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Figueiredo FB, Tomaselli PJ, Hallak J, Mattiello-Sverzut AC, Covaleski APPM, Sobreira CFDR, de Paula Gouvêa S, Marques W. Genetic diversity in hereditary axonal neuropathy: Analyzing 53 Brazilian children. J Peripher Nerv Syst 2024; 29:97-106. [PMID: 38375759 DOI: 10.1111/jns.12617] [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: 01/21/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND AND AIMS The genetic epidemiology of inherited neuropathies in children remains largely unknown. In this study, we specifically investigated the genetic profile of a Brazilian cohort of pediatric patients with pure or complex axonal neuropathies, a crucial knowledge in the near future for establishing treatment priorities and perspectives for this group of patients. METHODS Fifty-three pediatric patients who were assessed prior to reaching the age of 20, and who had clinical diagnoses of axonal hereditary neuropathy or presented with axonal neuropathy as the primary clinical feature, were included in the study. The recruitment of these cases took place from January 1, 2018, to December 31, 2020. The diagnosis was based on clinical and electrophysiological data. A molecular assessment was made using target-gene panel or whole-exome sequencing. Subsequently, segregation analysis was performed on available family members, and all candidate variants found were confirmed through Sanger. RESULTS A molecular diagnosis was reached in 68% of the patients (n = 36/53), considering only pathogenic and probably pathogenic variants. Variants in MFN2 (n = 15) and GJB1 (n = 3) accounted for half of the genetically confirmed patients (50%; n = 18/36). The other 18 genetically diagnosed patients had variants in several less common genes. INTERPRETATION Apart from MFN2 and GJB1 genes, universally recognized as a frequent cause of axonal neuropathies in most studied population, our Brazilian cohort of children with axonal neuropathies showed an important genetic heterogeneity, probably reflecting the multi ethnicity of the Brazilian population. Diagnostic, counseling, and future interventions should consider this characteristic.
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Affiliation(s)
- Fernanda Barbosa Figueiredo
- Neuroscience and Behavior Sciences Department, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Pedro José Tomaselli
- Neuroscience and Behavior Sciences Department, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Jaime Hallak
- Neuroscience and Behavior Sciences Department, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- National Institute of Sciences and Technology-INCT-Translational Medicine-CNPq/FAPESP, Ribeirao Preto, Brazil
| | | | | | | | - Silmara de Paula Gouvêa
- Neuroscience and Behavior Sciences Department, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Wilson Marques
- Neuroscience and Behavior Sciences Department, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- National Institute of Sciences and Technology-INCT-Translational Medicine-CNPq/FAPESP, Ribeirao Preto, Brazil
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Nishadham V, Santhoshkumar R, Nashi S, Vengalil S, Bardhan M, Polavarapu K, Sanka SB, Anjanappa RM, Kulanthaivelu K, Saini J, Chickabasaviah YT, Nalini A. A Novel Mutation in Frabin (FGD4) Causing a Mild Phenotype of CMT4H in an Indian Patient. J Neuromuscul Dis 2024; 11:221-232. [PMID: 38108359 PMCID: PMC10789318 DOI: 10.3233/jnd-230042] [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] [Accepted: 10/31/2023] [Indexed: 12/19/2023]
Abstract
Charcot-Marie-Tooth disease 4H(CMT4H) is an autosomal recessive demyelinating form of CMT caused by FGD4/FRABIN mutations. CMT4H is characterized by early onset and slowly progressing motor and sensory deficits in the distal extremities, along with foot deformities. We describe a patient with CMT4H who presented with rapidly progressing flaccid quadriparesis during the postpartum period, which improved significantly with steroid therapy. Magnetic resonance imaging and ultrasonography demonstrated considerable nerve thickening with increased cross-sectional area in the peripheral nerves. A nerve biopsy revealed significant demyelination and myelin outfolding. This is the first report of an Indian patient with a novel homozygous nonsense c.1672C>T (p.Arg558Ter) mutation in the FGD4 gene, expanding the mutational and phenotypic spectrum of this disease.
