1
|
Parmar JM, Laing NG, Kennerson ML, Ravenscroft G. Genetics of inherited peripheral neuropathies and the next frontier: looking backwards to progress forwards. J Neurol Neurosurg Psychiatry 2024:jnnp-2024-333436. [PMID: 38744462 DOI: 10.1136/jnnp-2024-333436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/10/2024] [Indexed: 05/16/2024]
Abstract
Inherited peripheral neuropathies (IPNs) encompass a clinically and genetically heterogeneous group of disorders causing length-dependent degeneration of peripheral autonomic, motor and/or sensory nerves. Despite gold-standard diagnostic testing for pathogenic variants in over 100 known associated genes, many patients with IPN remain genetically unsolved. Providing patients with a diagnosis is critical for reducing their 'diagnostic odyssey', improving clinical care, and for informed genetic counselling. The last decade of massively parallel sequencing technologies has seen a rapid increase in the number of newly described IPN-associated gene variants contributing to IPN pathogenesis. However, the scarcity of additional families and functional data supporting variants in potential novel genes is prolonging patient diagnostic uncertainty and contributing to the missing heritability of IPNs. We review the last decade of IPN disease gene discovery to highlight novel genes, structural variation and short tandem repeat expansions contributing to IPN pathogenesis. From the lessons learnt, we provide our vision for IPN research as we anticipate the future, providing examples of emerging technologies, resources and tools that we propose that will expedite the genetic diagnosis of unsolved IPN families.
Collapse
Affiliation(s)
- Jevin M Parmar
- Rare Disease Genetics and Functional Genomics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Nigel G Laing
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Preventive Genetics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, New South Wales, Australia
| | - Gianina Ravenscroft
- Rare Disease Genetics and Functional Genomics, Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Ng KWP, Chin HL, Chin AXY, Goh DLM. Using gene panels in the diagnosis of neuromuscular disorders: A mini-review. Front Neurol 2022; 13:997551. [PMID: 36313509 PMCID: PMC9602396 DOI: 10.3389/fneur.2022.997551] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/21/2022] [Indexed: 09/26/2023] Open
Abstract
The diagnosis of inherited neuromuscular disorders is challenging due to their genetic and phenotypic variability. Traditionally, neurophysiology and histopathology were primarily used in the initial diagnostic approach to these conditions. Sanger sequencing for molecular diagnosis was less frequently utilized as its application was a time-consuming and cost-intensive process. The advent and accessibility of next-generation sequencing (NGS) has revolutionized the evaluation process of genetically heterogenous neuromuscular disorders. Current NGS diagnostic testing approaches include gene panels, whole exome sequencing (WES), and whole genome sequencing (WGS). Gene panels are often the most widely used, being more accessible due to availability and affordability. In this mini-review, we describe the benefits and risks of clinical genetic testing. We also discuss the utility, benefits, challenges, and limitations of using gene panels in the evaluation of neuromuscular disorders.
Collapse
Affiliation(s)
- Kay W. P. Ng
- Division of Neurology, Department of Medicine, National University Hospital, Singapore, Singapore
| | - Hui-Lin Chin
- Division of Genetics and Metabolism, Department of Paediatrics, Khoo Teck Puat - National University Children's Medical Institute, National University Hospital, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Amanda X. Y. Chin
- Division of Neurology, Department of Medicine, National University Hospital, Singapore, Singapore
| | - Denise Li-Meng Goh
- Division of Genetics and Metabolism, Department of Paediatrics, Khoo Teck Puat - National University Children's Medical Institute, National University Hospital, Singapore, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| |
Collapse
|
4
|
Lescouzères L, Bordignon B, Bomont P. Development of a high-throughput tailored imaging method in zebrafish to understand and treat neuromuscular diseases. Front Mol Neurosci 2022; 15:956582. [PMID: 36204134 PMCID: PMC9530744 DOI: 10.3389/fnmol.2022.956582] [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: 05/30/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
The zebrafish (Danio rerio) is a vertebrate species offering multitude of advantages for the study of conserved biological systems in human and has considerably enriched our knowledge in developmental biology and physiology. Being equally important in medical research, the zebrafish has become a critical tool in the fields of diagnosis, gene discovery, disease modeling, and pharmacology-based therapy. Studies on the zebrafish neuromuscular system allowed for deciphering key molecular pathways in this tissue, and established it as a model of choice to study numerous motor neurons, neuromuscular junctions, and muscle diseases. Starting with the similarities of the zebrafish neuromuscular system with the human system, we review disease models associated with the neuromuscular system to focus on current methodologies employed to study them and outline their caveats. In particular, we put in perspective the necessity to develop standardized and high-resolution methodologies that are necessary to deepen our understanding of not only fundamental signaling pathways in a healthy tissue but also the changes leading to disease phenotype outbreaks, and offer templates for high-content screening strategies. While the development of high-throughput methodologies is underway for motility assays, there is no automated approach to quantify the key molecular cues of the neuromuscular junction. Here, we provide a novel high-throughput imaging methodology in the zebrafish that is standardized, highly resolutive, quantitative, and fit for drug screening. By providing a proof of concept for its robustness in identifying novel molecular players and therapeutic drugs in giant axonal neuropathy (GAN) disease, we foresee that this new tool could be useful for both fundamental and biomedical research.
Collapse
Affiliation(s)
- Léa Lescouzères
- ERC Team, Institut NeuroMyoGéne-PGNM, Inserm U1315, CNRS UMR 5261, Claude Bernard University Lyon 1, Lyon, France
| | - Benoît Bordignon
- Montpellier Ressources Imagerie, BioCampus, CNRS, INSERM, University of Montpellier, Montpellier, France
| | - Pascale Bomont
- ERC Team, Institut NeuroMyoGéne-PGNM, Inserm U1315, CNRS UMR 5261, Claude Bernard University Lyon 1, Lyon, France
| |
Collapse
|
5
|
Hsueh HW, Weng WC, Fan PC, Chien YH, Yang FJ, Lee WT, Lin RJ, Hwu WL, Yang CC, Lee NC. The diversity of hereditary neuromuscular diseases: Experiences from molecular diagnosis. J Formos Med Assoc 2022; 121:2574-2583. [PMID: 35821219 DOI: 10.1016/j.jfma.2022.06.012] [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: 07/07/2021] [Revised: 03/02/2022] [Accepted: 06/23/2022] [Indexed: 11/16/2022]
Abstract
BACKGROUND Hereditary neuromuscular diseases (NMDs) are a group of rare disorders, and the diagnosis of these diseases is a substantial burden for referral centers. Although next-generation sequencing (NGS) has identified a large number of genes associated with hereditary NMDs, the diagnostic rates still vary across centers. METHODS Patients with a suspected hereditary NMD were referred to neuromuscular specialists at the National Taiwan University Hospital. Molecular diagnoses were performed by employing a capture panel containing 194 genes associated with NMDs. RESULTS Among the 50 patients referred, 43 had a suspicion of myopathy, and seven had polyneuropathy. The overall diagnostic rate was 58%. Pathogenic variants in 19 genes were observed; the most frequent pathogenic variant found in this cohort (DYSF) was observed in only four patients, and 10 pathogenic variants were observed in one patient each. One case of motor neuron disease was clinically mistaken for myopathy. A positive family history increased the diagnostic rate (positive: 72.7% vs. negative: 56.3%). Fourteen patients with elevated plasma creatine kinase levels remained without a diagnosis. CONCLUSION The application of NGS in this single-center study proves the great diversity of hereditary NMDs. A capture panel is essential, but high-quality clinical and laboratory evaluations of patients are also indispensable.
