1
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Van Lent J, Prior R, Pérez Siles G, Cutrupi AN, Kennerson ML, Vangansewinkel T, Wolfs E, Mukherjee-Clavin B, Nevin Z, Judge L, Conklin B, Tyynismaa H, Clark AJ, Bennett DL, Van Den Bosch L, Saporta M, Timmerman V. Advances and challenges in modeling inherited peripheral neuropathies using iPSCs. Exp Mol Med 2024; 56:1348-1364. [PMID: 38825644 PMCID: PMC11263568 DOI: 10.1038/s12276-024-01250-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/21/2024] [Accepted: 03/18/2024] [Indexed: 06/04/2024] Open
Abstract
Inherited peripheral neuropathies (IPNs) are a group of diseases associated with mutations in various genes with fundamental roles in the development and function of peripheral nerves. Over the past 10 years, significant advances in identifying molecular disease mechanisms underlying axonal and myelin degeneration, acquired from cellular biology studies and transgenic fly and rodent models, have facilitated the development of promising treatment strategies. However, no clinical treatment has emerged to date. This lack of treatment highlights the urgent need for more biologically and clinically relevant models recapitulating IPNs. For both neurodevelopmental and neurodegenerative diseases, patient-specific induced pluripotent stem cells (iPSCs) are a particularly powerful platform for disease modeling and preclinical studies. In this review, we provide an update on different in vitro human cellular IPN models, including traditional two-dimensional monoculture iPSC derivatives, and recent advances in more complex human iPSC-based systems using microfluidic chips, organoids, and assembloids.
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Grants
- Wellcome Trust
- R01 NS119678 NINDS NIH HHS
- U01 ES032673 NIEHS NIH HHS
- DOC-PRO4 Universiteit Antwerpen (University of Antwerp)
- This work was supported in part by the University of Antwerp (DOC-PRO4 PhD fellowship to J.V.L. and TOP-BOF research grant no. 38694 to V.T.), the Association Française contre les Myopathies (AFM research grant no. 24063 to V.T.), Association Belge contre les Maladies Neuromusculaires (ABMM research grant no. 1 to J.V.L and V.T), the interuniversity research fund (iBOF project to. L.V.D.B, E.W. and V.T.). V.T. is part of the μNEURO Research Centre of Excellence of the University of Antwerp and is an active member of the European Network for Stem Cell Core Facilities (CorEUStem, COST Action CA20140). Work in the M.L.K group was supported by the NHMRC Ideas Grant (APP1186867), CMT Australia Grant awarded to M.L.K and G.P.-S and the Australian Medical Research Future Fund (MRFF) Genomics Health Futures Mission Grant 2007681. B.M.C. is supported by the American Academy of Neurology and the Passano Foundation. L.M.J. and B.R.C. are supported by the Charcot-Marie-Tooth Association, NINDS R01 NS119678, NIEHS U01 ES032673. H.T. is supported by Academy of Finland Centre of Excellence in Stem Cell Metabolism and Sigrid Juselius Foundation. Work in the D.L.B. group is supported by a Wellcome Investigator Grant (223149/Z/21/Z), the MRC (MR/T020113/1), and with funding from the MRC and Versus Arthritis to the PAINSTORM consortium as part of the Advanced Pain Discovery Platform (MR/W002388/1).
- Australian Medical Association (Australian Medical Association Limited)
- Universiteit Hasselt (UHasselt)
- American Academy of Neurology (AAN)
- Gladstone Institutes (J. David Gladstone Institutes)
- Academy of Finland (Suomen Akatemia)
- Academy of Medical Royal Colleges (AoMRC)
- Wellcome Trust (Wellcome)
- Oxford University Hospitals NHS Trust (Oxford University Hospitals National Health Service Trust)
- KU Leuven (Katholieke Universiteit Leuven)
- Vlaams Instituut voor Biotechnologie (Flanders Institute for Biotechnology)
- Miami University | Leonard M. Miller School of Medicine (Miller School of Medicine)
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Affiliation(s)
- Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, 2610, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born Bunge, 2610, Antwerp, Belgium
- Institute of Oncology Research (IOR), BIOS+, 6500, Bellinzona, Switzerland
- Università della Svizzera Italiana, 6900, Lugano, Switzerland
| | - Robert Prior
- Universitätsklinikum Bonn (UKB), University of Bonn, Bonn, Germany
| | - Gonzalo Pérez Siles
- Northcott Neuroscience Laboratory, ANZAC Research Institute Sydney Local Health District and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Anthony N Cutrupi
- Northcott Neuroscience Laboratory, ANZAC Research Institute Sydney Local Health District and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute Sydney Local Health District and Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Molecular Medicine Laboratory, Concord Hospital, Sydney, NSW, Australia
| | - Tim Vangansewinkel
- UHasselt - Hasselt University, BIOMED, Laboratory for Functional Imaging and Research on Stem Cells (FIERCE Lab), Agoralaan, 3590, Diepenbeek, Belgium
- VIB-Center for Brain and Disease Research, Laboratory of Neurobiology, 3000, Leuven, Belgium
| | - Esther Wolfs
- UHasselt - Hasselt University, BIOMED, Laboratory for Functional Imaging and Research on Stem Cells (FIERCE Lab), Agoralaan, 3590, Diepenbeek, Belgium
| | | | | | - Luke Judge
- Gladstone Institutes, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Bruce Conklin
- Gladstone Institutes, San Francisco, CA, USA
- Department of Ophthalmology, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Alex J Clark
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - David L Bennett
- Nuffield Department of Clinical Neuroscience, Oxford University, Oxford, UK
| | - Ludo Van Den Bosch
- VIB-Center for Brain and Disease Research, Laboratory of Neurobiology, 3000, Leuven, Belgium
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute, KU Leuven-University of Leuven, 3000, Leuven, Belgium
| | - Mario Saporta
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, 2610, Antwerp, Belgium.
- Laboratory of Neuromuscular Pathology, Institute Born Bunge, 2610, Antwerp, Belgium.
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2
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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.
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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
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3
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Allou L, Mundlos S. Disruption of regulatory domains and novel transcripts as disease-causing mechanisms. Bioessays 2023; 45:e2300010. [PMID: 37381881 DOI: 10.1002/bies.202300010] [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: 01/16/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023]
Abstract
Deletions, duplications, insertions, inversions, and translocations, collectively called structural variations (SVs), affect more base pairs of the genome than any other sequence variant. The recent technological advancements in genome sequencing have enabled the discovery of tens of thousands of SVs per human genome. These SVs primarily affect non-coding DNA sequences, but the difficulties in interpreting their impact limit our understanding of human disease etiology. The functional annotation of non-coding DNA sequences and methodologies to characterize their three-dimensional (3D) organization in the nucleus have greatly expanded our understanding of the basic mechanisms underlying gene regulation, thereby improving the interpretation of SVs for their pathogenic impact. Here, we discuss the various mechanisms by which SVs can result in altered gene regulation and how these mechanisms can result in rare genetic disorders. Beyond changing gene expression, SVs can produce novel gene-intergenic fusion transcripts at the SV breakpoints.