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Affiliation(s)
- Vikas Nishadham
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Rashmi Santhoshkumar
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Saraswati Nashi
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Seena Vengalil
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Mainak Bardhan
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Kiran Polavarapu
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Sai Bhargava Sanka
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Ram Murthy Anjanappa
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Karthik Kulanthaivelu
- Department of Neurointerventional and Imaging, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Jitender Saini
- Department of Neurointerventional and Imaging, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Yasha T. Chickabasaviah
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, Karnataka, India
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Kotaich F, Caillol D, Bomont P. Neurofilaments in health and Charcot-Marie-Tooth disease. Front Cell Dev Biol 2023; 11:1275155. [PMID: 38164457 PMCID: PMC10758125 DOI: 10.3389/fcell.2023.1275155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/02/2023] [Indexed: 01/03/2024] Open
Abstract
Neurofilaments (NFs) are the most abundant component of mature neurons, that interconnect with actin and microtubules to form the cytoskeleton. Specifically expressed in the nervous system, NFs present the particularity within the Intermediate Filament family of being formed by four subunits, the neurofilament light (NF-L), medium (NF-M), heavy (NF-H) proteins and α-internexin or peripherin. Here, we review the current knowledge on NF proteins and neurofilaments, from their domain structures and their model of assembly to the dynamics of their transport and degradation along the axon. The formation of the filament and its behaviour are regulated by various determinants, including post-transcriptional (miRNA and RBP proteins) and post-translational (phosphorylation and ubiquitination) modifiers. Altogether, the complex set of modifications enable the neuron to establish a stable but elastic NF array constituting the structural scaffold of the axon, while permitting the local expression of NF proteins and providing the dynamics necessary to fulfil local demands and respond to stimuli and injury. Thus, in addition to their roles in mechano-resistance, radial axonal outgrowth and nerve conduction, NFs control microtubule dynamics, organelle distribution and neurotransmission at the synapse. We discuss how the studies of neurodegenerative diseases with NF aggregation shed light on the biology of NFs. In particular, the NEFL and NEFH genes are mutated in Charcot-Marie-Tooth (CMT) disease, the most common inherited neurological disorder of the peripheral nervous system. The clinical features of the CMT forms (axonal CMT2E, CMT2CC; demyelinating CMT1F; intermediate I-CMT) with symptoms affecting the central nervous system (CNS) will allow us to further investigate the physiological roles of NFs in the brain. Thus, NF-CMT mouse models exhibit various degrees of sensory-motor deficits associated with CNS symptoms. Cellular systems brought findings regarding the dominant effect of NF-L mutants on NF aggregation and transport, although these have been recently challenged. Neurofilament detection without NF-L in recessive CMT is puzzling, calling for a re-examination of the current model in which NF-L is indispensable for NF assembly. Overall, we discuss how the fundamental and translational fields are feeding each-other to increase but also challenge our knowledge of NF biology, and to develop therapeutic avenues for CMT and neurodegenerative diseases with NF aggregation.
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Affiliation(s)
| | | | - Pascale Bomont
- ERC team, NeuroMyoGene Institute-Pathophysiology and Genetics of Neuron and Muscle, Inserm U1315, CNRS UMR5261, University of Lyon 1, Lyon, France
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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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Jung NY, Kwon HM, Nam DE, Tamanna N, Lee AJ, Kim SB, Choi BO, Chung KW. Peripheral Myelin Protein 22 Gene Mutations in Charcot-Marie-Tooth Disease Type 1E Patients. Genes (Basel) 2022; 13:genes13071219. [PMID: 35886002 PMCID: PMC9321036 DOI: 10.3390/genes13071219] [Citation(s) in RCA: 5] [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: 06/02/2022] [Revised: 06/27/2022] [Accepted: 07/04/2022] [Indexed: 02/04/2023] Open
Abstract
Duplication and deletion of the peripheral myelin protein 22 (PMP22) gene cause Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP), respectively, while point mutations or small insertions and deletions (indels) usually cause CMT type 1E (CMT1E) or HNPP. This study was performed to identify PMP22 mutations and to analyze the genotype−phenotype correlation in Korean CMT families. By the application of whole-exome sequencing (WES) and targeted gene panel sequencing (TS), we identified 14 pathogenic or likely pathogenic PMP22 mutations in 21 families out of 850 CMT families who were negative for 17p12 (PMP22) duplication. Most mutations were located in the well-conserved transmembrane domains. Of these, eight mutations were not reported in other populations. High frequencies of de novo mutations were observed, and the mutation sites of c.68C>G and c.215C>T were suggested as the mutational hotspots. Affected individuals showed an early onset-severe phenotype and late onset-mild phenotype, and more than 40% of the CMT1E patients showed hearing loss. Physical and electrophysiological symptoms of the CMT1E patients were more severely damaged than those of CMT1A while similar to CMT1B caused by MPZ mutations. Our results will be useful for the reference data of Korean CMT1E and the molecular diagnosis of CMT1 with or without hearing loss.
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Affiliation(s)
- Na Young Jung
- Department of Biological Sciences, Kongju National University, Gongju 32588, Korea; (N.Y.J.); (D.E.N.); (N.T.); (A.J.L.)
| | - Hye Mi Kwon
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
| | - Da Eun Nam
- Department of Biological Sciences, Kongju National University, Gongju 32588, Korea; (N.Y.J.); (D.E.N.); (N.T.); (A.J.L.)
| | - Nasrin Tamanna
- Department of Biological Sciences, Kongju National University, Gongju 32588, Korea; (N.Y.J.); (D.E.N.); (N.T.); (A.J.L.)
| | - Ah Jin Lee
- Department of Biological Sciences, Kongju National University, Gongju 32588, Korea; (N.Y.J.); (D.E.N.); (N.T.); (A.J.L.)
| | - Sang Beom Kim
- Department of Neurology, Kyung Hee University Hospital at Gangdong, Kyung Hee University School of Medicine, Seoul 05278, Korea;
| | - Byung-Ok Choi
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea;
- Cell & Gene Therapy Institute, Samsung Medical Center, Seoul 06351, Korea
- Correspondence: (B.-O.C.); (K.W.C.); Tel.: +82-2-3410-1296 (B.-O.C.); +82-41-850-8506 (K.W.C.)
| | - Ki Wha Chung
- Department of Biological Sciences, Kongju National University, Gongju 32588, Korea; (N.Y.J.); (D.E.N.); (N.T.); (A.J.L.)
- Correspondence: (B.-O.C.); (K.W.C.); Tel.: +82-2-3410-1296 (B.-O.C.); +82-41-850-8506 (K.W.C.)