Collapse
Affiliation(s)
- Hsueh-Wen Hsueh
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Chin Weng
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pi-Chuan Fan
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yin-Hsiu Chien
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Feng-Jung Yang
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan
| | - Wang-Tso Lee
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ru-Jen Lin
- Department of Neurology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
| | - Wuh-Liang Hwu
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Chih-Chao Yang
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Ni-Chung Lee
- Department of Pediatrics, National Taiwan University Hospital, Taipei, Taiwan; Department of Pediatrics, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.
| |
Collapse
|
6
|
Barbosa-Gouveia S, Vázquez-Mosquera ME, González-Vioque E, Hermida-Ameijeiras Á, Sánchez-Pintos P, de Castro MJ, León SR, Gil-Fournier B, Domínguez-González C, Camacho Salas A, Negrão L, Fineza I, Laranjeira F, Couce ML. Rapid Molecular Diagnosis of Genetically Inherited Neuromuscular Disorders Using Next-Generation Sequencing Technologies. J Clin Med 2022; 11:jcm11102750. [PMID: 35628876 PMCID: PMC9143479 DOI: 10.3390/jcm11102750] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/13/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023] Open
Abstract
Neuromuscular diseases are genetically highly heterogeneous, and differential diagnosis can be challenging. Over a 3-year period, we prospectively analyzed 268 pediatric and adult patients with a suspected diagnosis of inherited neuromuscular disorder (INMD) using comprehensive gene-panel analysis and next-generation sequencing. The rate of diagnosis increased exponentially with the addition of genes to successive versions of the INMD panel, from 31% for the first iteration (278 genes) to 40% for the last (324 genes). The global mean diagnostic rate was 36% (97/268 patients), with a diagnostic turnaround time of 4–6 weeks. Most diagnoses corresponded to muscular dystrophies/myopathies (68.37%) and peripheral nerve diseases (22.45%). The most common causative genes, TTN, RYR1, and ANO5, accounted for almost 30% of the diagnosed cases. Finally, we evaluated the utility of the differential diagnosis tool Phenomizer, which established a correlation between the phenotype and molecular findings in 21% of the diagnosed patients. In summary, comprehensive gene-panel analysis of all genes implicated in neuromuscular diseases facilitates a rapid diagnosis and provides a high diagnostic yield.
Collapse
Affiliation(s)
- Sofia Barbosa-Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
- Correspondence: (S.B.-G.); (M.L.C.); Tel.: +34-981-950-151 (M.L.C.)
| | - Maria Eugenia Vázquez-Mosquera
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
| | - Emiliano González-Vioque
- Department of Clinical Biochemistry, Puerta de Hierro-Majadahonda University Hospital, 28222 Majadahonda, Spain;
| | - Álvaro Hermida-Ameijeiras
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
| | - Paula Sánchez-Pintos
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
| | - Maria José de Castro
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
| | - Soraya Ramiro León
- Genetics Department, Hospital Universitario de Getafe, 28905 Madrid, Spain; (S.R.L.); (B.G.-F.)
| | - Belén Gil-Fournier
- Genetics Department, Hospital Universitario de Getafe, 28905 Madrid, Spain; (S.R.L.); (B.G.-F.)
| | - Cristina Domínguez-González
- Neuromuscular Unit, Imas12 Research Institute, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain;
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ana Camacho Salas
- Pediatric Neurology Unit, Hospital Universitario 12 de Octubre, Complutense University of Madrid, 28041 Madrid, Spain;
| | - Luis Negrão
- Neuromuscular Diseases Unit, Neurology Service, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal;
| | - Isabel Fineza
- Pediatric Neurology Department, Child Developmental Center, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra Coimbra Portugal, 3000-075 Coimbra, Portugal;
| | - Francisco Laranjeira
- Biochemical Genetics Unit, Centro de Genética Médica Doutor Jacinto Magalhães, 4050-466 Porto, Portugal;
| | - Maria Luz Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Paediatrics, Santiago de Compostela University Clinical Hospital, 15704 Santiago de Compostela, Spain; (M.E.V.-M.); (Á.H.-A.); (P.S.-P.); (M.J.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IDIS-Health Research Institute of Santiago de Compostela, Santiago de Compostela University Clinical Hospital, European Reference Network for Hereditary Metabolic Disorders (MetabERN), 15704 Santiago de Compostela, Spain
- Correspondence: (S.B.-G.); (M.L.C.); Tel.: +34-981-950-151 (M.L.C.)
| |
Collapse
|
7
|
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]
|
8
|
Laing NG, Ong RW, Ravenscroft G. Genetic neuromuscular disorders: what is the best that we can do? Neuromuscul Disord 2021; 31:1081-1089. [PMID: 34736628 DOI: 10.1016/j.nmd.2021.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/12/2021] [Indexed: 11/17/2022]
Abstract
The major advances in genetic neuromuscular disorders in the last 30 years have been: (a) identification of the genetic basis for hundreds of these disorders, (b) through knowing the genes, understanding their pathobiology and (c) subsequent implementation of evidence-based treatments for some of the disorders. New genomic technologies are providing precision diagnosis, mode of inheritance and likely prognosis for more patients than ever before. Parents of children with a genetic diagnosis can then use preimplantation or prenatal diagnosis to avoid having further affected children if they wish. But is this the best we can do for genetic neuromuscular disorders? Since the 1980s, it has been argued it would be better to identify Duchenne muscular dystrophy carrier mothers, rather than diagnose their affected sons. Carrier screening for recessive disorders can identify couples with a high chance of having affected children. It allows couples reproductive choice and can prevent infant morbidity and mortality and significant distress for families. Professional bodies in many countries now recommend prospective parents should be informed about carrier screening. Implementing and funding expensive therapies increases the cost-effectiveness of carrier screening, increasing its attractiveness to governments. Best practice for genetic neuromuscular disorders should include equitable access to carrier screening.