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Affiliation(s)
- Lila Allou
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Mundlos
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
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4
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Kim YG, Kwon H, Park JH, Nam SH, Ha C, Shin S, Heo WY, Kim HJ, Chung KW, Jang JH, Kim JW, Choi BO. Whole-genome sequencing in clinically diagnosed Charcot-Marie-Tooth disease undiagnosed by whole-exome sequencing. Brain Commun 2023; 5:fcad139. [PMID: 37180992 PMCID: PMC10174204 DOI: 10.1093/braincomms/fcad139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/16/2023] [Accepted: 04/27/2023] [Indexed: 05/16/2023] Open
Abstract
Whole-genome sequencing is the most comprehensive form of next-generation sequencing method. We aimed to assess the additional diagnostic yield of whole-genome sequencing in patients with clinically diagnosed Charcot-Marie-Tooth disease when compared with whole-exome sequencing, which has not been reported in the literature. Whole-genome sequencing was performed on 72 families whose genetic cause of clinically diagnosed Charcot-Marie-Tooth disease was not revealed after the whole-exome sequencing and 17p12 duplication screening. Among the included families, 14 (19.4%) acquired genetic diagnoses that were compatible with their phenotypes. The most common factor that led to the additional diagnosis in the whole-genome sequencing was genotype-driven analysis (four families, 4/14), in which a wider range of genes, not limited to peripheral neuropathy-related genes, were analysed. Another four families acquired diagnosis due to the inherent advantage of whole-genome sequencing such as better coverage than the whole-exome sequencing (two families, 2/14), structural variants (one family, 1/14) and non-coding variants (one family, 1/14). In conclusion, an evident gain in diagnostic yield was obtained from whole-genome sequencing of the whole-exome sequencing-negative cases. A wide range of genes, not limited to inherited peripheral neuropathy-related genes, should be targeted during whole-genome sequencing.
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Affiliation(s)
- Young-gon Kim
- Correspondence to: Jong-Won Kim, MD, PhD Department of Laboratory Medicine and Genetics, Samsung Medical Center 81 Irwon-ro, Gangnam-gu, Seoul 06351, South Korea E-mail:
| | | | - Jong-ho Park
- Clinical Genomics Center, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Soo Hyun Nam
- Cell and Gene Therapy Institute (CGTI), Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Changhee Ha
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Sunghwan Shin
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Won Young Heo
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Hye Jin Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Ki Wha Chung
- Department of Biological Sciences, Kongju National University, Gongju 32588, South Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Republic of Korea
- Clinical Genomics Center, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Byung-Ok Choi
- Correspondence may also be sent to: Byung-Ok Choi, MD, PhD Department of Neurology, Samsung Medical Center 81 Irwon-ro, Gangnam-gu, Seoul 06351, South Korea E-mail:
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5
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Identity-by-descent analysis of CMTX3 links three families through a common founder. J Hum Genet 2023; 68:47-49. [PMID: 36100665 PMCID: PMC9812773 DOI: 10.1038/s10038-022-01078-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/07/2022] [Accepted: 08/23/2022] [Indexed: 01/09/2023]
Abstract
A large 78 kb insertion from chromosome 8q24.3 into Xq27.1 was identified as the cause of CMTX3 in three families of European descent from Australia (CMT193, CMT180) and New Zealand/United Kingdom (CMT623). Using the relatedness tool XIBD to perform genome-wide identity-by-descent (IBD) analysis on 16 affected individuals from the three families demonstrated they all share the CMTX3 disease locus identical-by-descent, confirming the mutation arose in a common ancestor. Relationship estimation from IBD segment data has genetically linked all three families through 6th and 7th degree relatives.
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6
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Ding H, Luo J. MAMnet: detecting and genotyping deletions and insertions based on long reads and a deep learning approach. Brief Bioinform 2022; 23:6587170. [PMID: 35580841 DOI: 10.1093/bib/bbac195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/07/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Structural variations (SVs) play important roles in human genetic diversity; deletions and insertions are two common types of SVs that have been proven to be associated with genetic diseases. Hence, accurately detecting and genotyping SVs is significant for disease research. Despite the fact that long-read sequencing technologies have improved the field of SV detection and genotyping, there are still some challenges that prevent satisfactory results from being obtained. In this paper, we propose MAMnet, a fast and scalable SV detection and genotyping method based on long reads and a combination of convolutional neural network and long short-term network. MAMnet uses a deep neural network to implement sensitive SV detection with a novel prediction strategy. On real long-read sequencing datasets, we demonstrate that MAMnet outperforms Sniffles, SVIM, cuteSV and PBSV in terms of their F1 scores while achieving better scaling performance. The source code is available from https://github.com/micahvista/MAMnet.
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Affiliation(s)
- Hongyu Ding
- College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, 454003, China
| | - Junwei Luo
- College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, 454003, China
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7
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Boyling A, Perez-Siles G, Kennerson ML. Structural Variation at a Disease Mutation Hotspot: Strategies to Investigate Gene Regulation and the 3D Genome. Front Genet 2022; 13:842860. [PMID: 35401663 PMCID: PMC8990796 DOI: 10.3389/fgene.2022.842860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/21/2022] [Indexed: 12/18/2022] Open
Abstract
A rare form of X-linked Charcot-Marie-Tooth neuropathy, CMTX3, is caused by an interchromosomal insertion occurring at chromosome Xq27.1. Interestingly, eight other disease phenotypes have been associated with insertions (or insertion-deletions) occurring at the same genetic locus. To date, the pathogenic mechanism underlying most of these diseases remains unsolved, although local gene dysregulation has clearly been implicated in at least two phenotypes. The challenges of accessing disease-relevant tissue and modelling these complex genomic rearrangements has led to this research impasse. We argue that recent technological advancements can overcome many of these challenges, particularly induced pluripotent stem cells (iPSC) and their capacity to provide access to patient-derived disease-relevant tissue. However, to date these valuable tools have not been utilized to investigate the disease-associated insertions at chromosome Xq27.1. Therefore, using CMTX3 as a reference disease, we propose an experimental approach that can be used to explore these complex mutations, as well as similar structural variants located elsewhere in the genome. The mutational hotspot at Xq27.1 is a valuable disease paradigm with the potential to improve our understanding of the pathogenic consequences of complex structural variation, and more broadly, refine our knowledge of the multifaceted process of long-range gene regulation. Intergenic structural variation is a critically understudied class of mutation, although it is likely to contribute significantly to unsolved genetic disease.