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6
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Genetic Workup for Charcot–Marie–Tooth Neuropathy: A Retrospective Single-Site Experience Covering 15 Years. Life (Basel) 2022; 12:life12030402. [PMID: 35330153 PMCID: PMC8948690 DOI: 10.3390/life12030402] [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: 01/31/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 11/16/2022] Open
Abstract
Charcot–Marie–Tooth (CMT) disease is the most commonly inherited neurological disorder. This study includes patients affected by CMT during regular follow-ups at the CMT clinic in Genova, a neuromuscular university center in the northwest of Italy, with the aim of describing the genetic distribution of CMT subtypes in our cohort and reporting a peculiar phenotype. Since 2004, 585 patients (447 index cases) have been evaluated at our center, 64.9% of whom have a demyelinating neuropathy and 35.1% of whom have an axonal neuropathy. A genetic diagnosis was achieved in 66% of all patients, with the following distribution: CMT1A (48%), HNPP (14%), CMT1X (13%), CMT2A (5%), and P0-related neuropathies (7%), accounting all together for 87% of all the molecularly defined neuropathies. Interestingly, we observe a peculiar phenotype with initial exclusive lower limb involvement as well as lower limb involvement that is maintained over time, which we have defined as a “strictly length-dependent” phenotype. Most patients with this clinical presentation shared variants in either HSPB1 or MPZ genes. The identification of distinctive phenotypes such as this one may help to address genetic diagnosis. In conclusion, we describe our diagnostic experiences as a multidisciplinary outpatient clinic, combining a gene-by-gene approach or targeted gene panels based on clinical presentation.
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Kim HJ, Kim SB, Kim HS, Kwon HM, Park JH, Lee AJ, Lim SO, Nam SH, Hong YB, Chung KW, Choi BO. Phenotypic heterogeneity in patients with NEFL-related Charcot-Marie-Tooth disease. Mol Genet Genomic Med 2022; 10:e1870. [PMID: 35044100 PMCID: PMC8830812 DOI: 10.1002/mgg3.1870] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/12/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022] Open
Abstract
Charcot–Marie–Tooth disease (CMT) is the most common hereditary peripheral neuropathy. Mutations in the neurofilament light polypeptide (NEFL) gene produce diverse clinical phenotypes, including demyelinating (CMT1F), axonal (CMT2E), and intermediate (CMTDIG) neuropathies. From 2005 to 2020, 1,143 Korean CMT families underwent gene sequencing, and we investigated the clinical, genetic, and neuroimaging spectra of NEFL‐related CMT patients. Ten NEFL mutations in 17 families (1.49%) were identified, of which three (p.L312P, p.Y443N, and p.K467N) were novel. Eight de novo cases were identified at a rate of 0.47 based on a cosegregation analysis. The age of onset was ≤3 years in five cases (13.5%). The patients revealed additional features including delayed walking, ataxia, dysphagia, dysarthria, dementia, ptosis, waddling gait, tremor, hearing loss, and abnormal visual evoked potential. Signs of ataxia were found in 26 patients (70.3%). In leg MRI analyses, various degrees of intramuscular fat infiltration were found. All compartments were evenly affected in CMT1F patients. The anterior and anterolateral compartments were affected in CMT2E, and the posterior compartment was affected in CMTDIG. Thus, NEFL‐related CMT patients showed phenotypic heterogeneities. This study's clinical, genetic, and neuroimaging results could be helpful in the evaluation of novel NEFL variants and differential diagnosis against other CMT subtypes.
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Affiliation(s)
- Hye Jin Kim
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea.,Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sang Beom Kim
- Department of Neurology, Kyung Hee University Hospital at Gangdong, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Hyun Su Kim
- Department of Radiology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hye Mi Kwon
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae Hong Park
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ah Jin Lee
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Si On Lim
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Soo Hyun Nam
- Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul, Korea
| | - Young Bin Hong
- Department of Biochemistry, College of Medicine, Dong-A University, Busan, Korea
| | - Ki Wha Chung
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Byung-Ok Choi
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea.,Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul, Korea
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8
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Narayanaswami P, Živković S. Molecular and Genetic Therapies. Neuromuscul Disord 2022. [DOI: 10.1016/b978-0-323-71317-7.00011-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Gangfuß A, Schara-Schmidt U, Roos A. [Genomics and proteomics in the research of neuromuscular diseases]. DER NERVENARZT 2021; 93:114-121. [PMID: 34622318 DOI: 10.1007/s00115-021-01201-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/04/2021] [Indexed: 11/30/2022]
Abstract
Neurological diseases affect 3-5% of children and, apart from cardiovascular diseases and cancer, represent the most prominent cause of morbidity and mortality in adults and particularly in the aged population of western Europe. Neuromuscular disorders are a subgroup of neurological diseases and often have a genetic origin, which leads to familial clustering. Despite the enormous progress in the analysis of the genome, such as by sequence analysis of coding regions of deoxyribonucleic acid or even the entire deoxyribonucleic acid sequence, in approximately 50% of the patients suffering from rare forms of neurological diseases the genetic cause remains unsolved. The reasons for this limited detection rate are presented in this article. If a treatment concept is available, under certain conditions this can have an impact on the adequate and early treatment of these patients. Considering neuromuscular disorders as a paradigm, this article reports on the advantages of the inclusion of next generation sequencing analysis-based DNA investigations as an omics technology (genomics) and the advantage of the integration with protein analyses (proteomics). A special focus is on the combination of genomics and proteomics in the sense of a proteogenomic approach in the diagnostics and research of these diseases. Along this line, this article presents a proteogenomic approach in the context of a multidisciplinary project aiming towards improved diagnostic work-up and future treatment of patients with neuromuscular diseases; "NMD-GPS: gene and protein signatures as a global positioning system in patients suffering from neuromuscular diseases".
