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Simon A. [Omics to serve myology]. Med Sci (Paris) 2023; 39 Hors série n° 1:22-27. [PMID: 37975766 DOI: 10.1051/medsci/2023136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
Despite efforts in biomedical research, pathophysiological mechanisms and therapeutic targets of diseases remain difficult to identify. The development of high-throughput techniques led to the advent of innovatve technologies called omics. They aim at characterizing as exhaustively as possible a set of molecules: genes, RNAs, proteins, metabolites, etc. These a priori methods allow a precise molecular characterization of diseases and a better understanding of complex pathophysiological mechanisms. In this paper, we will review most omics approaches, their integration and their applications in the context of myology.
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Affiliation(s)
- Alix Simon
- IGBMC - CNRS UMR 7104 - Inserm U 1258, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, France
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2
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Nicolau S, Milone M, Liewluck T. Guidelines for genetic testing of muscle and neuromuscular junction disorders. Muscle Nerve 2021; 64:255-269. [PMID: 34133031 DOI: 10.1002/mus.27337] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022]
Abstract
Despite recent advances in the understanding of inherited muscle and neuromuscular junction diseases, as well as the advent of a wide range of genetic tests, patients continue to face delays in diagnosis of sometimes treatable disorders. These guidelines outline an approach to genetic testing in such disorders. Initially, a patient's phenotype is evaluated to identify myopathies requiring directed testing, including myotonic dystrophies, facioscapulohumeral muscular dystrophy, oculopharyngeal muscular dystrophy, mitochondrial myopathies, dystrophinopathies, and oculopharyngodistal myopathy. Initial investigation in the remaining patients is generally a comprehensive gene panel by next-generation sequencing. Broad panels have a higher diagnostic yield and can be cost-effective. Due to extensive phenotypic overlap and treatment implications, genes responsible for congenital myasthenic syndromes should be included when evaluating myopathy patients. For patients whose initial genetic testing is negative or inconclusive, phenotypic re-evaluation is warranted, along with consideration of genes and variants not included initially, as well as their acquired mimickers.
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Affiliation(s)
- Stefan Nicolau
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Teerin Liewluck
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
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Karakaya M, Storbeck M, Strathmann EA, Delle Vedove A, Hölker I, Altmueller J, Naghiyeva L, Schmitz-Steinkrüger L, Vezyroglou K, Motameny S, Alawbathani S, Thiele H, Polat AI, Okur D, Boostani R, Karimiani EG, Wunderlich G, Ardicli D, Topaloglu H, Kirschner J, Schrank B, Maroofian R, Magnusson O, Yis U, Nürnberg P, Heller R, Wirth B. Targeted sequencing with expanded gene profile enables high diagnostic yield in non-5q-spinal muscular atrophies. Hum Mutat 2018; 39:1284-1298. [PMID: 29858556 DOI: 10.1002/humu.23560] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/14/2018] [Accepted: 05/30/2018] [Indexed: 11/08/2022]
Abstract
Spinal muscular atrophies (SMAs) are a heterogeneous group of disorders characterized by muscular atrophy, weakness, and hypotonia due to suspected lower motor neuron degeneration (LMND). In a large cohort of 3,465 individuals suspected with SMA submitted for SMN1 testing to our routine diagnostic laboratory, 48.8% carried a homozygous SMN1 deletion, 2.8% a subtle mutation, and an SMN1 deletion, whereas 48.4% remained undiagnosed. Recently, several other genes implicated in SMA/LMND have been reported. Despite several efforts to establish a diagnostic algorithm for non-5q-SMA (SMA without deletion or point mutations in SMN1 [5q13.2]), data from large-scale studies are not available. We tested the clinical utility of targeted sequencing in non-5q-SMA by developing two different gene panels. We first analyzed 30 individuals with a small panel including 62 genes associated with LMND using IonTorrent-AmpliSeq target enrichment. Then, additional 65 individuals were tested with a broader panel encompassing up to 479 genes implicated in neuromuscular diseases (NMDs) with Agilent-SureSelect target enrichment. The NMD panel provided a higher diagnostic yield (33%) than the restricted LMND panel (13%). Nondiagnosed cases were further subjected to exome or genome sequencing. Our experience supports the use of gene panels covering a broad disease spectrum for diseases that are highly heterogeneous and clinically difficult to differentiate.