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Affiliation(s)
- Alexandra Boyling
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- *Correspondence: Alexandra Boyling, ; Marina L. Kennerson,
| | - Gonzalo Perez-Siles
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Marina L. Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Molecular Medicine Laboratory, Concord Repatriation General Hospital, Sydney, NSW, Australia
- *Correspondence: Alexandra Boyling, ; Marina L. Kennerson,
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8
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Boschann F, Moreno DA, Mensah MA, Sczakiel HL, Skipalova K, Holtgrewe M, Mundlos S, Fischer-Zirnsak B. Xq27.1 palindrome mediated interchromosomal insertion likely causes familial congenital bilateral laryngeal abductor paralysis (Plott syndrome). J Hum Genet 2022; 67:405-410. [PMID: 35095096 PMCID: PMC9233990 DOI: 10.1038/s10038-022-01018-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 01/27/2023]
Abstract
Bilateral laryngeal abductor paralysis is a rare entity and the second most common cause of stridor in newborns. So far, no conclusive genetic or chromosomal aberration has been reported for X-linked isolated bilateral vocal cord paralysis, also referred to as Plott syndrome. Via whole genome sequencing (WGS), we identified a complex interchromosomal insertion in a large family with seven affected males. The 404 kb inserted fragment originates from chromosome 10q21.3, contains no genes and is inserted inversionally into the intergenic chromosomal region Xq27.1, 82 kb centromeric to the nearest gene SOX3. The patterns found at the breakpoint junctions resemble typical characteristics that arise in replication-based mechanisms with long-distance template switching. Non protein-coding insertions into the same genomic region have been described to result in different phenotypes, indicating that the phenotypic outcome likely depends on the introduction of regulatory elements. In conclusion, our data adds Plott syndrome as another entity, likely caused by the insertion of non-coding DNA into the intergenic chromosomal region Xq27.1. In this regard, we demonstrate the importance of WGS as a powerful diagnostic test in unsolved genetic diseases, as this genomic rearrangement has not been detected by current first-line diagnostic tests, i.e., exome sequencing and chromosomal microarray analysis.
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9
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Ki CS. Recent Advances in the Clinical Application of Next-Generation Sequencing. Pediatr Gastroenterol Hepatol Nutr 2021; 24:1-6. [PMID: 33505888 PMCID: PMC7813577 DOI: 10.5223/pghn.2021.24.1.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have changed the process of genetic diagnosis from a gene-by-gene approach to syndrome-based diagnostic gene panel sequencing (DPS), diagnostic exome sequencing (DES), and diagnostic genome sequencing (DGS). A priori information on the causative genes that might underlie a genetic condition is a prerequisite for genetic diagnosis before conducting clinical NGS tests. Theoretically, DPS, DES, and DGS do not require any information on specific candidate genes. Therefore, clinical NGS tests sometimes detect disease-related pathogenic variants in genes underlying different conditions from the initial diagnosis. These clinical NGS tests are expensive, but they can be a cost-effective approach for the rapid diagnosis of rare disorders with genetic heterogeneity, such as the glycogen storage disease, familial intrahepatic cholestasis, lysosomal storage disease, and primary immunodeficiency. In addition, DES or DGS may find novel genes that that were previously not linked to human diseases.
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10
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Mortreux J, Bacquet J, Boyer A, Alazard E, Bellance R, Giguet-Valard AG, Cerino M, Krahn M, Audic F, Chabrol B, Laugel V, Desvignes JP, Béroud C, Nguyen K, Verschueren A, Lévy N, Attarian S, Delague V, Missirian C, Bonello-Palot N. Identification of novel pathogenic copy number variations in Charcot-Marie-Tooth disease. J Hum Genet 2019; 65:313-323. [PMID: 31852984 DOI: 10.1038/s10038-019-0710-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/03/2019] [Accepted: 12/08/2019] [Indexed: 12/13/2022]
Abstract
Charcot-Marie-Tooth disease (CMT) is a hereditary sensory-motor neuropathy characterized by a strong clinical and genetic heterogeneity. Over the past few years, with the occurrence of whole-exome sequencing (WES) or whole-genome sequencing (WGS), the molecular diagnosis rate has been improved by allowing the screening of more than 80 genes at one time. In CMT, except the recurrent PMP22 duplication accounting for about 60% of pathogenic variations, pathogenic copy number variations (CNVs) are rarely reported and only a few studies screening specifically CNVs have been performed. The aim of the present study was to screen for CNVs in the most prevalent genes associated with CMT in a cohort of 200 patients negative for the PMP22 duplication. CNVs were screened using the Exome Depth software on next generation sequencing (NGS) data obtained by targeted capture and sequencing of a panel of 81 CMT associated genes. Deleterious CNVs were identified in four patients (2%), in four genes: GDAP1, LRSAM1, GAN, and FGD4. All CNVs were confirmed by high-resolution oligonucleotide array Comparative Genomic Hybridization (aCGH) and/or quantitative PCR. By identifying four new CNVs in four different genes, we demonstrate that, although they are rare mutational events in CMT, CNVs might contribute significantly to mutational spectrum of Charcot-Marie-Tooth disease and should be searched in routine NGS diagnosis. This strategy increases the molecular diagnosis rate of patients with neuropathy.
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Affiliation(s)
- J Mortreux
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - J Bacquet
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - A Boyer
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France
| | - E Alazard
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France
| | - R Bellance
- Centre de référence Caribéen pour les maladies neuromusculaires, CeRCa, Hôpital Pierre-Zobda-Quitman, CHU de Martinique, France
| | - A G Giguet-Valard
- Centre de référence Caribéen pour les maladies neuromusculaires, CeRCa, Hôpital Pierre-Zobda-Quitman, CHU de Martinique, France
| | - M Cerino
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - M Krahn
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - F Audic
- Centre de référence des maladies neuromusculaires, Hôpital de la Timone enfant, Assistance-Publique Hôpitaux de Marseille, Marseille, France
| | - B Chabrol
- Centre de référence des maladies neuromusculaires, Hôpital de la Timone enfant, Assistance-Publique Hôpitaux de Marseille, Marseille, France
| | - V Laugel
- Centre de référence des maladies neuromusculaires, Service de pédiatrie, CHU Strasbourg, France
| | - J P Desvignes
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - C Béroud
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - K Nguyen
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - A Verschueren
- Centre de référence des maladies neuromusculaires, Hôpital de la Timone Adulte, Assistance-Publique Hôpitaux de Marseille, Marseille, France
| | - N Lévy
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - S Attarian
- Centre de référence des maladies neuromusculaires, Hôpital de la Timone Adulte, Assistance-Publique Hôpitaux de Marseille, Marseille, France
| | - V Delague
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - C Missirian
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France
| | - N Bonello-Palot
- Département de génétique médicale, Hôpital Timone enfants, Assistance-Publique Hôpitaux de Marseille, Marseille, France. .,Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France.