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Affiliation(s)
- Andrea Gangfuß
- Abteilung für Neuropädiatrie, Universitätsmedizin Essen, Hufelandstrasse 55, 45147, Essen, Deutschland
| | - Ulrike Schara-Schmidt
- Abteilung für Neuropädiatrie, Universitätsmedizin Essen, Hufelandstrasse 55, 45147, Essen, Deutschland
| | - Andreas Roos
- Abteilung für Neuropädiatrie, Universitätsmedizin Essen, Hufelandstrasse 55, 45147, Essen, Deutschland. .,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Kanada.
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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.
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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
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11
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Stone EJ, Kolb SJ, Brown A. A review and analysis of the clinical literature on Charcot-Marie-Tooth disease caused by mutations in neurofilament protein L. Cytoskeleton (Hoboken) 2021; 78:97-110. [PMID: 33993654 PMCID: PMC10174713 DOI: 10.1002/cm.21676] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 01/22/2023]
Abstract
Charcot-Marie-Tooth disease (CMT) is one of the most common inherited neurological disorders and can be caused by mutations in over 100 different genes. One of the causative genes is NEFL on chromosome 8 which encodes neurofilament light protein (NEFL), one of five proteins that co-assemble to form neurofilaments. At least 34 different CMT-causing mutations in NEFL have been reported which span the head, rod, and tail domains of the protein. The majority of these mutations are inherited dominantly, but some are inherited recessively. The resulting disease is classified variably in clinical reports based on electrodiagnostic studies as either axonal (type 2; CMT2E), demyelinating (type 1; CMT1F), or a form intermediate between the two (dominant intermediate; DI-CMTG). In this article, we first present a brief introduction to CMT and neurofilaments. We then collate and analyze the data from the clinical literature on the disease classification, age of onset and electrodiagnostic test results for the various mutations. We find that mutations in the head, rod, and tail domains can all cause disease with early onset and profound neurological impairment, with a trend toward greater severity for head domain mutations. We also find that the disease classification does not correlate with specific mutation or domain. In fact, different individuals with the same mutation can be classified as having axonal, demyelinating, or dominant intermediate forms of the disease. This suggests that the classification of the disease as CMT2E, CMT1F or DI-CMTG has more to do with variable disease presentation than to differences in the underlying disease mechanism, which is most likely primarily axonal in all cases.
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Affiliation(s)
- Elizabeth J Stone
- Department of Neuroscience, Ohio State University, Columbus, Ohio, USA.,Neuroscience Graduate Program, Ohio State University, Columbus, Ohio, USA
| | - Stephen J Kolb
- Department of Neurology, Ohio State University, Columbus, Ohio, USA.,Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, Ohio, USA
| | - Anthony Brown
- Department of Neuroscience, Ohio State University, Columbus, Ohio, USA
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12
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Yubero D, Natera-de Benito D, Pijuan J, Armstrong J, Martorell L, Fernàndez G, Maynou J, Jou C, Roldan M, Ortez C, Nascimento A, Hoenicka J, Palau F. The Increasing Impact of Translational Research in the Molecular Diagnostics of Neuromuscular Diseases. Int J Mol Sci 2021; 22:4274. [PMID: 33924139 PMCID: PMC8074304 DOI: 10.3390/ijms22084274] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
The diagnosis of neuromuscular diseases (NMDs) has been progressively evolving from the grouping of clinical symptoms and signs towards the molecular definition. Optimal clinical, biochemical, electrophysiological, electrophysiological, and histopathological characterization is very helpful to achieve molecular diagnosis, which is essential for establishing prognosis, treatment and genetic counselling. Currently, the genetic approach includes both the gene-targeted analysis in specific clinically recognizable diseases, as well as genomic analysis based on next-generation sequencing, analyzing either the clinical exome/genome or the whole exome or genome. However, as of today, there are still many patients in whom the causative genetic variant cannot be definitely established and variants of uncertain significance are often found. In this review, we address these drawbacks by incorporating two additional biological omics approaches into the molecular diagnostic process of NMDs. First, functional genomics by introducing experimental cell and molecular biology to analyze and validate the variant for its biological effect in an in-house translational diagnostic program, and second, incorporating a multi-omics approach including RNA-seq, metabolomics, and proteomics in the molecular diagnosis of neuromuscular disease. Both translational diagnostics programs and omics are being implemented as part of the diagnostic process in academic centers and referral hospitals and, therefore, an increase in the proportion of neuromuscular patients with a molecular diagnosis is expected. This improvement in the process and diagnostic performance of patients will allow solving aspects of their health problems in a precise way and will allow them and their families to take a step forward in their lives.
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Affiliation(s)
- Dèlia Yubero
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Daniel Natera-de Benito
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.N.-d.B.); (C.O.)
| | - Jordi Pijuan
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Judith Armstrong
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Loreto Martorell
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Guerau Fernàndez
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Joan Maynou
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
| | - Cristina Jou
- Department of Pathology, Hospital Sant Joan de Déu, Pediatric Biobank for Research, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Mònica Roldan
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Confocal Microscopy and Cellular Imaging Unit, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain
| | - Carlos Ortez
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.N.-d.B.); (C.O.)
