MFN2, providing insight into the types of evidence that support VUS resolution and informing expectations of reclassification rates. Conclusions These data provide guidance for clinicians using genetic testing to diagnose neuromuscular disorders and represent one of the largest studies demonstrating the utility of NGS-based testing for these disorders.
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Affiliation(s)
- Thomas L Winder
- Invitae Corporation (T.L.W., C.A.T., S.K., H.W., J.M.W., J.Z.W., A.E., R.T., R.L.N., S.A.), San Francisco, CA; Volunteer Faculty (R.L.N.), University of California, San Francisco; and Center for Genetic Medicine (E.M.M.), Northwestern University, Evanston, IL
| | - Christopher A Tan
- Invitae Corporation (T.L.W., C.A.T., S.K., H.W., J.M.W., J.Z.W., A.E., R.T., R.L.N., S.A.), San Francisco, CA; Volunteer Faculty (R.L.N.), University of California, San Francisco; and Center for Genetic Medicine (E.M.M.), Northwestern University, Evanston, IL
| | - Sarah Klemm
- Invitae Corporation (T.L.W., C.A.T., S.K., H.W., J.M.W., J.Z.W., A.E., R.T., R.L.N., S.A.), San Francisco, CA; Volunteer Faculty (R.L.N.), University of California, San Francisco; and Center for Genetic Medicine (E.M.M.), Northwestern University, Evanston, IL
| | - Hannah White
- Invitae Corporation (T.L.W., C.A.T., S.K., H.W., J.M.W., J.Z.W., A.E., R.T., R.L.N., S.A.), San Francisco, CA; Volunteer Faculty (R.L.N.), University of California, San Francisco; and Center for Genetic Medicine (E.M.M.), Northwestern University, Evanston, IL
| | - Jody M Westbrook
- Invitae Corporation (T.L.W., C.A.T., S.K., H.W., J.M.W., J.Z.W., A.E., R.T., R.L.N., S.A.), San Francisco, CA; Volunteer Faculty (R.L.N.), University of California, San Francisco; and Center for Genetic Medicine (E.M.M.), Northwestern University, Evanston, IL
| | - James Z Wang
- Invitae Corporation (T.L.W., C.A.T., S.K., H.W., J.M.W., J.Z.W., A.E., R.T., R.L.N., S.A.), San Francisco, CA; Volunteer Faculty (R.L.N.), University of California, San Francisco; and Center for Genetic Medicine (E.M.M.), Northwestern University, Evanston, IL
| | - Ali Entezam
- Invitae Corporation (T.L.W., C.A.T., S.K., H.W., J.M.W., J.Z.W., A.E., R.T., R.L.N., S.A.), San Francisco, CA; Volunteer Faculty (R.L.N.), University of California, San Francisco; and Center for Genetic Medicine (E.M.M.), Northwestern University, Evanston, IL
| | - Rebecca Truty
- Invitae Corporation (T.L.W., C.A.T., S.K., H.W., J.M.W., J.Z.W., A.E., R.T., R.L.N., S.A.), San Francisco, CA; Volunteer Faculty (R.L.N.), University of California, San Francisco; and Center for Genetic Medicine (E.M.M.), Northwestern University, Evanston, IL
| | - Robert L Nussbaum
- Invitae Corporation (T.L.W., C.A.T., S.K., H.W., J.M.W., J.Z.W., A.E., R.T., R.L.N., S.A.), San Francisco, CA; Volunteer Faculty (R.L.N.), University of California, San Francisco; and Center for Genetic Medicine (E.M.M.), Northwestern University, Evanston, IL
| | - Elizabeth M McNally
- Invitae Corporation (T.L.W., C.A.T., S.K., H.W., J.M.W., J.Z.W., A.E., R.T., R.L.N., S.A.), San Francisco, CA; Volunteer Faculty (R.L.N.), University of California, San Francisco; and Center for Genetic Medicine (E.M.M.), Northwestern University, Evanston, IL
| | - Swaroop Aradhya
- Invitae Corporation (T.L.W., C.A.T., S.K., H.W., J.M.W., J.Z.W., A.E., R.T., R.L.N., S.A.), San Francisco, CA; Volunteer Faculty (R.L.N.), University of California, San Francisco; and Center for Genetic Medicine (E.M.M.), Northwestern University, Evanston, IL
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10
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Välipakka S, Savarese M, Sagath L, Arumilli M, Giugliano T, Udd B, Hackman P. Improving Copy Number Variant Detection from Sequencing Data with a Combination of Programs and a Predictive Model. J Mol Diagn 2020; 22:40-49. [DOI: 10.1016/j.jmoldx.2019.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/25/2019] [Accepted: 08/08/2019] [Indexed: 12/18/2022] Open
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11