Collapse
Affiliation(s)
- Nigel G Laing
- QEII Medical Centre, Neurogenetic Diseases Group, Harry Perkins Institute of Medical Research and University of Western Australia, 6 Verdun Street, Nedlands, Western Australia 6009, Australia; Neurogenetic Unit, Department of Diagnostic Genomics, PathWest Laboratory Medicine, West Australian Department of Health, QEII Medical Centre, Nedlands, Western Australia 6009, Australia.
| | - Royston W Ong
- QEII Medical Centre, Neurogenetic Diseases Group, Harry Perkins Institute of Medical Research and University of Western Australia, 6 Verdun Street, Nedlands, Western Australia 6009, Australia
| | - Gianina Ravenscroft
- QEII Medical Centre, Neurogenetic Diseases Group, Harry Perkins Institute of Medical Research and University of Western Australia, 6 Verdun Street, Nedlands, Western Australia 6009, Australia; School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia 6009, Australia
| |
Collapse
|
9
|
Megarbane A, Bizzari S, Deepthi A, Sabbagh S, Mansour H, Chouery E, Hmaimess G, Jabbour R, Mehawej C, Alame S, Hani A, Hasbini D, Ghanem I, Koussa S, Al-Ali MT, Obeid M, Talea DB, Lefranc G, Levy N, Leturcq F, El Hayek S, Delague V, Urtizberea A. A 20-year Clinical and Genetic Neuromuscular Cohort Analysis in Lebanon: An International Effort. J Neuromuscul Dis 2021; 9:193-210. [PMID: 34602496 PMCID: PMC8842757 DOI: 10.3233/jnd-210652] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Clinical and molecular data on the occurrence and frequency of inherited neuromuscular disorders (NMD) in the Lebanese population is scarce. OBJECTIVE This study aims to provide a retrospective overview of hereditary NMDs based on our clinical consultations in Lebanon. METHODS Clinical and molecular data of patients referred to a multi-disciplinary consultation for neuromuscular disorders over a 20-year period (1999-2019) was reviewed. RESULTS A total of 506 patients were diagnosed with 62 different disorders encompassing 10 classes of NMDs. 103 variants in 49 genes were identified. In this cohort, 81.4%of patients were diagnosed with motor neuron diseases and muscular dystrophies, with almost half of these described with spinal muscular atrophy (SMA) (40.3%of patients). We estimate a high SMA incidence of 1 in 7,500 births in Lebanon. Duchenne and Becker muscular dystrophy were the second most frequently diagnosed NMDs (17%of patients). The latter disorders were associated with the highest number of variants (39) identified in this study. A highly heterogeneous presentation of Limb Girdle Muscular Dystrophy and Charcot-Marie-Tooth disease was notably identified. The least common disorders (5.5%of patients) involved congenital, metabolic, and mitochondrial myopathies, congenital myasthenic syndromes, and myotonic dystrophies. A review of the literature for selected NMDs in Lebanon is provided. CONCLUSIONS Our study indicates a high prevalence and underreporting of heterogeneous forms of NMDs in Lebanon- a major challenge with many novel NMD treatments in the pipeline. This report calls for a regional NMD patient registry.
Collapse
Affiliation(s)
- Andre Megarbane
- Department of Human Genetics, Gilbert and Rose-Mary Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon.,Institut Jérôme Lejeune, Paris, France
| | | | | | - Sandra Sabbagh
- Department of Pediatrics, Hôtel Dieu de France Hospital, Beirut, Lebanon
| | - Hicham Mansour
- Department of Pediatrics, Saint George Hospital, Balamand University, Beirut, Lebanon
| | - Eliane Chouery
- Department of Human Genetics, Gilbert and Rose-Mary Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Ghassan Hmaimess
- Department of Pediatrics, Saint George Hospital, Balamand University, Beirut, Lebanon
| | - Rosette Jabbour
- Department of Neurology, Saint George Hospital, Balamand University, Beirut, Lebanon
| | - Cybel Mehawej
- Department of Human Genetics, Gilbert and Rose-Mary Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Saada Alame
- Department of Neuropediatrics, Lebanese University, Beirut, Lebanon
| | - Abeer Hani
- Departments of Pediatrics and Neurology, Gilbert and Rose-Mary Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Dana Hasbini
- Department of Pediatric Neurology, Rafic Hariri University Hospital, Beirut, Lebanon
| | - Ismat Ghanem
- Department of Orthopedics, Hotel Dieu de France Hospital, Beirut, Lebanon
| | - Salam Koussa
- Department of Neurology, Geitaoui Lebanese University Hospital, Beirut, Lebanon
| | | | - Marc Obeid
- Genetic laboratory, American University of Science and Technology, Lebanon
| | - Diana Bou Talea
- Genetic laboratory, American University of Science and Technology, Lebanon
| | - Gerard Lefranc
- Institut de Génétique Humaine, UMR 9002 CNRS-Université de Montpellier, France
| | - Nicolas Levy
- Aix Marseille Univ, Inserm, MMG, U 1251, Marseille, France
| | | | | | | | | |
Collapse
|
10
|
Gburek-Augustat J, Schoene-Bake JC, Bültmann E, Haack T, Buchert R, Synofzik M, Biskup S, Feuerhake F, Sorge I, Hartmann H. Pitfalls in Genetic Diagnostics: Why Phenotyping is Essential. Neuropediatrics 2021; 52:274-283. [PMID: 33791999 DOI: 10.1055/s-0041-1726306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
New genetic testing technologies have revolutionized medicine within the past years. It is foreseeable that the development will continue with the introduction of new techniques. Nevertheless, despite improved technology, an exact clinical description of the phenotype is still necessary and it is important to critically question findings, both before initiating genetic testing and when interpreting the results. We present four brief case vignettes to point out difficulties associated with correctly interpreting genetic findings.