- Division of Pediatrics, Clinic Institute of Medicine & Dermatology, Hospital Clínic, University of Barcelona School of Medicine and Health Sciences, 08950 Barcelona, Spain
| | - Andrés Nascimento
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
- Neuromuscular Unit, Department of Pediatric Neurology, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.N.-d.B.); (C.O.)
| | - Janet Hoenicka
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
| | - Francesc Palau
- Department of Genetic and Molecular Medicine—IPER, Hospital Sant Joan de Déu and Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; (D.Y.); (J.A.); (L.M.); (G.F.); (J.M.); (M.R.)
- Center for Biomedical Research Network on Rare Diseases (CIBERER), ISCIII, 08950 Barcelona, Spain;
- Laboratory of Neurogenetics and Molecular Medicine—IPER, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
- Department of Pathology, Hospital Sant Joan de Déu, Pediatric Biobank for Research, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain;
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13
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Jiang H, Guo C, Xie J, Pan J, Huang Y, Li M, Guo Y. Case report: exome sequencing achieved a definite diagnosis in a Chinese family with muscle atrophy. BMC Neurol 2021; 21:96. [PMID: 33653295 PMCID: PMC7923504 DOI: 10.1186/s12883-021-02093-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/04/2021] [Indexed: 11/25/2022] Open
Abstract
Background Due to large genetic and phenotypic heterogeneity, the conventional workup for Charcot-Marie-Tooth (CMT) diagnosis is often underpowered, leading to diagnostic delay or even lack of diagnosis. In the present study, we explored how bioinformatics analysis on whole-exome sequencing (WES) data can be used to diagnose patients with CMT disease efficiently. Case presentation The proband is a 29-year-old female presented with a severe amyotrophy and distal skeletal deformity that plagued her family for over 20 years since she was 5-year-old. No other aberrant symptoms were detected in her speaking, hearing, vision, and intelligence. Similar symptoms manifested in her younger brother, while her parents and her older brother showed normal. To uncover the genetic causes of this disease, we performed exome sequencing for the proband and her parents. Subsequent bioinformatics analysis on the KGGSeq platform and further Sanger sequencing identified a novel homozygous GDAP1 nonsense mutation (c.218C > G, p.Ser73*) that responsible for the family. This genetic finding then led to a quick diagnosis of CMT type 4A (CMT4A), confirmed by nerve conduction velocity and electromyography examination of the patients. Conclusions The patients with severe muscle atrophy and distal skeletal deformity were caused by a novel homozygous nonsense mutation in GDAP1 (c.218C > G, p.Ser73*), and were diagnosed as CMT4A finally. This study expanded the mutation spectrum of CMT disease and demonstrated how affordable WES could be effectively employed for the clinical diagnosis of unexplained phenotypes. Supplementary Information The online version contains supplementary material available at 10.1186/s12883-021-02093-z.
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Affiliation(s)
- Hui Jiang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Diseases Control (SYSU), Sun Yat-sen University, Guangzhou, 510080, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Chunmiao Guo
- Department of Neurology, The Second Affiliated Hospital, Fujian University of Medical Science, Quanzhou, 362000, China
| | - Jie Xie
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Diseases Control (SYSU), Sun Yat-sen University, Guangzhou, 510080, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Jingxin Pan
- Department of Hematology, The Second Affiliated Hospital, Fujian University of Medical Science, Quanzhou, 362000, China
| | - Ying Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Diseases Control (SYSU), Sun Yat-sen University, Guangzhou, 510080, China.,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (SYSU), Sun Yat-sen University, Guangzhou, 510080, China. .,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong, China. .,State Key Laboratory for Cognitive and Brain Sciences, The University of Hong Kong, Hong Kong SAR, China.
| | - Yibin Guo
- Key Laboratory of Tropical Diseases Control (SYSU), Sun Yat-sen University, Guangzhou, 510080, China. .,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,School of Medicine, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
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14
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Kim HS, Kim HJ, Nam SH, Kim SB, Choi YJ, Lee KS, Chung KW, Yoon YC, Choi BO. Clinical and Neuroimaging Features in Charcot-Marie-Tooth Patients with GDAP1 Mutations. J Clin Neurol 2021; 17:52-62. [PMID: 33480199 PMCID: PMC7840330 DOI: 10.3988/jcn.2021.17.1.52] [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: 06/30/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 01/04/2023] Open
Abstract
Background and Purpose Mutations in the ganglioside-induced differentiation-associated protein 1 gene (GDAP1) are known to cause Charcot-Marie-Tooth disease (CMT). These mutations are very rare in most countries, but not in certain Mediterranean countries. The purpose of this study was to identify the clinical and neuroimaging characteristics of Korean CMT patients with GDAP1 mutations. Methods Gene sequencing was applied to 1,143 families in whom CMT had been diagnosed from 2005 to 2020. PMP22 duplication was found in 344 families, and whole-exome sequencing was performed in 699 patients. Magnetic resonance imaging (MRI) were obtained using either a 1.5-T or 3.0-T MRI system. Results We found ten patients from eight families with GDAP1 mutations: five with autosomal dominant (AD) CMT type 2K (three families with p.R120W and two families with p.Q218E) and three with autosomal recessive (AR) intermediate CMT type A (two families with homozygous p.H256R and one family with p.P111H and p.V219G mutations). The frequency was about 1.0% exclusive of the PMP22 duplication, which is similar to that in other Asian countries. There were clinical differences among AD GDAP1 patients according to mutation sites. Surprisingly, fat infiltrations evident in lower-limb MRI differed between AD and AR patients. The posterior-compartment muscles in the calf were affected early and predominantly in AD patients, whereas AR patients showed fat infiltration predominantly in the anterolateral-compartment muscles. Conclusions This is the first cohort report on Korean patients with GDAP1 mutations. The patients with AD and AR inheritance routes exhibited different clinical and neuroimaging features in the lower extremities. We believe that these results will help to expand the knowledge of the clinical, genetic, and neuroimaging features of CMT.