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Karakaya M, Storbeck M, Strathmann EA, Delle Vedove A, Hölker I, Altmueller J, Naghiyeva L, Schmitz-Steinkrüger L, Vezyroglou K, Motameny S, Alawbathani S, Thiele H, Polat AI, Okur D, Boostani R, Karimiani EG, Wunderlich G, Ardicli D, Topaloglu H, Kirschner J, Schrank B, Maroofian R, Magnusson O, Yis U, Nürnberg P, Heller R, Wirth B. Targeted sequencing with expanded gene profile enables high diagnostic yield in non-5q-spinal muscular atrophies. Hum Mutat 2018; 39:1284-1298. [PMID: 29858556 DOI: 10.1002/humu.23560] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/14/2018] [Accepted: 05/30/2018] [Indexed: 11/08/2022]
Abstract
Spinal muscular atrophies (SMAs) are a heterogeneous group of disorders characterized by muscular atrophy, weakness, and hypotonia due to suspected lower motor neuron degeneration (LMND). In a large cohort of 3,465 individuals suspected with SMA submitted for SMN1 testing to our routine diagnostic laboratory, 48.8% carried a homozygous SMN1 deletion, 2.8% a subtle mutation, and an SMN1 deletion, whereas 48.4% remained undiagnosed. Recently, several other genes implicated in SMA/LMND have been reported. Despite several efforts to establish a diagnostic algorithm for non-5q-SMA (SMA without deletion or point mutations in SMN1 [5q13.2]), data from large-scale studies are not available. We tested the clinical utility of targeted sequencing in non-5q-SMA by developing two different gene panels. We first analyzed 30 individuals with a small panel including 62 genes associated with LMND using IonTorrent-AmpliSeq target enrichment. Then, additional 65 individuals were tested with a broader panel encompassing up to 479 genes implicated in neuromuscular diseases (NMDs) with Agilent-SureSelect target enrichment. The NMD panel provided a higher diagnostic yield (33%) than the restricted LMND panel (13%). Nondiagnosed cases were further subjected to exome or genome sequencing. Our experience supports the use of gene panels covering a broad disease spectrum for diseases that are highly heterogeneous and clinically difficult to differentiate.
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Affiliation(s)
- Mert Karakaya
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Markus Storbeck
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Eike A Strathmann
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Andrea Delle Vedove
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Irmgard Hölker
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Janine Altmueller
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Leyla Naghiyeva
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Lea Schmitz-Steinkrüger
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Katharina Vezyroglou
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Susanne Motameny
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Salem Alawbathani
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Ayse Ipek Polat
- Dokuz Eylül University, Department of Pediatric Neurology, Izmir, Turkey
| | - Derya Okur
- Dokuz Eylül University, Department of Pediatric Neurology, Izmir, Turkey
| | - Reza Boostani
- Mashhad University of Medical Sciences, Department of Neurology, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Next Generation Genetic Polyclinic, Mashhad, Iran.,Razavi Cancer Research Center, Razavi Hospital, Imam Reza International University, Mashhad, Iran
| | | | - Didem Ardicli
- Hacettepe University, Department of Pediatric Neurology, Ankara, Turkey
| | - Haluk Topaloglu
- Hacettepe University, Department of Pediatric Neurology, Ankara, Turkey
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Bertold Schrank
- DKD HELIOS Kliniken, Department of Neurology, Wiesbaden, Germany
| | - Reza Maroofian
- Genetics and Molecular Cell Sciences Research Centre, St George's University of London, London, UK
| | | | - Uluc Yis
- Dokuz Eylül University, Department of Pediatric Neurology, Izmir, Turkey
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Raoul Heller
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
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12
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Howell RR, Zuchner S. MOVR-NeuroMuscular ObserVational Research, a unified data hub for neuromuscular diseases. Genet Med 2018; 21:536-538. [PMID: 29934516 DOI: 10.1038/s41436-018-0086-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/01/2018] [Indexed: 11/09/2022] Open
Affiliation(s)
- R Rodney Howell
- Chairman of the Board, Muscular Dystrophy Association, Miami, Florida, USA.