Collapse
Affiliation(s)
- Janina Gburek-Augustat
- Division of Neuropediatrics, University Hospital, Hospital for Children and Adolescents, Leipzig, Germany.,Clinic for Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Hannover, Germany.,Department of Neuropediatrics, Developmental Neurology, Social Paediatrics, University Children's Hospital Tuebingen, Tuebingen, Germany
| | - Jan-Christoph Schoene-Bake
- Clinic for Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Hannover, Germany.,Gemeinschaftspraxis fuer Humangenetik, Hamburg, Germany
| | - Eva Bültmann
- Institute of Diagnostic and Interventional Neuroradiology, Hannover Medical School, Hannover, Germany
| | - Tobias Haack
- Department of Medical Genetics and Applied Genomics, Rare Disease Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Rebecca Buchert
- Department of Medical Genetics and Applied Genomics, Rare Disease Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Matthis Synofzik
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Saskia Biskup
- CeGaT GmbH, Center for Genomics and Transcriptomics, Tübingen, Germany
| | | | - Ina Sorge
- Department of Pediatric Radiology, University Hospital Leipzig, Leipzig, Germany
| | - Hans Hartmann
- Clinic for Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Hannover, Germany
| |
Collapse
|
11
|
Zhong X, Cui S, Liu L, Yang Y, Kong X. DMD/BMD prenatal diagnosis and treatment expectation in a single centre in China for 15 years. BMC Med Genomics 2021; 14:181. [PMID: 34238289 PMCID: PMC8268296 DOI: 10.1186/s12920-021-01024-8] [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: 09/12/2020] [Accepted: 06/28/2021] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE DMD/BMD prenatal diagnosis for 931 foetuses. BACKGROUND DMD is the most common fatal X-linked recessive muscular disease. There is no effective clinical treatment method at present. Accurate gene diagnosis and prenatal diagnosis technology are important ways for early detection, early prevention and early treatment. METHODS A total of 931 prenatal diagnoses were performed for pregnant women with a definite family history of DMD or a history of DMD childbirth between 2005 and 2019. This report may be considered the largest DMD prenatal diagnosis report in a single centre worldwide. Multiple ligation-dependent probe amplification (MLPA) and next-generation sequencing were used in combination. Techniques and short tandem repeat (STR) linkage analysis were used to determine the location of the DMD gene mutation in the pregnant woman and then to detect the DMD gene in the foetuses. RESULTS There were 872 families in our study. Among all 931 foetuses, 20.73% (193/931) were males expected to develop DMD and 16.33% (152/931) were female carriers. In addition, gonadal mosaicism was observed in 5 mothers, and gene recombination was identified in three foetuses. The results of the prenatal diagnosis were consistent with the results of the CPK analysis, and the results of the prenatal diagnosis were 100% accurate. CONCLUSIONS MLPA and Sanger sequencing, when combined with STR linkage analyses, can provide an accurate and rapid prenatal diagnosis. Due to the high de novo rate, prenatal diagnosis and genetic counselling should be given great attention.
Collapse
Affiliation(s)
- Xingjian Zhong
- The Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Rd., Erqi District, Zhengzhou, Henan Province, China
| | - Siying Cui
- The Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Rd., Erqi District, Zhengzhou, Henan Province, China
| | - Lina Liu
- The Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Rd., Erqi District, Zhengzhou, Henan Province, China
| | - Yuxia Yang
- The Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Rd., Erqi District, Zhengzhou, Henan Province, China.
| | - Xiangdong Kong
- The Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Rd., Erqi District, Zhengzhou, Henan Province, China.
| |
Collapse
|
12
|
Felice KJ, Whitaker CH, Khorasanizadeh S. Diagnostic yield of advanced genetic testing in patients with hereditary neuropathies: A retrospective single-site study. Muscle Nerve 2021; 64:454-461. [PMID: 34232518 DOI: 10.1002/mus.27368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 06/29/2021] [Accepted: 07/04/2021] [Indexed: 11/09/2022]
Abstract
INTRODUCTION/AIMS Advanced genetic testing including next-generation sequencing (AGT/NGS) has facilitated DNA testing in the clinical setting and greatly expanded new gene discovery for the Charcot-Marie-Tooth neuropathies and other hereditary neuropathies (CMT/HN). Herein, we report AGT/NGS results, clinical findings, and diagnostic yield in a cohort of CMT/HN patients evaluated at our neuropathy care center. METHODS We reviewed the medical records of all patients with suspected CMT/HN who underwent AGT/NGS at the Hospital for Special Care from January 2017 through January 2020. Patients with variants reported as pathogenic or likely pathogenic were included for further clinical review. RESULTS We ordered AGT/NGS on 108 patients with suspected CMT/HN. Of these, pathogenic or likely pathogenic variants were identified in 17 patients (diagnostic yield, 15.7%), including 6 (35%) with PMP22 duplications; 3 (18%) with MPZ variants; 2 (12%) with MFN2 variants; and 1 each with NEFL, IGHMBP2, GJB1, BSCL2, DNM2, and TTR variants. Diagnostic yield increased to 31.0% for patients with a positive family history. DISCUSSION AGT/NGS panels can provide specific genetic diagnoses for a subset of patients with CMT/HN disorders, which improves disease and genetic counseling and prepares patients for disease-focused therapies. Despite these advancements, many patients with known or suspected CMT/HN disorders remain without a specific genetic diagnosis. Continued advancements in genetic testing, such as multiomic technology and better understanding of genotype-phenotype correlation, will further improve detection rates for patients with suspected CMT/HN disorders.
Collapse
Affiliation(s)
- Kevin J Felice
- Department of Neuromuscular Medicine, Hospital for Special Care, New Britain, Connecticut, USA
| | - Charles H Whitaker
- Department of Neuromuscular Medicine, Hospital for Special Care, New Britain, Connecticut, USA
| | - Sadaf Khorasanizadeh
- Department of Neuromuscular Medicine, Hospital for Special Care, New Britain, Connecticut, USA
| |
Collapse
|
13
|
Bowen BM, Truty R, Aradhya S, Bristow SL, Johnson BA, Morales A, Tan CA, Westbrook MJ, Winder TL, Chavez JC. SMA Identified: Clinical and Molecular Findings From a Sponsored Testing Program for Spinal Muscular Atrophy in More Than 2,000 Individuals. Front Neurol 2021; 12:663911. [PMID: 34025568 PMCID: PMC8134668 DOI: 10.3389/fneur.2021.663911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/09/2021] [Indexed: 12/31/2022] Open
Abstract
Background: Spinal muscular atrophy (SMA) linked to chromosome 5q is an inherited progressive neuromuscular disorder with a narrow therapeutic window for optimal treatment. Although genetic testing provides a definitive molecular diagnosis that can facilitate access to effective treatments, limited awareness and other barriers may prohibit widespread testing. In this study, the clinical and molecular findings of SMA Identified—a no-charge sponsored next-generation sequencing (NGS)-based genetic testing program for SMA diagnosis—are reported. Methods: Between March 2018 and March 2020, unrelated individuals who had a confirmed or suspected SMA diagnosis or had a family history of SMA were eligible. All individuals underwent diagnostic genetic testing for SMA at clinician discretion. In total, 2,459 individuals were tested and included in this analysis. An NGS-based approach interrogated sequence and copy number of SMN1 and SMN2. Variants were confirmed by multiplex ligation-dependent probe amplification sequencing. Individuals were categorized according to genetic test results: diagnostic (two pathogenic SMN1 variants), nearly diagnostic (SMN1 exon-7 deletion with a variant of uncertain significance [VUS] in SMN1 or SMN2), indeterminate VUS (one VUS in SMN1 or SMN2), carrier (heterozygous SMN1 deletion only), or negative (no pathogenic variants or VUS in SMN1 or SMN2). Diagnostic yield was calculated. Genetic test results were analyzed based on clinician-reported clinical features and genetic modifiers (SMN2 copy number and SMN2 c.859G>C). Results: In total, 2,459 unrelated individuals (mean age 24.3 ± 23.0 years) underwent diagnostic testing. The diagnostic yield for diagnostic plus nearly diagnostic results was 31.3% (n = 771/2,459). Age of onset and clinical presentation varied considerably for individuals and was dependent on SMN2 copy number. Homozygous deletions represented the most common genetic etiology (96.2%), with sequence variants also observed in probands with clinical diagnoses of SMA. Conclusions: Using a high-yield panel test in a no-charge sponsored program early in the diagnostic odyssey may open the door for medical interventions in a substantial number of individuals with SMA. These findings have potential implications for clinical management of probands and their families.