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Affiliation(s)
- Hyun Su Kim
- Department of Radiology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hye Jin Kim
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea.,Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Soo Hyun Nam
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sang Beom Kim
- Department of Neurology, Kyung Hee University Hospital at Gangdong, Kyung Hee University School of Medicine, Seoul, Korea
| | - Yu Jin Choi
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Kyung Suk Lee
- Department of Physics Education, Kongju National University, Gongju, Korea
| | - Ki Wha Chung
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Young Cheol Yoon
- Department of Radiology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Byung Ok Choi
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea.,Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul, Korea.
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15
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Chen P, Yu X, Huang H, Zeng W, He X, Liu M, Huang B. Evaluation of Ion Torrent next-generation sequencing for thalassemia diagnosis. J Int Med Res 2020; 48:300060520967778. [PMID: 33342339 PMCID: PMC7754798 DOI: 10.1177/0300060520967778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
INTRODUCTION To evaluate a next-generation sequencing (NGS) workflow in the screening and diagnosis of thalassemia. METHODS In this prospective study, blood samples were obtained from people undergoing genetic screening for thalassemia at our centre in Guangzhou, China. Genomic DNA was polymerase chain reaction (PCR)-amplified and sequenced using the Ion Torrent system and results compared with traditional genetic analyses. RESULTS Of the 359 subjects, 148 (41%) were confirmed to have thalassemia. Variant detection identified 35 different types including the most common. Identification of the mutational sites by NGS were consistent with those identified by Sanger sequencing and Gap-PCR. The sensitivity and specificities of the Ion Torrent NGS were 100%. In a separate test of 16 samples, results were consistent when repeated ten times. CONCLUSION Our NGS workflow based on the Ion Torrent sequencer was successful in the detection of large deletions and non-deletional defects in thalassemia with high accuracy and repeatability.
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Affiliation(s)
- Peisong Chen
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xuegao Yu
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hao Huang
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wentao Zeng
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaohong He
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Min Liu
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Bin Huang
- Department of Clinical Laboratory, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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16
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Zhong M, Luo Q, Ye T, Zhu X, Chen X, Liu J. Identification of Candidate Genes Associated with Charcot-Marie-Tooth Disease by Network and Pathway Analysis. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1353516. [PMID: 33029488 PMCID: PMC7532371 DOI: 10.1155/2020/1353516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/21/2020] [Accepted: 08/12/2020] [Indexed: 12/15/2022]
Abstract
Charcot-Marie-Tooth Disease (CMT) is the most common clinical genetic disease of the peripheral nervous system. Although many studies have focused on elucidating the pathogenesis of CMT, few focuses on achieving a systematic analysis of biology to decode the underlying pathological molecular mechanisms and the mechanism of its disease remains to be elucidated. So our study may provide further useful insights into the molecular mechanisms of CMT based on a systematic bioinformatics analysis. In the current study, by reviewing the literatures deposited in PUBMED, we identified 100 genes genetically related to CMT. Then, the functional features of the CMT-related genes were examined by R software and KOBAS, and the selected biological process crosstalk was visualized with the software Cytoscape. Moreover, CMT specific molecular network analysis was conducted by the Molecular Complex Detection (MCODE) Algorithm. The biological function enrichment analysis suggested that myelin sheath, axon, peripheral nervous system, mitochondrial function, various metabolic processes, and autophagy played important roles in CMT development. Aminoacyl-tRNA biosynthesis, metabolic pathways, and vasopressin-regulated water reabsorption were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway network, suggesting that these pathways may play key roles in CMT occurrence and development. According to the crosstalk, the biological processes could be roughly divided into a correlative module and two separate modules. MCODE clusters showed that in top 3 clusters, 13 of CMT-related genes were included in the network and 30 candidate genes were discovered which might be potentially related to CMT. The study may help to update the new understanding of the pathogenesis of CMT and expand the potential genes of CMT for further exploration.
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Affiliation(s)
- Min Zhong
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, 646000 Sichuan, China
| | - Qing Luo
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, 646000 Sichuan, China
| | - Ting Ye
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, 646000 Sichuan, China
| | - XiDan Zhu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, 646000 Sichuan, China
| | - Xiu Chen
- Department of Neurology, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, 646000 Sichuan, China
| | - JinBo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, 25 Taiping Street, Luzhou, 646000 Sichuan, China
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17
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Advances in the diagnosis of inherited neuromuscular diseases and implications for therapy development. Lancet Neurol 2020; 19:522-532. [PMID: 32470424 DOI: 10.1016/s1474-4422(20)30028-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/19/2022]
Abstract
Advances in DNA sequencing technologies have resulted in a near doubling, in under 10 years, of the number of causal genes identified for inherited neuromuscular disorders. However, around half of patients, whether children or adults, do not receive a molecular diagnosis after initial diagnostic workup. Massively parallel technologies targeting RNA, proteins, and metabolites are being increasingly used to diagnose these unsolved cases. The use of these technologies to delineate pathways, biomarkers, and therapeutic targets has led to new approaches entering the drug development pipeline. However, these technologies might give rise to misleading conclusions if used in isolation, and traditional techniques including comprehensive neurological evaluation, histopathology, and biochemistry continue to have a crucial role in diagnostics. For optimal diagnosis, prognosis, and precision medicine, no single ruling technology exists. Instead, an interdisciplinary approach combining novel and traditional neurological techniques with computer-aided analysis and international data sharing is needed to advance the diagnosis and treatment of neuromuscular disorders.