| | - Stephan Zuchner
- Department of Human Genetics at the University of Miami and Member, Scientific Advisory Board to the MDA, Miami, Florida, USA
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13
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Punetha J, Kesari A, Uapinyoying P, Giri M, Clarke NF, Waddell LB, North KN, Ghaoui R, O'Grady GL, Oates EC, Sandaradura SA, Bönnemann CG, Donkervoort S, Plotz PH, Smith EC, Tesi-Rocha C, Bertorini TE, Tarnopolsky MA, Reitter B, Hausmanowa-Petrusewicz I, Hoffman EP. Targeted Re-Sequencing Emulsion PCR Panel for Myopathies: Results in 94 Cases. J Neuromuscul Dis 2018; 3:209-225. [PMID: 27854218 DOI: 10.3233/jnd-160151] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Molecular diagnostics in the genetic myopathies often requires testing of the largest and most complex transcript units in the human genome (DMD, TTN, NEB). Iteratively targeting single genes for sequencing has traditionally entailed high costs and long turnaround times. Exome sequencing has begun to supplant single targeted genes, but there are concerns regarding coverage and needed depth of the very large and complex genes that frequently cause myopathies. OBJECTIVE To evaluate efficiency of next-generation sequencing technologies to provide molecular diagnostics for patients with previously undiagnosed myopathies. METHODS We tested a targeted re-sequencing approach, using a 45 gene emulsion PCR myopathy panel, with subsequent sequencing on the Illumina platform in 94 undiagnosed patients. We compared the targeted re-sequencing approach to exome sequencing for 10 of these patients studied. RESULTS We detected likely pathogenic mutations in 33 out of 94 patients with a molecular diagnostic rate of approximately 35%. The remaining patients showed variants of unknown significance (35/94 patients) or no mutations detected in the 45 genes tested (26/94 patients). Mutation detection rates for targeted re-sequencing vs. whole exome were similar in both methods; however exome sequencing showed better distribution of reads and fewer exon dropouts. CONCLUSIONS Given that costs of highly parallel re-sequencing and whole exome sequencing are similar, and that exome sequencing now takes considerably less laboratory processing time than targeted re-sequencing, we recommend exome sequencing as the standard approach for molecular diagnostics of myopathies.