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11
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Middelkamp S, Vlaar JM, Giltay J, Korzelius J, Besselink N, Boymans S, Janssen R, de la Fonteijne L, van Binsbergen E, van Roosmalen MJ, Hochstenbach R, Giachino D, Talkowski ME, Kloosterman WP, Cuppen E. Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants. Genome Med 2019; 11:79. [PMID: 31801603 PMCID: PMC6894143 DOI: 10.1186/s13073-019-0692-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/14/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Genomic structural variants (SVs) can affect many genes and regulatory elements. Therefore, the molecular mechanisms driving the phenotypes of patients carrying de novo SVs are frequently unknown. METHODS We applied a combination of systematic experimental and bioinformatic methods to improve the molecular diagnosis of 39 patients with multiple congenital abnormalities and/or intellectual disability harboring apparent de novo SVs, most with an inconclusive diagnosis after regular genetic testing. RESULTS In 7 of these cases (18%), whole-genome sequencing analysis revealed disease-relevant complexities of the SVs missed in routine microarray-based analyses. We developed a computational tool to predict the effects on genes directly affected by SVs and on genes indirectly affected likely due to the changes in chromatin organization and impact on regulatory mechanisms. By combining these functional predictions with extensive phenotype information, candidate driver genes were identified in 16/39 (41%) patients. In 8 cases, evidence was found for the involvement of multiple candidate drivers contributing to different parts of the phenotypes. Subsequently, we applied this computational method to two cohorts containing a total of 379 patients with previously detected and classified de novo SVs and identified candidate driver genes in 189 cases (50%), including 40 cases whose SVs were previously not classified as pathogenic. Pathogenic position effects were predicted in 28% of all studied cases with balanced SVs and in 11% of the cases with copy number variants. CONCLUSIONS These results demonstrate an integrated computational and experimental approach to predict driver genes based on analyses of WGS data with phenotype association and chromatin organization datasets. These analyses nominate new pathogenic loci and have strong potential to improve the molecular diagnosis of patients with de novo SVs.
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Affiliation(s)
- Sjors Middelkamp
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Judith M Vlaar
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Jacques Giltay
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Jerome Korzelius
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
- Max Planck Institute for Biology of Aging, Cologne, Germany
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Roel Janssen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Lisanne de la Fonteijne
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Markus J van Roosmalen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands
| | - Ron Hochstenbach
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Daniela Giachino
- Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, 10043, Orbassano, Italy
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wigard P Kloosterman
- Department of Genetics, University Medical Center Utrecht, 3584 EA, Utrecht, the Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX, Utrecht, the Netherlands.
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12
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Next-generation sequencing in Charcot-Marie-Tooth disease: opportunities and challenges. Nat Rev Neurol 2019; 15:644-656. [PMID: 31582811 DOI: 10.1038/s41582-019-0254-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2019] [Indexed: 01/08/2023]
Abstract
Charcot-Marie-Tooth disease and the related disorders hereditary motor neuropathy and hereditary sensory neuropathy, collectively termed CMT, are the commonest group of inherited neuromuscular diseases, and they exhibit wide phenotypic and genetic heterogeneity. CMT is usually characterized by distal muscle atrophy, often with foot deformity, weakness and sensory loss. In the past decade, next-generation sequencing (NGS) technologies have revolutionized genomic medicine and, as these technologies are being applied to clinical practice, they are changing our diagnostic approach to CMT. In this Review, we discuss the application of NGS technologies, including disease-specific gene panels, whole-exome sequencing, whole-genome sequencing (WGS), mitochondrial sequencing and high-throughput transcriptome sequencing, to the diagnosis of CMT. We discuss the growing challenge of variant interpretation and consider how the clinical phenotype can be combined with genetic, bioinformatic and functional evidence to assess the pathogenicity of genetic variants in patients with CMT. WGS has several advantages over the other techniques that we discuss, which include unparalleled coverage of coding, non-coding and intergenic areas of both nuclear and mitochondrial genomes, the ability to identify structural variants and the opportunity to perform genome-wide dense homozygosity mapping. We propose an algorithm for incorporating WGS into the CMT diagnostic pathway.
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13
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Bamshad MJ, Nickerson DA, Chong JX. Mendelian Gene Discovery: Fast and Furious with No End in Sight. Am J Hum Genet 2019; 105:448-455. [PMID: 31491408 DOI: 10.1016/j.ajhg.2019.07.011] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/16/2019] [Indexed: 10/26/2022] Open
Abstract
Gene discovery for Mendelian conditions (MCs) offers a direct path to understanding genome function. Approaches based on next-generation sequencing applied at scale have dramatically accelerated gene discovery and transformed genetic medicine. Finding the genetic basis of ∼6,000-13,000 MCs yet to be delineated will require both technical and computational innovation, but will rely to a larger extent on meaningful data sharing.
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14
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Si N, Meng X, Zhao Z, Xia W, Zhang X. A 105 kb interstitial insertion in the Xq27.1 palindrome from pseudoautosomal region PAR1 causes a novel X-linked recessive compound phenotype. J Transl Med 2019; 17:138. [PMID: 31036090 PMCID: PMC6489244 DOI: 10.1186/s12967-019-1887-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic disorders present a wide spectrum of unrelated clinical entities that result from genomic rearrangements. Interstitial insertions requiring three points of breakage are rare genomic rearrangement events. The pseudoautosomal region PAR1, homologous between the Xp22 and Yp11 loci, has a high crossover and recombination rate. A 180 bp human-specific palindrome at Xq27.1 appears to be a hotspot for genomic rearrangement, and several genetic diseases/phenotypes associated with Xq27.1 palindrome-driven genomic rearrangement have been reported. Here we investigate a Chinese family with an extremely rare X-linked compound phenotype that remains undiagnosed. We attempt to identify underlying genetic causes by an integrated genome analysis. METHODS A five-generation Chinese family with a distinct X-linked compound phenotype was recruited. Peripheral blood samples were collected and genomic DNA was extracted. Systemic physical and lab examinations were performed to evaluate the phenotype. An integrated genomic analysis was performed. Genotyping and linkage analysis were conducted to map the disease locus. Whole exome sequencing was performed to detect mutations in coding region. Whole genome sequencing was used to detect single nucleotide variations, small insertions, small deletions, or large structural variations. Copy number variation scanning was also performed on the genome scale. Interstitial insertion was confirmed by gap-PCR and quantitative-PCR, and breakpoint junctions were identified by genome walking and direct sequencing. Expression of products of genes nearby to the Xq27.1 palindrome was measured in peripheral blood from patients and unrelated controls via quantitative-PCR. RESULTS The identified compound phenotype of genu varum, cubitus valgus, and everted lipsdoes not match any reported clinical entities. Fine mapping and linkage analysis identified a candidate interval of 4 Mb on the X chromosome. No potential coding region mutations were detected. A 105 kb genomic fragment of PAR1 containing no coding genes was duplicated and inserted into the center of a human-specific palindrome at Xq27.1. The interstitial insertion fully cosegregated with the family phenotype. No expression of FGF13 or SOX3 was detected in peripheral blood from the proband or unrelated controls. CONCLUSION We report an extremely rare phenotype associated with an infrequently-seen genomic rearrangement. The novel compound phenotype is X-linked and characterized by genu varum, cubitus valgus, and everted lips. A 105 kb interstitial insertion of a PAR1 fragment into the Xq27.1 palindrome is associated with the phenotype in the family. The present study identified the underlying genetic cause of the phenotype, expanding the spectrum of known human-specific Xq27.1 palindrome insertion events and associated phenotypes.