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18
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Abstract
PURPOSE OF REVIEW Charcot-Marie-Tooth (CMT) disease and related disorders are the commonest group of inherited neuromuscular diseases and represent a heterogeneous group of disorders. This review will cover recent advances in genetic diagnosis and the evolving genetic and phenotype landscape of this disease group. We will review recent evidence of the increasingly recognized phenotypic overlap with other neurodegenerative conditions including hereditary spastic paraplegia, hereditary ataxias and mitochondrial diseases and highlight the importance of deep phenotyping to inform genetic diagnosis and prognosis. RECENT FINDINGS Through whole exome sequencing and multicentre collaboration new genes are being identified as causal for CMT expanding the genetic heterogeneity of this condition. In addition, an increasing number of variants have been identified in genes known to cause complex inherited diseases in which the peripheral neuropathy is part of the disorder and may be the presenting feature. The recent discovery of a repeat expansion in the RFC1 gene in cerebellar ataxia, neuropathy, vestibular areflexia syndrome highlights the prevalence of late-onset recessive conditions which have historically been considered to cause early-onset disease. SUMMARY CMT is an evolving field with considerable phenotypic and genetic heterogeneity and deep phenotyping remains a cornerstone in contemporary CMT diagnostics.
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19
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Cortese A, Wilcox JE, Polke JM, Poh R, Skorupinska M, Rossor AM, Laura M, Tomaselli PJ, Houlden H, Shy ME, Reilly MM. Targeted next-generation sequencing panels in the diagnosis of Charcot-Marie-Tooth disease. Neurology 2019; 94:e51-e61. [PMID: 31827005 PMCID: PMC7011687 DOI: 10.1212/wnl.0000000000008672] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/24/2019] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE To investigate the effectiveness of targeted next-generation sequencing (NGS) panels in achieving a molecular diagnosis in Charcot-Marie-Tooth disease (CMT) and related disorders in a clinical setting. METHODS We prospectively enrolled 220 patients from 2 tertiary referral centers, one in London, United Kingdom (n = 120), and one in Iowa (n = 100), in whom a targeted CMT NGS panel had been requested as a diagnostic test. PMP22 duplication/deletion was previously excluded in demyelinating cases. We reviewed the genetic and clinical data upon completion of the diagnostic process. RESULTS After targeted NGS sequencing, a definite molecular diagnosis, defined as a pathogenic or likely pathogenic variant, was reached in 30% of cases (n = 67). The diagnostic rate was similar in London (32%) and Iowa (29%). Variants of unknown significance were found in an additional 33% of cases. Mutations in GJB1, MFN2, and MPZ accounted for 39% of cases that received genetic confirmation, while the remainder of positive cases had mutations in diverse genes, including SH3TC2, GDAP1, IGHMBP2, LRSAM1, FDG4, and GARS, and another 12 less common genes. Copy number changes in PMP22, MPZ, MFN2, SH3TC2, and FDG4 were also accurately detected. A definite genetic diagnosis was more likely in cases with an early onset, a positive family history of neuropathy or consanguinity, and a demyelinating neuropathy. CONCLUSIONS NGS panels are effective tools in the diagnosis of CMT, leading to genetic confirmation in one-third of cases negative for PMP22 duplication/deletion, thus highlighting how rarer and previously undiagnosed subtypes represent a relevant part of the genetic landscape of CMT.
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Affiliation(s)
- Andrea Cortese
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Janel E Wilcox
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - James M Polke
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Roy Poh
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Mariola Skorupinska
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Alexander M Rossor
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Matilde Laura
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Pedro J Tomaselli
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Henry Houlden
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Michael E Shy
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City
| | - Mary M Reilly
- From the MRC Centre for Neuromuscular Diseases (A.C., J.M.P., R.P., M.S., A.M.R., M.L., P.J.T., H.H., M.M.R.), Department of Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, UCL Queen Square Institute of Neurology, London, UK; Department of Brain and Behavioral Sciences (A.C.), University of Pavia, Italy; and the Department of Neurology (J.E.W., M.E.S.), University of Iowa Carver College of Medicine, Iowa City.
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20
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Stone EJ, Uchida A, Brown A. Charcot-Marie-Tooth disease Type 2E/1F mutant neurofilament proteins assemble into neurofilaments. Cytoskeleton (Hoboken) 2019; 76:423-439. [PMID: 31574566 DOI: 10.1002/cm.21566] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/30/2019] [Accepted: 09/13/2019] [Indexed: 11/12/2022]
Abstract
Charcot-Marie-Tooth disease Type 2E/1F (CMT2E/1F) is a peripheral neuropathy caused by mutations in neurofilament protein L (NFL), which is one of five neurofilament subunit proteins that co-assemble to form neurofilaments in vivo. Prior studies on cultured cells have shown that CMT2E/1F mutations disrupt neurofilament assembly and lead to protein aggregation, suggesting a possible disease mechanism. However, electron microscopy of axons in peripheral nerve biopsies from patients has revealed accumulations of neurofilament polymers of normal appearance and no evidence of protein aggregates. To reconcile these observations, we reexamined the assembly of seven CMT2E/1F NFL mutants in cultured cells. None of the mutants assembled into homopolymers in SW13vim- cells, but P8R, P22S, L268/269P, and P440/441L mutant NFL assembled into heteropolymers in the presence of neurofilament protein M (NFM) alone, and N98S, Q332/333P, and E396/397K mutant NFL assembled in the presence of NFM and peripherin. P8R, P22S, N98S, L268/269P, E396/397K, and P440/441L mutant NFL co-assembled into neurofilaments with endogenous NFL, NFM, and α-internexin in cultured neurons, although the N98S and E396/397K mutants showed reduced filament incorporation, and the Q332/333P mutant showed limited incorporation. We conclude that all the mutants are capable of assembling into neurofilaments, but for some of the mutants this was dependent on the identity of the other neurofilament proteins available for co-assembly, and most likely also their relative expression level. Thus, caution should be exercised when drawing conclusions about the assembly capacity of CMT2E/1F mutants based on transient transfections in cultured cells.