Collapse
|
14
|
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”.
Collapse
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;
| |
Collapse
|
15
|
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".
Collapse
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
| |
Collapse
|
16
|
Hannah-Shmouni F, Al-Shahoumi R, Brady LI, Wu L, Frei J, Tarnopolsky MA. Dual molecular diagnoses in a neurometabolic specialty clinic. Am J Med Genet A 2020; 185:766-773. [PMID: 33369152 DOI: 10.1002/ajmg.a.62034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/05/2020] [Accepted: 12/06/2020] [Indexed: 11/08/2022]
Abstract
Reports of patients with concomitant diagnoses of two inherited genetic disorders, sometimes referred to as "double trouble," have appeared intermittently in the medical literature. We report eight additional cases with dual diagnoses of two genetic conditions. All cases had a phenotype atypical for their primary diagnosis, leading to the search for a second genetic diagnosis. These cases highlight the importance of the history, physical examination and continued work-up if the phenotype of the patient falls drastically outside what has been reported with their primary diagnosis. Some of the diagnoses of the patients presented here (e.g., Myotonic Dystrophy Type 1, fascioscapulohumeral muscular dystrophy) would not have been identified by genetic testing done on a next generation sequencing backbone (e.g., panel or exome sequencing). When the clinical picture is atypical or more severe than expected the possibility of a dual diagnosis (double trouble) should be considered. Identification of a second genetic condition can impact management and genetic counseling.
Collapse
Affiliation(s)
- Fady Hannah-Shmouni
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Rashid Al-Shahoumi
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Lauren I Brady
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Lily Wu
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Julia Frei
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Mark A Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| |
Collapse
|
17
|
Galleni Leão L, Santos Souza L, Nogueira L, Pavanello RDCM, Gurgel-Giannetti J, Reed UC, Oliveira ASB, Cuperman T, Cotta A, FPaim J, Zatz M, Vainzof M. Dominant or recessive mutations in the RYR1 gene causing central core myopathy in Brazilian patients. ACTA MYOLOGICA : MYOPATHIES AND CARDIOMYOPATHIES : OFFICIAL JOURNAL OF THE MEDITERRANEAN SOCIETY OF MYOLOGY 2020; 39:274-282. [PMID: 33458582 PMCID: PMC7783440 DOI: 10.36185/2532-1900-030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 11/06/2022]
Abstract
Central Core Disease (CCD) is an inherited neuromuscular disorder characterized by the presence of cores in muscle biopsy. CCD is caused by mutations in the RYR1 gene. This gene encodes the ryanodine receptor 1, which is an intracellular calcium release channel from the sarcoplasmic reticulum to the cytosol in response to depolarization of the plasma membrane. Mutations in this gene are also associated with susceptibility to Malignant Hyperthermia (MHS). In this study, we evaluated 20 families with clinical and histological characteristics of CCD to identify primary mutations in patients, for diagnosis and genetic counseling of the families. We identified variants in the RYR1 gene in 19/20 families. The molecular pathogenicity was confirmed in 16 of them. Most of these variants (22/23) are missense and unique in the families. Two variants were recurrent in two different families. We identified six families with biallelic mutations, five compound heterozygotes with no consanguinity, and one homozygous, with consanguineous parents, resulting in 30% of cases with possible autosomal recessive inheritance. We identified seven novel variants, four of them classified as pathogenic. In one family, we identified two mutations in exon 102, segregating in cis, suggesting an additive effect of two mutations in the same allele. This work highlights the importance of using Next-Generation Sequencing technology for the molecular diagnosis of genetic diseases when a very large gene is involved, associated to a broad distribution of the mutations along it. These data also influence the prevention through adequate genetic counseling for the families and cautions against malignant hyperthermia susceptibility.
Collapse
Affiliation(s)
- Leonardo Galleni Leão
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Lucas Santos Souza
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Letícia Nogueira
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | | | - Juliana Gurgel-Giannetti
- Depart of Pediatrics, Medical School of Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Umbertina C Reed
- Department of Neurology, Medical School of the University of Sao Paulo, São Paulo, Brazil
| | - Acary S B Oliveira
- Department of Neurology and Neurosurgery, Division of Neuromuscular Disorders, Federal University of São Paulo (Unifesp), São Paulo SP, Brazil
| | - Thais Cuperman
- Department of Neurology and Neurosurgery, Division of Neuromuscular Disorders, Federal University of São Paulo (Unifesp), São Paulo SP, Brazil
| | - Ana Cotta
- Department of Pathology SARAH Network of Rehabilitation Hospitals, Belo Horizonte, MG, Brazil
| | - Julia FPaim
- Department of Pathology SARAH Network of Rehabilitation Hospitals, Belo Horizonte, MG, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Mariz Vainzof
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
18
|
Whole Exome Sequencing as a Diagnostic Tool for Unidentified Muscular Dystrophy in a Vietnamese Family. Diagnostics (Basel) 2020; 10:diagnostics10100741. [PMID: 32987775 PMCID: PMC7598670 DOI: 10.3390/diagnostics10100741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 11/17/2022] Open
Abstract
Muscular dystrophies are a group of heterogeneous clinical and genetic disorders. Two siblings presented with characteristics like muscular dystrophy, abnormal white matter, and elevated serum creatine kinase level. The high throughput of whole exome sequencing (WES) makes it an efficient tool for obtaining a precise diagnosis without the need for immunohistochemistry. WES was performed in the two siblings and their parents, followed by prioritization of variants and validation by Sanger sequencing. Very rare variants with moderate to high predicted impact in genes associated with neuromuscular disorders were selected. We identified two pathogenic missense variants, c.778C>T (p.H260Y) and c.2987G>A (p.C996Y), in the LAMA2 gene (NM_000426.3), in the homozygous state in two siblings, and in the heterozygous state in their unaffected parents, which were confirmed by Sanger sequencing. Variant c.2987G>A has not been reported previously. These variants may lead to a change in the structure and function of laminin-α2, a member of the family of laminin-211, which is an extracellular matrix protein that functions to stabilize the basement membrane of muscle fibers during contractions. Overall, WES enabled an accurate diagnosis of both patients with LAMA2-related muscular dystrophy and expanded the spectrum of missense variants in LAMA2.