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Affiliation(s)
- Nuo Si
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Xiaolu Meng
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Zhen Zhao
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Weibo Xia
- Department of Endocrinology, Key Laboratory of Endocrinology, Ministry of Health, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
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15
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Bick D, Jones M, Taylor SL, Taft RJ, Belmont J. Case for genome sequencing in infants and children with rare, undiagnosed or genetic diseases. J Med Genet 2019; 56:783-791. [PMID: 31023718 PMCID: PMC6929710 DOI: 10.1136/jmedgenet-2019-106111] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/19/2019] [Indexed: 01/01/2023]
Abstract
Up to 350 million people worldwide suffer from a rare disease, and while the individual diseases are rare, in aggregate they represent a substantial challenge to global health systems. The majority of rare disorders are genetic in origin, with children under the age of five disproportionately affected. As these conditions are difficult to identify clinically, genetic and genomic testing have become the backbone of diagnostic testing in this population. In the last 10 years, next-generation sequencing technologies have enabled testing of multiple disease genes simultaneously, ranging from targeted gene panels to exome sequencing (ES) and genome sequencing (GS). GS is quickly becoming a practical first-tier test, as cost decreases and performance improves. A growing number of studies demonstrate that GS can detect an unparalleled range of pathogenic abnormalities in a single laboratory workflow. GS has the potential to deliver unbiased, rapid and accurate molecular diagnoses to patients across diverse clinical indications and complex presentations. In this paper, we discuss clinical indications for testing and historical testing paradigms. Evidence supporting GS as a diagnostic tool is supported by superior genomic coverage, types of pathogenic variants detected, simpler laboratory workflow enabling shorter turnaround times, diagnostic and reanalysis yield, and impact on healthcare.
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Affiliation(s)
- David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Marilyn Jones
- Rady Children's Hospital San Diego, San Diego, California, USA
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16
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Kanhangad M, Cornett K, Brewer MH, Nicholson GA, Ryan MM, Smith RL, Subramanian GM, Young HK, Züchner S, Kennerson ML, Burns J, Menezes MP. Unique clinical and neurophysiologic profile of a cohort of children with CMTX3. Neurology 2018; 90:e1706-e1710. [PMID: 29626178 PMCID: PMC10681066 DOI: 10.1212/wnl.0000000000005479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/21/2018] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To describe in detail the clinical profile of Charcot-Marie-Tooth disease subtype 3 (CMTX3) to aid appropriate genetic testing and rehabilitative therapy. METHODS We reviewed the clinical and neurophysiologic profile and CMT Pediatric Scale (CMTPedS) assessments of 11 children with CMTX3. RESULTS Compared with the more common forms of CMT, CMT1A and CMTX, CMTX3 was characterized by early onset with early and progressive hand weakness. Most affected children were symptomatic within the first 2 years of life. The most common presentation was foot deformity in the first year of life. CMTPedS analysis in these children revealed that CMTX3 progressed more rapidly (4.3 ± 4.1 points over 2 years, n = 7) than CMT1A and CMTX1. Grip strength in affected boys was 2 SDs below age- and sex-matched normative reference values (z score -2.05 ± 1.32) in the second decade of life. The most severely affected individual was wheelchair bound at 14 years of age, and 2 individuals had no movement in the small muscles of the hand in the second decade of life. Nerve conduction studies showed a demyelinating sensorimotor neuropathy with motor conduction velocity ≤23 m/s. CONCLUSIONS CMTX3 had an earlier onset, severe hand weakness, and more rapidly progressive disability compared to the more common forms of CMT. Understanding the unique phenotype of CMTX3 is essential for directing genetic testing because the CMTX3 insertion will not be seen on a routine microarray or neuromuscular gene panel. Early diagnosis will enable rehabilitation to be started early in this rapidly progressive neuropathy.
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Affiliation(s)
- Manoj Kanhangad
- From the T.Y. Nelson Department of Neurology and Neurosurgery (M.K., M.P.M.) and Institute for Neuroscience and Muscle Research (K.C., J.B., M.P.M.), The Children's Hospital at Westmead; University of Sydney (K.C., M.H.B., G.A.N., H.K.Y., M.L.K., J.B., M.P.M.); Northcott Neuroscience Laboratory (M.H.B., G.A.N., M.L.K.), ANZAC Research Institute, Concord; Molecular Medicine Laboratory (G.A.N., M.L.K.), Concord Repatriation General Hospital, New South Wales; Department of Neurology (M.M.R.), Royal Children's Hospital; Murdoch Children's Research Institute (M.M.R.); Department of Paediatrics (M.M.R.), University of Melbourne, Parkville, Victoria; Department of Neurology (R.L.S., G.M.S.), John Hunter Children's Hospital, and University Faculty of Health, Newcastle; Department of Paediatrics (H.K.Y.), Royal North Shore Hospital, St. Leonards, New South Wales, Australia; Department of Human Genetics (S.Z.), Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, FL; and Paediatric Gait Analysis Service of New South Wales (J.B.), Sydney Children's Hospitals Network (Randwick and Westmead), Australia
| | - Kayla Cornett
- From the T.Y. Nelson Department of Neurology and Neurosurgery (M.K., M.P.M.) and Institute for Neuroscience and Muscle Research (K.C., J.B., M.P.M.), The Children's Hospital at Westmead; University of Sydney (K.C., M.H.B., G.A.N., H.K.Y., M.L.K., J.B., M.P.M.); Northcott Neuroscience Laboratory (M.H.B., G.A.N., M.L.K.), ANZAC Research Institute, Concord; Molecular Medicine Laboratory (G.A.N., M.L.K.), Concord Repatriation General Hospital, New South Wales; Department of Neurology (M.M.R.), Royal Children's Hospital; Murdoch Children's Research Institute (M.M.R.); Department of Paediatrics (M.M.R.), University of Melbourne, Parkville, Victoria; Department of Neurology (R.L.S., G.M.S.), John Hunter Children's Hospital, and University Faculty of Health, Newcastle; Department of Paediatrics (H.K.Y.), Royal North Shore Hospital, St. Leonards, New South Wales, Australia; Department of Human Genetics (S.Z.), Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, FL; and Paediatric Gait Analysis Service of New South Wales (J.B.), Sydney Children's Hospitals Network (Randwick and Westmead), Australia