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Affiliation(s)
- Jaya Punetha
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA.,Department of Integrative Systems Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Akanchha Kesari
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA
| | - Prech Uapinyoying
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA.,Department of Integrative Systems Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Mamta Giri
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA
| | - Nigel F Clarke
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Leigh B Waddell
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Kathryn N North
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia.,Murdoch Childrens Research Institute, Melbourne, Australia; Department of Paediatrics, Faculty of Medicine, University of Melbourne, Melbourne, Australia
| | - Roula Ghaoui
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Gina L O'Grady
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Emily C Oates
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Sarah A Sandaradura
- INMR, The Children's Hospital at Westmead & Discipline of Paediatrics and Child Health, University of Sydney, Sydney, Australia
| | - Carsten G Bönnemann
- National Institute of Neurological Disorders and Stroke/NIH, Porter Neuroscience Research Center, Bethesda, MD, USA
| | - Sandra Donkervoort
- National Institute of Neurological Disorders and Stroke/NIH, Porter Neuroscience Research Center, Bethesda, MD, USA
| | - Paul H Plotz
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Edward C Smith
- Department of Pediatrics, Division of Pediatric Neurology, Duke University Medical Center, Durham, NC, USA
| | - Carolina Tesi-Rocha
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA
| | - Tulio E Bertorini
- Department of Neurology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mark A Tarnopolsky
- Departments of Pediatrics and Medicine, McMaster University, Neuromuscular Disease Clinic, Health Sciences Centre, ON, Canada
| | - Bernd Reitter
- Children's Hospital, Johannes Gutenberg University, Mainz, Germany
| | | | - Eric P Hoffman
- Research Center for Genetic Medicine, Children's National Medical Center, Washington DC, USA.,Department of Integrative Systems Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
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14
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Congenital myopathies: disorders of excitation-contraction coupling and muscle contraction. Nat Rev Neurol 2018; 14:151-167. [PMID: 29391587 DOI: 10.1038/nrneurol.2017.191] [Citation(s) in RCA: 177] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The congenital myopathies are a group of early-onset, non-dystrophic neuromuscular conditions with characteristic muscle biopsy findings, variable severity and a stable or slowly progressive course. Pronounced weakness in axial and proximal muscle groups is a common feature, and involvement of extraocular, cardiorespiratory and/or distal muscles can implicate specific genetic defects. Central core disease (CCD), multi-minicore disease (MmD), centronuclear myopathy (CNM) and nemaline myopathy were among the first congenital myopathies to be reported, and they still represent the main diagnostic categories. However, these entities seem to belong to a much wider phenotypic spectrum. To date, congenital myopathies have been attributed to mutations in over 20 genes, which encode proteins implicated in skeletal muscle Ca2+ homeostasis, excitation-contraction coupling, thin-thick filament assembly and interactions, and other mechanisms. RYR1 mutations are the most frequent genetic cause, and CCD and MmD are the most common subgroups. Next-generation sequencing has vastly improved mutation detection and has enabled the identification of novel genetic backgrounds. At present, management of congenital myopathies is largely supportive, although new therapeutic approaches are reaching the clinical trial stage.
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15
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Harris E, Topf A, Barresi R, Hudson J, Powell H, Tellez J, Hicks D, Porter A, Bertoli M, Evangelista T, Marini-Betollo C, Magnússon Ó, Lek M, MacArthur D, Bushby K, Lochmüller H, Straub V. Exome sequences versus sequential gene testing in the UK highly specialised Service for Limb Girdle Muscular Dystrophy. Orphanet J Rare Dis 2017; 12:151. [PMID: 28877744 PMCID: PMC5588739 DOI: 10.1186/s13023-017-0699-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/22/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Limb girdle muscular dystrophies are a group of rare and genetically heterogeneous diseases that share proximal weakness as a common feature; however they are often lacking very specific phenotypic features to allow an accurate differential diagnosis based on the clinical signs only, limiting the diagnostic rate using phenotype driven genetic testing. Next generation sequencing provides an opportunity to obtain molecular diagnoses for undiagnosed patients, as well as identifying novel genetic causes of muscle diseases. We performed whole exome sequencing (WES) on 104 affected individuals from 75 families in who standard gene by gene testing had not yielded a diagnosis. For comparison we also evaluated the diagnostic rate using sequential gene by gene testing for 91 affected individuals from 84 families over a 2 year period. RESULTS Patients selected for WES had undergone more extensive prior testing than those undergoing standard genetic testing and on average had had 8 genes screened already. In this extensively investigated cohort WES identified the genetic diagnosis in 28 families (28/75, 37%), including the identification of the novel gene ZAK and two unpublished genes. WES of a single affected individual with sporadic disease yielded a diagnosis in 13/38 (34%) of cases. In comparison, conventional gene by gene testing provided a genetic diagnosis in 28/84 (33%) families. Titinopathies and collagen VI related dystrophy were the most frequent diagnoses made by WES. Reasons why mutations in known genes were not identified previously included atypical phenotypes, reassignment of pathogenicity of variants, and in one individual mosaicism for a COL6A1 mutation which was undetected by prior direct sequencing. CONCLUSION WES was able to overcome many limitations of standard testing and achieved a higher rate of diagnosis than standard testing even in this cohort of extensively investigated patients. Earlier application of WES is therefore likely to yield an even higher diagnostic rate. We obtained a high diagnosis rate in simplex cases and therefore such individuals should be included in exome or genome sequencing projects. Disease due to somatic mosaicism may be increasingly recognised due to the increased sensitivity of next generation sequencing techniques to detect low level mosaicism.