Collapse
|
19
|
Tan CA, Westbrook MJ, Truty R, Kvitek DJ, Kennemer M, Winder TL, Shieh PB. Incorporating Spinal Muscular Atrophy Analysis by Next-Generation Sequencing into a Comprehensive Multigene Panel for Neuromuscular Disorders. Genet Test Mol Biomarkers 2020; 24:616-624. [PMID: 32721234 DOI: 10.1089/gtmb.2019.0282] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background: Spinal muscular atrophy (SMA) is traditionally molecularly diagnosed by multiplex ligation-dependent probe amplification or quantitative polymerase chain reaction (qPCR). SMA analyses are not routinely incorporated into gene panel analyses for individuals with suspected SMA or broader neuromuscular indications. Aim: We sought to determine whether a next-generation sequencing (NGS) approach that integrates SMA analyses into a multigene neuromuscular disorders panel could detect undiagnosed SMA. Materials and Methods: Sequence and copy number variants of the SMN1/SMN2 genes were simultaneously analyzed in samples from 5304 unselected individuals referred for testing using an NGS-based 122-gene neuromuscular panel. This diagnostic approach was validated using DNA from 68 individuals who had been previously diagnosed with SMA via quantitative PCR for SMN1/SMN2. Results: Homozygous loss of SMN1 was detected in 47 unselected individuals. Heterozygous loss of SMN1 was detected in 118 individuals; 8 had an indeterminate variant in "SMN1 or SMN2" that supported an SMA diagnosis but required additional disambiguation. Of the remaining SMA carriers, 44 had pathogenic variants in other genes. Concordance rates between NGS and qPCR were 100% and 93% for SMN1 and SMN2 copy numbers, respectively. Where there was disagreement, phenotypes were more consistent with the SMN2 results from NGS. Conclusion: Integrating NGS-based SMA testing into a multigene neuromuscular panel allows a single assay to diagnose SMA while comprehensively assessing the spectrum of variants that can occur in individuals with broad differential diagnoses or nonspecific/overlapping neuromuscular features.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Perry B Shieh
- Department of Neurology, University of California, Los Angeles, Los Angeles, California, USA
| |
Collapse
|
20
|
Salmaninejad A, Motaee J, Farjami M, Alimardani M, Esmaeilie A, Pasdar A. Next-generation sequencing and its application in diagnosis of retinitis pigmentosa. Ophthalmic Genet 2020; 40:393-402. [PMID: 31755340 DOI: 10.1080/13816810.2019.1675178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Retinitis Pigmentosa (RP) is a major cause of heritable human blindness with a high genetic heterogeneity. It is characterized by the initial degeneration of rod photoreceptors followed by cone photoreceptors. RP is also a prominent reason of visual impairment, by a global prevalence of 1:4000. RP is usually specified with nyctalopia in puberty, followed by concentric visual field loss, that reflects the main impairment of rod photoreceptors; later in the life, as disease progresses, because of cone dysfunction, central vision loss also occurs. A precise molecular diagnosis is crucial for disease characterization and clinical prognosis. DNA sequencing is a powerful tool for deciphering various causes of different human diseases. The arrival of next-generation sequencing (NGS) technologies has diminished sequencing cost and considerably augmented the throughput, making whole-genome sequencing (WGS) a conceivable way for obtaining comprehensive genomic data and a more precise clinical decision. Nevertheless, the advantages gained from NGS technologies are among a number of challenges that must be sufficiently addressed before this technique can be altered from an investigation tools to a helpful method in routine clinical practices. This article aims to provide an overview about NGS technology and its related platforms. The challenges in the analysis and choosing an appropriate NGS method likewise their potential applications in clinical diagnosis are also discussed. The merit of such technique has been reflected in some recent studies where it is shown that using NGS and molecular information could help with clinical diagnosis, providing potential treatment options or changes, up-to-date family counseling and management.
Collapse
Affiliation(s)
- Arash Salmaninejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshid Motaee
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahsa Farjami
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maliheh Alimardani
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Alireza Pasdar
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine,Medical School, University of Aberdeen, Foresterhill, Aberdeen, UK
| |
Collapse
|
21
|
Ghaoui R, Needham M. Investigation of hereditary muscle disorders in the genomic era. ADVANCES IN CLINICAL NEUROSCIENCE & REHABILITATION 2020. [DOI: 10.47795/ayyz8676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
22
|
Thuriot F, Gravel E, Buote C, Doyon M, Lapointe E, Marcoux L, Larue S, Nadeau A, Chénier S, Waters PJ, Jacques PÉ, Gravel S, Lévesque S. Molecular diagnosis of muscular diseases in outpatient clinics: A Canadian perspective. NEUROLOGY-GENETICS 2020; 6:e408. [PMID: 32337335 PMCID: PMC7164974 DOI: 10.1212/nxg.0000000000000408] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 01/24/2020] [Indexed: 12/18/2022]
Abstract
Objective To evaluate the diagnostic yield of an 89-gene panel in a large cohort of patients with suspected muscle disorders and to compare the diagnostic yield of gene panel and exome sequencing approaches. Methods We tested 1,236 patients from outpatient clinics across Canada using a gene panel and performed exome sequencing for 46 other patients with sequential analysis of 89 genes followed by all mendelian genes. Sequencing and analysis were performed in patients with muscle weakness or symptoms suggestive of a muscle disorder and showing at least 1 supporting clinical laboratory. Results We identified a molecular diagnosis in 187 (15.1%) of the 1,236 patients tested with the 89-gene panel. Diagnoses were distributed across 40 different genes, but 6 (DMD, RYR1, CAPN3, PYGM, DYSF, and FKRP) explained about half of all cases. Cardiac anomalies, positive family history, age <60 years, and creatine kinase >1,000 IU/L were all associated with increased diagnostic yield. Exome sequencing identified a diagnosis in 10 (21.7%) of the 46 patients tested. Among these, 3 were attributed to genes not included in the 89-gene panel. Despite differences in median coverage, only 1 of the 187 diagnoses that were identified on gene panel in the 1,236 patients could have been potentially missed if exome sequencing had been performed instead. Conclusions Our study supports the use of gene panel testing in patients with suspected muscle disorders from outpatient clinics. It also shows that exome sequencing has a low risk of missing diagnoses compared with gene panel, while potentially increasing the diagnostic yield of patients with muscle disorders.