| | - Megan H Brewer
- From the T.Y. Nelson Department of Neurology and Neurosurgery (M.K., M.P.M.) and Institute for Neuroscience and Muscle Research (K.C., J.B., M.P.M.), The Children's Hospital at Westmead; University of Sydney (K.C., M.H.B., G.A.N., H.K.Y., M.L.K., J.B., M.P.M.); Northcott Neuroscience Laboratory (M.H.B., G.A.N., M.L.K.), ANZAC Research Institute, Concord; Molecular Medicine Laboratory (G.A.N., M.L.K.), Concord Repatriation General Hospital, New South Wales; Department of Neurology (M.M.R.), Royal Children's Hospital; Murdoch Children's Research Institute (M.M.R.); Department of Paediatrics (M.M.R.), University of Melbourne, Parkville, Victoria; Department of Neurology (R.L.S., G.M.S.), John Hunter Children's Hospital, and University Faculty of Health, Newcastle; Department of Paediatrics (H.K.Y.), Royal North Shore Hospital, St. Leonards, New South Wales, Australia; Department of Human Genetics (S.Z.), Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, FL; and Paediatric Gait Analysis Service of New South Wales (J.B.), Sydney Children's Hospitals Network (Randwick and Westmead), Australia
| | - Garth A Nicholson
- From the T.Y. Nelson Department of Neurology and Neurosurgery (M.K., M.P.M.) and Institute for Neuroscience and Muscle Research (K.C., J.B., M.P.M.), The Children's Hospital at Westmead; University of Sydney (K.C., M.H.B., G.A.N., H.K.Y., M.L.K., J.B., M.P.M.); Northcott Neuroscience Laboratory (M.H.B., G.A.N., M.L.K.), ANZAC Research Institute, Concord; Molecular Medicine Laboratory (G.A.N., M.L.K.), Concord Repatriation General Hospital, New South Wales; Department of Neurology (M.M.R.), Royal Children's Hospital; Murdoch Children's Research Institute (M.M.R.); Department of Paediatrics (M.M.R.), University of Melbourne, Parkville, Victoria; Department of Neurology (R.L.S., G.M.S.), John Hunter Children's Hospital, and University Faculty of Health, Newcastle; Department of Paediatrics (H.K.Y.), Royal North Shore Hospital, St. Leonards, New South Wales, Australia; Department of Human Genetics (S.Z.), Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, FL; and Paediatric Gait Analysis Service of New South Wales (J.B.), Sydney Children's Hospitals Network (Randwick and Westmead), Australia
| | - Monique M Ryan
- From the T.Y. Nelson Department of Neurology and Neurosurgery (M.K., M.P.M.) and Institute for Neuroscience and Muscle Research (K.C., J.B., M.P.M.), The Children's Hospital at Westmead; University of Sydney (K.C., M.H.B., G.A.N., H.K.Y., M.L.K., J.B., M.P.M.); Northcott Neuroscience Laboratory (M.H.B., G.A.N., M.L.K.), ANZAC Research Institute, Concord; Molecular Medicine Laboratory (G.A.N., M.L.K.), Concord Repatriation General Hospital, New South Wales; Department of Neurology (M.M.R.), Royal Children's Hospital; Murdoch Children's Research Institute (M.M.R.); Department of Paediatrics (M.M.R.), University of Melbourne, Parkville, Victoria; Department of Neurology (R.L.S., G.M.S.), John Hunter Children's Hospital, and University Faculty of Health, Newcastle; Department of Paediatrics (H.K.Y.), Royal North Shore Hospital, St. Leonards, New South Wales, Australia; Department of Human Genetics (S.Z.), Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, FL; and Paediatric Gait Analysis Service of New South Wales (J.B.), Sydney Children's Hospitals Network (Randwick and Westmead), Australia
| | - Robert L Smith
- From the T.Y. Nelson Department of Neurology and Neurosurgery (M.K., M.P.M.) and Institute for Neuroscience and Muscle Research (K.C., J.B., M.P.M.), The Children's Hospital at Westmead; University of Sydney (K.C., M.H.B., G.A.N., H.K.Y., M.L.K., J.B., M.P.M.); Northcott Neuroscience Laboratory (M.H.B., G.A.N., M.L.K.), ANZAC Research Institute, Concord; Molecular Medicine Laboratory (G.A.N., M.L.K.), Concord Repatriation General Hospital, New South Wales; Department of Neurology (M.M.R.), Royal Children's Hospital; Murdoch Children's Research Institute (M.M.R.); Department of Paediatrics (M.M.R.), University of Melbourne, Parkville, Victoria; Department of Neurology (R.L.S., G.M.S.), John Hunter Children's Hospital, and University Faculty of Health, Newcastle; Department of Paediatrics (H.K.Y.), Royal North Shore Hospital, St. Leonards, New South Wales, Australia; Department of Human Genetics (S.Z.), Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, FL; and Paediatric Gait Analysis Service of New South Wales (J.B.), Sydney Children's Hospitals Network (Randwick and Westmead), Australia
| | - Gopinath M Subramanian
- From the T.Y. Nelson Department of Neurology and Neurosurgery (M.K., M.P.M.) and Institute for Neuroscience and Muscle Research (K.C., J.B., M.P.M.), The Children's Hospital at Westmead; University of Sydney (K.C., M.H.B., G.A.N., H.K.Y., M.L.K., J.B., M.P.M.); Northcott Neuroscience Laboratory (M.H.B., G.A.N., M.L.K.), ANZAC Research Institute, Concord; Molecular Medicine Laboratory (G.A.N., M.L.K.), Concord Repatriation General Hospital, New South Wales; Department of Neurology (M.M.R.), Royal Children's Hospital; Murdoch Children's Research Institute (M.M.R.); Department of Paediatrics (M.M.R.), University of Melbourne, Parkville, Victoria; Department of Neurology (R.L.S., G.M.S.), John Hunter Children's Hospital, and University Faculty of Health, Newcastle; Department of Paediatrics (H.K.Y.), Royal North Shore Hospital, St. Leonards, New South Wales, Australia; Department of Human Genetics (S.Z.), Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, FL; and Paediatric Gait Analysis Service of New South Wales (J.B.), Sydney Children's Hospitals Network (Randwick and Westmead), Australia
| | - Helen K Young
- From the T.Y. Nelson Department of Neurology and Neurosurgery (M.K., M.P.M.) and Institute for Neuroscience and Muscle Research (K.C., J.B., M.P.M.), The Children's Hospital at Westmead; University of Sydney (K.C., M.H.B., G.A.N., H.K.Y., M.L.K., J.B., M.P.M.); Northcott Neuroscience Laboratory (M.H.B., G.A.N., M.L.K.), ANZAC Research Institute, Concord; Molecular Medicine Laboratory (G.A.N., M.L.K.), Concord Repatriation General Hospital, New South Wales; Department of Neurology (M.M.R.), Royal Children's Hospital; Murdoch Children's Research Institute (M.M.R.); Department of Paediatrics (M.M.R.), University of Melbourne, Parkville, Victoria; Department of Neurology (R.L.S., G.M.S.), John Hunter Children's Hospital, and University Faculty of Health, Newcastle; Department of Paediatrics (H.K.Y.), Royal North Shore Hospital, St. Leonards, New South Wales, Australia; Department of Human Genetics (S.Z.), Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, FL; and Paediatric Gait Analysis Service of New South Wales (J.B.), Sydney Children's Hospitals Network (Randwick and Westmead), Australia