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Affiliation(s)
- Mert Karakaya
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Markus Storbeck
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Eike A Strathmann
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Andrea Delle Vedove
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Irmgard Hölker
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Janine Altmueller
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Leyla Naghiyeva
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Lea Schmitz-Steinkrüger
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Katharina Vezyroglou
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Susanne Motameny
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Salem Alawbathani
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Ayse Ipek Polat
- Dokuz Eylül University, Department of Pediatric Neurology, Izmir, Turkey
| | - Derya Okur
- Dokuz Eylül University, Department of Pediatric Neurology, Izmir, Turkey
| | - Reza Boostani
- Mashhad University of Medical Sciences, Department of Neurology, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Next Generation Genetic Polyclinic, Mashhad, Iran.,Razavi Cancer Research Center, Razavi Hospital, Imam Reza International University, Mashhad, Iran
| | | | - Didem Ardicli
- Hacettepe University, Department of Pediatric Neurology, Ankara, Turkey
| | - Haluk Topaloglu
- Hacettepe University, Department of Pediatric Neurology, Ankara, Turkey
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Bertold Schrank
- DKD HELIOS Kliniken, Department of Neurology, Wiesbaden, Germany
| | - Reza Maroofian
- Genetics and Molecular Cell Sciences Research Centre, St George's University of London, London, UK
| | | | - Uluc Yis
- Dokuz Eylül University, Department of Pediatric Neurology, Izmir, Turkey
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Raoul Heller
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
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Krahn M, Cerino M, Campana-Salort E, Cossée M. [Towards a national standardisation of NGS studies in the diagnosis of myopathies]. Med Sci (Paris) 2017; 33 Hors série n°1:30-33. [PMID: 29139383 DOI: 10.1051/medsci/201733s106] [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
Affiliation(s)
- Martin Krahn
- Aix Marseille Université, Inserm UMR_S 910, GMGF, 13385, Marseille, France - APHM, Département de Génétique Médicale, Hôpital Timone Enfants, 13385, Marseille, France
| | - Mathieu Cerino
- Aix Marseille Université, Inserm UMR_S 910, GMGF, 13385, Marseille, France - APHM, Département de Génétique Médicale, Hôpital Timone Enfants, 13385, Marseille, France
| | - Emmanuelle Campana-Salort
- Aix Marseille Université, Inserm UMR_S 910, GMGF, 13385, Marseille, France - APHM, Hôpital Timone, Centre de référence des maladies neuromusculaires et de la SLA, Marseille, France
| | - Mireille Cossée
- CHRU Montpellier, Laboratoire de Génétique moléculaire, Montpellier, France - Université Montpellier, Laboratoire de Génétique de maladies rares, Montpellier, France
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Hackman P, Udd B, Bönnemann CG, Ferreiro A. 219th ENMC International Workshop Titinopathies International database of titin mutations and phenotypes, Heemskerk, The Netherlands, 29 April-1 May 2016. Neuromuscul Disord 2017; 27:396-407. [PMID: 28214268 DOI: 10.1016/j.nmd.2017.01.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/12/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Peter Hackman
- Folkhälsan Institute of Genetics, University of Helsinki, Finland.
| | - Bjarne Udd
- Neuromuscular Research Center, Tampere University, Finland
| | | | - Ana Ferreiro
- Unité de Biologie Fonctionnelle et Adaptative, Université Paris Diderot/CNRS, France; Reference Center for Neuromuscular Disorders, Pitié-Salpêtrière Hospital, AP-HP, France
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Gorokhova S, Cerino M, Mathieu Y, Courrier S, Desvignes JP, Salgado D, Béroud C, Krahn M, Bartoli M. Comparing targeted exome and whole exome approaches for genetic diagnosis of neuromuscular disorders. Appl Transl Genom 2015; 7:26-31. [PMID: 27054082 PMCID: PMC4803780 DOI: 10.1016/j.atg.2015.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 12/30/2022]
Abstract
Massively parallel sequencing is rapidly becoming a widely used method in genetic diagnostics. However, there is still no clear consensus as to which approach can most efficiently identify the pathogenic mutations carried by a given patient, while avoiding false negative and false positive results. We developed a targeted exome approach (MyoPanel2) in order to optimize genetic diagnosis of neuromuscular disorders. Using this approach, we were able to analyse 306 genes known to be mutated in myopathies as well as in related disorders, obtaining 98.8% target sequence coverage at 20 ×. Moreover, MyoPanel2 was able to detect 99.7% of 11,467 known mutations responsible for neuromuscular disorders. We have then used several quality control parameters to compare performance of the targeted exome approach with that of whole exome sequencing. The results of this pilot study of 140 DNA samples suggest that targeted exome sequencing approach is an efficient genetic diagnostic test for most neuromuscular diseases.
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Affiliation(s)
- Svetlana Gorokhova
- Aix Marseille University, INSERM, GMGF, UMR_S 910, 13385, Marseille, France
| | - Mathieu Cerino
- Aix Marseille University, INSERM, GMGF, UMR_S 910, 13385, Marseille, France; APHM, Department de Medical Genetics, Timone Children's Hospital, Marseille, France
| | - Yves Mathieu
- Aix Marseille University, INSERM, GMGF, UMR_S 910, 13385, Marseille, France
| | - Sébastien Courrier
- Aix Marseille University, INSERM, GMGF, UMR_S 910, 13385, Marseille, France
| | | | - David Salgado
- Aix Marseille University, INSERM, GMGF, UMR_S 910, 13385, Marseille, France
| | - Christophe Béroud
- Aix Marseille University, INSERM, GMGF, UMR_S 910, 13385, Marseille, France
| | - Martin Krahn
- Aix Marseille University, INSERM, GMGF, UMR_S 910, 13385, Marseille, France; APHM, Department de Medical Genetics, Timone Children's Hospital, Marseille, France
| | - Marc Bartoli
- Aix Marseille University, INSERM, GMGF, UMR_S 910, 13385, Marseille, France
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