Collapse
Affiliation(s)
- Fanny Thuriot
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Elaine Gravel
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Caroline Buote
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Marianne Doyon
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Elvy Lapointe
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Lydia Marcoux
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Sandrine Larue
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Amélie Nadeau
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Sébastien Chénier
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Paula J Waters
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Pierre-Étienne Jacques
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Serge Gravel
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| | - Sébastien Lévesque
- Department of Pediatrics (F.T., E.G., C.B., M.D., L.M., A.N., S.C., P.J.W., S.G., S. Lévesque), Université de Sherbrooke; Sherbrooke Genomic Medicine (F.T., E.G., C.B., S.G., S. Lévesque); RNomic's Platform (E.L.), Université de Sherbrooke; Department of Neurology (S. Larue), Notre-Dame Hospital, Université de Montréal; Department of Biology (P.-É.J.), Université de Sherbrooke; and Department of Computer Sciences (P.-É.J.), Université de Sherbrooke, Quebec, Canada
| |
Collapse
|
23
|
Kong X, Zhong X, Liu L, Cui S, Yang Y, Kong L. Genetic analysis of 1051 Chinese families with Duchenne/Becker Muscular Dystrophy. BMC MEDICAL GENETICS 2019; 20:139. [PMID: 31412794 PMCID: PMC6694523 DOI: 10.1186/s12881-019-0873-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 08/05/2019] [Indexed: 01/03/2023]
Abstract
Background Duchenne Muscular Dystrophy (DMD) is the most common muscle disease in children, and there are no effective therapies for DMD or Becker Muscular Dystrophy (BMD). Currently, targeted gene therapy treatments have emerged. As a result, genetic diagnosis is the basis of treatment. In addition, genetic and prenatal diagnosis significantly reduces their incidence rates. This study combines the application of multiplex ligation-dependent probe amplification technology (MLPA) and “next-generation” sequencing technology (NGS) as the most economical and efficient method of diagnosis. Therefore, in the diagnosis of DMD/BMD, patients’ MLPA data are first used to detect DMD gene deletions or duplications, and NGS and Sanger sequencing are then applied to exclude MLPA-negative samples. Meanwhile, polymerase chain reaction (PCR) is used to detect single exon deletions to exclude false-positives in MLPA caused by point mutations. Methods In this study, we recruited 1051 proband families of DMD from 2016 to 2018 and had access to information that could identify individual participants during or after data collection. Patients who were diagnosed with DMD were first tested by MLPA. MLPA results with single exon deletions were validated with PCR amplification and Sanger sequencing. The negative results of MLPA were further analysed with NGS and validated by Sanger sequencing. For novel missense mutations, phenotype-genotype correlations were analysed using PolyPhen2 and mutation taster. All methods were performed in accordance with the relevant guidelines and regulations. Results DMD mutations were identified in 1029 families (97.91%, 1029/1051). Large deletions, duplications, and small mutations accounted for 70.41% (740/1051), 8.28% (87/1051), and 19.12% (201/1051) of all cases, respectively. There were 205 small mutation types, 53 of which were novel. The rate of de novo mutations was 39.45% (187/474) and was higher in large duplications (49.53%, 157/317). Among 68 asymptomatic patients (< 3 years old) with unexplained persistent hyperCKaemia upon conventional physical examination, 63 were diagnosed as DMD/BMD according to genetic diagnosis. Conclusion Our results expand the spectrum of DMD mutations, which could contribute to the treatment of DMD/BMD and provide an effective diagnosis method. Thus, the combination of MLPA, NGS and Sanger sequencing is of great significance for family analysis, gene diagnosis and gene therapy.
Collapse
Affiliation(s)
- Xiangdong Kong
- The Genetics and Prenatal Diagnosis Center of the First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Rd, Erqi District, Zhengzhou, Henan Province, China.
| | - Xingjian Zhong
- The Genetics and Prenatal Diagnosis Center of the First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Rd, Erqi District, Zhengzhou, Henan Province, China
| | - Lina Liu
- The Genetics and Prenatal Diagnosis Center of the First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Rd, Erqi District, Zhengzhou, Henan Province, China
| | - Siying Cui
- The Genetics and Prenatal Diagnosis Center of the First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Rd, Erqi District, Zhengzhou, Henan Province, China
| | - Yuxia Yang
- The Genetics and Prenatal Diagnosis Center of the First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Rd, Erqi District, Zhengzhou, Henan Province, China
| | - Lingrong Kong
- The Genetics and Prenatal Diagnosis Center of the First Affiliated Hospital of Zhengzhou University, No. 1, Jianshe East Rd, Erqi District, Zhengzhou, Henan Province, China
| |
Collapse
|
24
|
Isackson PJ, Wang J, Zia M, Spurgeon P, Levesque A, Bard J, James S, Nowak N, Lee TK, Vladutiu GD. RYR1 and CACNA1S genetic variants identified with statin-associated muscle symptoms. Pharmacogenomics 2018; 19:1235-1249. [PMID: 30325262 PMCID: PMC6563124 DOI: 10.2217/pgs-2018-0106] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/31/2018] [Indexed: 11/21/2022] Open
Abstract
AIM To examine the genetic differences between subjects with statin-associated muscle symptoms and statin-tolerant controls. MATERIALS & METHODS Next-generation sequencing was used to characterize the exomes of 76 subjects with severe statin-associated muscle symptoms and 50 statin-tolerant controls. RESULTS 12 probably pathogenic variants were found within the RYR1 and CACNA1S genes in 16% of cases with severe statin-induced myopathy representing a fourfold increase over variants found in statin-tolerant controls. Subjects with probably pathogenic RYR1 or CACNA1S variants had plasma CK 5X to more than 400X the upper limit of normal in addition to having muscle symptoms. CONCLUSIONS Genetic variants within the RYR1 and CACNA1S genes are likely to be a major contributor to the susceptibility to statin-associated muscle symptoms.