| | - Stephan Züchner
- From the T.Y. Nelson Department of Neurology and Neurosurgery (M.K., M.P.M.) and Institute for Neuroscience and Muscle Research (K.C., J.B., M.P.M.), The Children's Hospital at Westmead; University of Sydney (K.C., M.H.B., G.A.N., H.K.Y., M.L.K., J.B., M.P.M.); Northcott Neuroscience Laboratory (M.H.B., G.A.N., M.L.K.), ANZAC Research Institute, Concord; Molecular Medicine Laboratory (G.A.N., M.L.K.), Concord Repatriation General Hospital, New South Wales; Department of Neurology (M.M.R.), Royal Children's Hospital; Murdoch Children's Research Institute (M.M.R.); Department of Paediatrics (M.M.R.), University of Melbourne, Parkville, Victoria; Department of Neurology (R.L.S., G.M.S.), John Hunter Children's Hospital, and University Faculty of Health, Newcastle; Department of Paediatrics (H.K.Y.), Royal North Shore Hospital, St. Leonards, New South Wales, Australia; Department of Human Genetics (S.Z.), Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, FL; and Paediatric Gait Analysis Service of New South Wales (J.B.), Sydney Children's Hospitals Network (Randwick and Westmead), Australia
| | - Marina L Kennerson
- From the T.Y. Nelson Department of Neurology and Neurosurgery (M.K., M.P.M.) and Institute for Neuroscience and Muscle Research (K.C., J.B., M.P.M.), The Children's Hospital at Westmead; University of Sydney (K.C., M.H.B., G.A.N., H.K.Y., M.L.K., J.B., M.P.M.); Northcott Neuroscience Laboratory (M.H.B., G.A.N., M.L.K.), ANZAC Research Institute, Concord; Molecular Medicine Laboratory (G.A.N., M.L.K.), Concord Repatriation General Hospital, New South Wales; Department of Neurology (M.M.R.), Royal Children's Hospital; Murdoch Children's Research Institute (M.M.R.); Department of Paediatrics (M.M.R.), University of Melbourne, Parkville, Victoria; Department of Neurology (R.L.S., G.M.S.), John Hunter Children's Hospital, and University Faculty of Health, Newcastle; Department of Paediatrics (H.K.Y.), Royal North Shore Hospital, St. Leonards, New South Wales, Australia; Department of Human Genetics (S.Z.), Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, FL; and Paediatric Gait Analysis Service of New South Wales (J.B.), Sydney Children's Hospitals Network (Randwick and Westmead), Australia
| | - Joshua Burns
- From the T.Y. Nelson Department of Neurology and Neurosurgery (M.K., M.P.M.) and Institute for Neuroscience and Muscle Research (K.C., J.B., M.P.M.), The Children's Hospital at Westmead; University of Sydney (K.C., M.H.B., G.A.N., H.K.Y., M.L.K., J.B., M.P.M.); Northcott Neuroscience Laboratory (M.H.B., G.A.N., M.L.K.), ANZAC Research Institute, Concord; Molecular Medicine Laboratory (G.A.N., M.L.K.), Concord Repatriation General Hospital, New South Wales; Department of Neurology (M.M.R.), Royal Children's Hospital; Murdoch Children's Research Institute (M.M.R.); Department of Paediatrics (M.M.R.), University of Melbourne, Parkville, Victoria; Department of Neurology (R.L.S., G.M.S.), John Hunter Children's Hospital, and University Faculty of Health, Newcastle; Department of Paediatrics (H.K.Y.), Royal North Shore Hospital, St. Leonards, New South Wales, Australia; Department of Human Genetics (S.Z.), Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, FL; and Paediatric Gait Analysis Service of New South Wales (J.B.), Sydney Children's Hospitals Network (Randwick and Westmead), Australia
| | - Manoj P Menezes
- From the T.Y. Nelson Department of Neurology and Neurosurgery (M.K., M.P.M.) and Institute for Neuroscience and Muscle Research (K.C., J.B., M.P.M.), The Children's Hospital at Westmead; University of Sydney (K.C., M.H.B., G.A.N., H.K.Y., M.L.K., J.B., M.P.M.); Northcott Neuroscience Laboratory (M.H.B., G.A.N., M.L.K.), ANZAC Research Institute, Concord; Molecular Medicine Laboratory (G.A.N., M.L.K.), Concord Repatriation General Hospital, New South Wales; Department of Neurology (M.M.R.), Royal Children's Hospital; Murdoch Children's Research Institute (M.M.R.); Department of Paediatrics (M.M.R.), University of Melbourne, Parkville, Victoria; Department of Neurology (R.L.S., G.M.S.), John Hunter Children's Hospital, and University Faculty of Health, Newcastle; Department of Paediatrics (H.K.Y.), Royal North Shore Hospital, St. Leonards, New South Wales, Australia; Department of Human Genetics (S.Z.), Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, FL; and Paediatric Gait Analysis Service of New South Wales (J.B.), Sydney Children's Hospitals Network (Randwick and Westmead), Australia.
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Cutrupi AN, Brewer MH, Nicholson GA, Kennerson M. Structural variations causing inherited peripheral neuropathies: A paradigm for understanding genomic organization, chromatin interactions, and gene dysregulation. Mol Genet Genomic Med 2018; 6:422-433. [PMID: 29573232 PMCID: PMC6014456 DOI: 10.1002/mgg3.390] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/09/2018] [Accepted: 03/01/2018] [Indexed: 11/16/2022] Open
Abstract
Inherited peripheral neuropathies (IPNs) are a clinically and genetically heterogeneous group of diseases affecting the motor and sensory peripheral nerves. IPNs have benefited from gene discovery and genetic diagnosis using next-generation sequencing with over 80 causative genes available for testing. Despite this success, up to 50% of cases remain genetically unsolved. In the absence of protein coding mutations, noncoding DNA or structural variation (SV) mutations are a possible explanation. The most common IPN, Charcot-Marie-Tooth neuropathy type 1A (CMT1A), is caused by a 1.5 Mb duplication causing trisomy of the dosage sensitive gene PMP22. Using genome sequencing, we recently identified two large genomic rearrangements causing IPN subtypes X-linked CMT (CMTX3) and distal hereditary motor neuropathy (DHMN1), thereby expanding the spectrum of SV mutations causing IPN. Understanding how newly discovered SVs can cause IPN may serve as a useful paradigm to examine the role of topologically associated domains (TADs), chromatin interactions, and gene dysregulation in disease. This review will describe the growing role of SV in the pathogenesis of IPN and the importance of considering this type of mutation in Mendelian diseases where protein coding mutations cannot be identified.