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Affiliation(s)
- Elizabeth Harris
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Ana Topf
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Rita Barresi
- Muscle Immunoanalysis Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE2 4AZ, UK
| | - Judith Hudson
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Helen Powell
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - James Tellez
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Debbie Hicks
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Anna Porter
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Marta Bertoli
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Teresinha Evangelista
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Chiara Marini-Betollo
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | | | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
| | - Daniel MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
| | - Kate Bushby
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Hanns Lochmüller
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Volker Straub
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK. .,Newcastle University John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle upon Tyne, UK.
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16
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A novel recessive TTN founder variant is a common cause of distal myopathy in the Serbian population. Eur J Hum Genet 2017; 25:572-581. [PMID: 28295036 DOI: 10.1038/ejhg.2017.16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 01/11/2017] [Accepted: 01/22/2017] [Indexed: 12/16/2022] Open
Abstract
Variants in the TTN gene have been associated with distal myopathies and other distinctive phenotypes involving skeletal and cardiac muscle. Through whole-exome sequencing we identified a novel stop-gain variant (c.107635C>T, p.(Gln35879Ter)) in the TTN gene, coding a part of the M-line of titin, in 14 patients with autosomal recessive distal myopathy and Serbian ancestry. All patients share a common 1 Mb core haplotype associated with c.107635C>T, suggesting a founder variant. In compound heterozygotes, nine other TTN variants were identified: four stop-gain, three frameshift, one missense and one splice donor variant. Patients homozygous for the common variant did not show significant clinical differences to the compound heterozygous patients. The clinical presentation of all patients was an adult onset distal myopathy with predominant lower limb involvement. In addition, most patients had normal to mildly elevated serum creatine kinase levels, myopathic electromyograms, normal cardiologic and respiratory tests and muscle pathology consistent with a dystrophic process. In this study, we describe a distinct phenotype for patients with distal myopathy associated with novel recessive TTN variants including a Serbian founder variant. Our results expand the phenotypic and genetic spectrum of titinopathies and will facilitate the diagnosis of this condition in patients of Serbian origin.
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17
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Thompson R, Straub V. Limb-girdle muscular dystrophies - international collaborations for translational research. Nat Rev Neurol 2016; 12:294-309. [PMID: 27033376 DOI: 10.1038/nrneurol.2016.35] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The limb-girdle muscular dystrophies (LGMDs) are a diverse group of genetic neuromuscular conditions that usually manifest in the proximal muscles of the hip and shoulder girdles. Since the identification of the first gene associated with the phenotype in 1994, an extensive body of research has identified the genetic defects responsible for over 30 LGMD subtypes, revealed an increasingly varied phenotypic spectrum, and exposed the need to move towards a systems-based understanding of the molecular pathways affected. New sequencing technologies, including whole-exome and whole-genome sequencing, are continuing to expand the range of genes and phenotypes associated with the LGMDs, and new computational approaches are helping clinicians to adapt to this new genomic medicine paradigm. However, 60 years on from the first description of LGMD, no curative therapies exist, and systematic exploration of the natural history is still lacking. To enable rapid translation of basic research to the clinic, well-phenotyped and genetically characterized patient cohorts are a necessity, and appropriate outcome measures and biomarkers must be developed through natural history studies. Here, we review the international collaborations that are addressing these translational research issues, and the lessons learned from large-scale LGMD sequencing programmes.
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Affiliation(s)
- Rachel Thompson
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Volker Straub
- The John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
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