Collapse
Affiliation(s)
- Paul J Isackson
- Department of Pediatrics, State University of New York at Buffalo, NY 14203, USA
| | - Jianxin Wang
- Center for Computational Research, State University of New York at Buffalo, NY 14203, USA
| | - Mohammad Zia
- Center for Computational Research, State University of New York at Buffalo, NY 14203, USA
| | - Paul Spurgeon
- Center for Computational Research, State University of New York at Buffalo, NY 14203, USA
| | - Adrian Levesque
- Center for Computational Research, State University of New York at Buffalo, NY 14203, USA
| | - Jonathan Bard
- Center for Computational Research, State University of New York at Buffalo, NY 14203, USA
| | - Smitha James
- New York State Center of Excellence in Bioinformatics & Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Norma Nowak
- New York State Center of Excellence in Bioinformatics & Life Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Biochemistry, Jacobs School of Medicine & Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Tae Keun Lee
- Department of Pediatrics, State University of New York at Buffalo, NY 14203, USA
| | - Georgirene D Vladutiu
- Department of Pediatrics, State University of New York at Buffalo, NY 14203, USA
- Departments of Neurology & Pathology & Anatomical Sciences, University at Buffalo, Buffalo, NY 14214, USA
| |
Collapse
|
25
|
Castiglioni C, Lozano-Arango A. Atrofias musculares espinales no asociadas a SMN1. REVISTA MÉDICA CLÍNICA LAS CONDES 2018. [DOI: 10.1016/j.rmclc.2018.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
26
|
Nuevas herramientas diagnósticas de biología molecular en enfermedades neuromusculares. REVISTA MÉDICA CLÍNICA LAS CONDES 2018. [DOI: 10.1016/j.rmclc.2018.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
27
|
Next-generation sequencing in neuromuscular diseases: Erratum. Curr Opin Neurol 2018; 31:232. [DOI: 10.1097/wco.0000000000000552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
28
|
Haskell GT, Adams MC, Fan Z, Amin K, Guzman Badillo RJ, Zhou L, Bizon C, Chahin N, Greenwood RS, Milko LV, Shiloh-Malawsky Y, Crooks KR, Strande N, Tennison M, Tilley CR, Brandt A, Wilhelmsen KC, Weck K, Evans JP, Berg JS. Diagnostic utility of exome sequencing in the evaluation of neuromuscular disorders. NEUROLOGY-GENETICS 2018; 4:e212. [PMID: 29417091 PMCID: PMC5798313 DOI: 10.1212/nxg.0000000000000212] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/12/2017] [Indexed: 12/14/2022]
Abstract
Objective To evaluate the diagnostic yield and workflow of genome-scale sequencing in patients with neuromuscular disorders (NMDs). Methods We performed exome sequencing in 93 undiagnosed patients with various NMDs for whom a molecular diagnosis was not yet established. Variants on both targeted and broad diagnostic gene lists were identified. Prior diagnostic tests were extracted from the patient's medical record to evaluate the use of exome sequencing in the context of their prior diagnostic workup. Results The overall diagnostic yield of exome sequencing in our cohort was 12.9%, with one or more pathogenic or likely pathogenic variants identified in a causative gene associated with the patient's disorder. Targeted gene lists had the same diagnostic yield as a broad NMD gene list in patients with clear neuropathy or myopathy phenotypes, but evaluation of a broader set of disease genes was needed for patients with complex NMD phenotypes. Most patients with NMD had undergone prior testing, but only 10/16 (63%) of these procedures, such as muscle biopsy, were informative in pointing to a final molecular diagnosis. Conclusions Genome-scale sequencing or analysis of a panel of relevant genes used early in the evaluation of patients with NMDs can provide or clarify a diagnosis and minimize invasive testing in many cases.
Collapse
Affiliation(s)
- Gloria T Haskell
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Michael C Adams
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Zheng Fan
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Krunal Amin
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Roberto J Guzman Badillo
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Linran Zhou
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Christopher Bizon
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Nizar Chahin
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Robert S Greenwood
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Laura V Milko
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Yael Shiloh-Malawsky
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Kristy R Crooks
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Natasha Strande
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Michael Tennison
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Christian R Tilley
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Alicia Brandt
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Kirk C Wilhelmsen
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Karen Weck
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - James P Evans
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| | - Jonathan S Berg
- Department of Pathology (G.T.H.), Duke University, Durham, NC; The Ohio State University Wexner Medical Center (M.C.A.), Columbus, OH; Department of Neurology (Z.F., R.S.G., Y.S.-M., M.T., K.C.W.), Department of Genetics (K.A., R.J.G.B., L.Z., L.V.M., C.R.T., A.B., K.C.W., K.W., J.P.E., J.S.B.), Lineberger Comprehensive Cancer Center (J.P.E., J.S.B.), and Department of Pathology and Lab Medicine (N.S., K.W.), University of North Carolina at Chapel Hill; Renaissance Computing Institute (C.B., K.C.W.), Chapel Hill, NC; Oregon Health and Science University (N.C.), Portland; and Department of Pathology (K.R.C.), University of Colorado, Denver
| |
Collapse
|
29
|
Fernández-Marmiesse A, Gouveia S, Couce ML. NGS Technologies as a Turning Point in Rare Disease Research , Diagnosis and Treatment. Curr Med Chem 2018; 25:404-432. [PMID: 28721829 PMCID: PMC5815091 DOI: 10.2174/0929867324666170718101946] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/19/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023]
Abstract
Approximately 25-50 million Americans, 30 million Europeans, and 8% of the Australian population have a rare disease. Rare diseases are thus a common problem for clinicians and account for enormous healthcare costs worldwide due to the difficulty of establishing a specific diagnosis. In this article, we review the milestones achieved in our understanding of rare diseases since the emergence of next-generation sequencing (NGS) technologies and analyze how these advances have influenced research and diagnosis. The first half of this review describes how NGS has changed diagnostic workflows and provided an unprecedented, simple way of discovering novel disease-associated genes. We focus particularly on metabolic and neurodevelopmental disorders. NGS has enabled cheap and rapid genetic diagnosis, highlighted the relevance of mosaic and de novo mutations, brought to light the wide phenotypic spectrum of most genes, detected digenic inheritance or the presence of more than one rare disease in the same patient, and paved the way for promising new therapies. In the second part of the review, we look at the limitations and challenges of NGS, including determination of variant causality, the loss of variants in coding and non-coding regions, and the detection of somatic mosaicism variants and epigenetic mutations, and discuss how these can be overcome in the near future.
Collapse
Affiliation(s)
- Ana Fernández-Marmiesse
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sofía Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - María L. Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| |
Collapse
|
30
|
Nga Brignol T. Génétique : Apport du séquençage de nouvelle génération (NGS) dans le diagnostic des maladies neuromusculaires. Med Sci (Paris) 2016. [DOI: 10.1051/medsci/201632s212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|