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Affiliation(s)
- Anthony N. Cutrupi
- Northcott Neuroscience LaboratoryANZAC Research InstituteSydneyNSWAustralia
- Sydney Medical SchoolUniversity of SydneySydneyNSWAustralia
| | - Megan H. Brewer
- Northcott Neuroscience LaboratoryANZAC Research InstituteSydneyNSWAustralia
- Sydney Medical SchoolUniversity of SydneySydneyNSWAustralia
| | - Garth A. Nicholson
- Northcott Neuroscience LaboratoryANZAC Research InstituteSydneyNSWAustralia
- Sydney Medical SchoolUniversity of SydneySydneyNSWAustralia
- Molecular Medicine LaboratoryConcord HospitalSydneyNSWAustralia
| | - Marina L. Kennerson
- Northcott Neuroscience LaboratoryANZAC Research InstituteSydneyNSWAustralia
- Sydney Medical SchoolUniversity of SydneySydneyNSWAustralia
- Molecular Medicine LaboratoryConcord HospitalSydneyNSWAustralia
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Abstract
PURPOSE OF REVIEW Charcot-Marie-Tooth disease (CMT) and related neuropathies represent a heterogeneous group of hereditary disorders. The present review will discuss the most recent advances in the field. RECENT FINDINGS Knowledge of CMT epidemiology and frequency of the main associated genes is increasing, with an overall prevalence estimated at 10-28/100 000. In the last years, the huge number of newly uncovered genes, thanks to next-generation sequencing techniques, is challenging the current classification of CMT. During the last 18 months other genes have been associated with CMT, such as PMP2, MORC2, NEFH, MME, and DGAT2. For the most common forms of CMT, numerous promising compounds are under study in cellular and animal models, mainly targeting either the protein degradation pathway or the protein overexpression. Consequently, efforts are devoted to develop responsive outcome measures and biomarkers for this overall slowly progressive disorder, with quantitative muscle MRI resulting the most sensitive-to-change measure. SUMMARY This is a rapidly evolving field where better understanding of pathophysiology is paving the way to develop potentially effective treatments, part of which will soon be tested in patients. Intense research is currently devoted to prepare clinical trials and develop responsive outcome measures.
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Cornett KMD, Menezes MP, Shy RR, Moroni I, Pagliano E, Pareyson D, Estilow T, Yum SW, Bhandari T, Muntoni F, Laura M, Reilly MM, Finkel RS, Eichinger KJ, Herrmann DN, Bray P, Halaki M, Shy ME, Burns J. Natural history of Charcot-Marie-Tooth disease during childhood. Ann Neurol 2017; 82:353-359. [PMID: 28796392 DOI: 10.1002/ana.25009] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/04/2017] [Accepted: 08/04/2017] [Indexed: 11/12/2022]
Abstract
OBJECTIVE To determine the rate of disease progression in a longitudinal natural history study of children with Charcot-Marie-Tooth (CMT) disease. METHODS Two hundred six (103 female) participants aged 3 to 20 years enrolled in the Inherited Neuropathies Consortium were assessed at baseline and 2 years. Demographic, anthropometric, and diagnostic information were collected. Disease progression was assessed with the CMT Pediatric Scale (CMTPedS), a reliable Rasch-built linearly weighted disability scale evaluating fine and gross motor function, strength, sensation, and balance. RESULTS On average, CMTPedS Total scores progressed at a rate of 2.4 ± 4.9 over 2 years (14% change from baseline; p < 0.001). There was no difference between males and females (mean difference, 0.5; 95% confidence interval [CI], -0.9 to 1.9; p = 0.49). The most responsive CMTPedS items were dorsiflexion strength (z-score change, -0.3; 95% CI, -0.6 to -0.05; p = 0.02), balance (z-score change, -1.0; 95% CI, -1.9 to -0.09; p = 0.03), and long jump (z-score change, -0.4; 95% CI, -0.7 to -0.02; p = 0.04). Of the most common genetic subtypes, 111 participants with CMT1A/PMP22 duplication progressed by 1.8 ± 4.2 (12% change from baseline; p < 0.001), 9 participants with CMT1B/MPZ mutation progressed by 2.2 ± 5.1 (11% change), 6 participants with CMT2A/MFN2 mutation progressed by 6.2 ± 7.9 (23% change), and 7 participants with CMT4C/SH3TC2 mutations progressed by 3.0 ± 4.5 (12% change). Participants with CMT2A progressed faster than CMT1A (mean difference, -4.4; 95% CI, -8.1 to -0.8; p = 0.02). Children with CMT1A progressed consistently through early childhood (3-10 years) and adolescence (11-20 years; mean difference, 1.1; 95% CI, -0.6 to 2.7; p = 0.19), whereas CMT2A appeared to progress faster during early childhood than adolescence (mean difference, 10.0; 95% CI, -2.2 to 22.2; p = 0.08). INTERPRETATION Using the CMTPedS as an outcome measure of disease severity, children with CMT progress at a significant rate over 2 years. Understanding the rate at which children with CMT deteriorate is essential for adequately powering trials of disease-modifying interventions. Ann Neurol 2017;82:353-359.
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Affiliation(s)
- Kayla M D Cornett
- The University of Sydney, Sydney Children's Hospitals Network (Randwick and Westmead, Sydney, New South Wales, Australia
| | - Manoj P Menezes
- The University of Sydney, Sydney Children's Hospitals Network (Randwick and Westmead, Sydney, New South Wales, Australia.,Paediatrics and Child Health, University of Sydney, Sydney, New South Wales, Australia
| | - Rosemary R Shy
- Carver College of Medicine, Department of Pediatrics, University of Iowa, Iowa City, IA
| | - Isabella Moroni
- IRCCS Foundation, Carlo Besta Neurological Institute, Milan, Italy
| | | | - Davide Pareyson
- IRCCS Foundation, Carlo Besta Neurological Institute, Milan, Italy
| | - Timothy Estilow
- Neuromuscular Program, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Sabrina W Yum
- Division of Neurology, The Children's Hospital of Philadelphia, Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Trupti Bhandari
- UCL Institute of Child Health & Great Ormond Street Hospital, London, United Kingdom
| | - Francesco Muntoni
- UCL Institute of Child Health & Great Ormond Street Hospital, London, United Kingdom
| | - Matilde Laura
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Mary M Reilly
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, United Kingdom
| | - Richard S Finkel
- Neuromuscular Program, Division of Neurology, Nemours Children's Hospital, Orlando, FL
| | | | | | - Paula Bray
- The University of Sydney, Sydney Children's Hospitals Network (Randwick and Westmead, Sydney, New South Wales, Australia
| | - Mark Halaki
- Paediatrics and Child Health, University of Sydney, Sydney, New South Wales, Australia
| | - Michael E Shy
- Carver College of Medicine, Department of Neurology, University of Iowa, Iowa City, IA
| | - Joshua Burns
- The University of Sydney, Sydney Children's Hospitals Network (Randwick and Westmead, Sydney, New South Wales, Australia.,Paediatrics and Child Health, University of Sydney, Sydney, New South Wales, Australia
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20
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Allamand V. Génétique : Une insertion de 78 kb du chromosome 8 au locus CMTX3 à l’origine d’une forme de neuropathie de type Charcot-Marie-Tooth. Med Sci (Paris) 2016. [DOI: 10.1051/medsci/201632s211] [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
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