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Affiliation(s)
- Elizabeth J Stone
- Department of Neuroscience, Ohio State University, Columbus, Ohio.,Neuroscience Graduate Program, Ohio State University, Columbus, Ohio
| | - Atsuko Uchida
- Department of Neuroscience, Ohio State University, Columbus, Ohio
| | - Anthony Brown
- Department of Neuroscience, Ohio State University, Columbus, Ohio
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21
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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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22
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He J, Guo L, Lin S, Chen W, Xu G, Cai B, Xu L, Hong J, Qiu L, Wang N, Chen W. ATP1A1mutations cause intermediate Charcot‐Marie‐Tooth disease. Hum Mutat 2019; 40:2334-2343. [DOI: 10.1002/humu.23886] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/18/2019] [Accepted: 07/30/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Jin He
- Department of Neurology and Institute of Neurology, First Affiliated HospitalFujian Medical University Fuzhou China
- Fujian Key Laboratory of Molecular NeurologyFujian Medical University Fuzhou China
| | - Lingling Guo
- Department of Neurology and Institute of Neurology, First Affiliated HospitalFujian Medical University Fuzhou China
| | - Shan Lin
- Department of Neurology and Institute of Neurology, First Affiliated HospitalFujian Medical University Fuzhou China
| | - Wenfeng Chen
- Institute of Life SciencesFuzhou University Fuzhou China
| | - Guorong Xu
- Department of Neurology and Institute of Neurology, First Affiliated HospitalFujian Medical University Fuzhou China
| | - Bin Cai
- Department of Neurology and Institute of Neurology, First Affiliated HospitalFujian Medical University Fuzhou China
- Fujian Key Laboratory of Molecular NeurologyFujian Medical University Fuzhou China
| | - Liuqing Xu
- Department of Neurology and Institute of Neurology, First Affiliated HospitalFujian Medical University Fuzhou China
| | - Jingmei Hong
- Department of Neurology and Institute of Neurology, First Affiliated HospitalFujian Medical University Fuzhou China
| | - Liangliang Qiu
- Department of Neurology and Institute of Neurology, First Affiliated HospitalFujian Medical University Fuzhou China
| | - Ning Wang
- Department of Neurology and Institute of Neurology, First Affiliated HospitalFujian Medical University Fuzhou China
- Fujian Key Laboratory of Molecular NeurologyFujian Medical University Fuzhou China
| | - Wanjin Chen
- Department of Neurology and Institute of Neurology, First Affiliated HospitalFujian Medical University Fuzhou China
- Fujian Key Laboratory of Molecular NeurologyFujian Medical University Fuzhou China
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23
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Charcot-Marie-Tooth 2F (Hsp27 mutations): A review. Neurobiol Dis 2019; 130:104505. [PMID: 31212070 DOI: 10.1016/j.nbd.2019.104505] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 12/13/2022] Open
Abstract
Charcot-Marie-Tooth disease is a commonly inherited form of neuropathy. Although named over 100 years ago, identification of subtypes of Charcot-Marie-Tooth has rapidly expanded in the preceding decades with the advancement of genetic sequencing, including type 2F (CMT2F), due to mutations in heat shock protein 27 (Hsp27). However, despite CMT being one of the most common inherited neurological diseases, definitive mechanistic models of pathology and effective treatments for CMT2F are lacking. This review extensively profiles the published literature on CMT2F and distal hereditary motor neuropathy II (dHMN II), a similar neuropathy with exclusively motor symptoms that is also due to mutations in Hsp27. This includes a review of case reports and sequencing studies detailing disease course. Included are tables listing of all known published mutations of Hsp27 that cause symptoms of CMT2F and dHMN II. Furthermore, pathological mechanisms are assessed. While many groups have established pathologies relating to defective chaperone function, cellular neurofilament and microtubule structure and function, and mitochondrial and metabolic dysfunction, there are still discrepancies in results between different model systems. Moreover, initial mouse models have also produced promising results with similar phenotypes to humans, however discrepancies still exist. Both patient-focused and scientific studies have demonstrated variability in phenotypes even considering specific mutations. Given the clinical heterogeneity in presentation, CMT2F and dHMN II likely result from similar pathological mechanisms of the same general disease process that may present distinctly due to other genetic and environment influences. Determining how these influences exert their effects to produce pathology contributing to the disease phenotype will be a major future challenge ahead in the field.
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24
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Li LX, Zhao SY, Liu ZJ, Ni W, Li HF, Xiao BG, Wu ZY. Improving molecular diagnosis of Chinese patients with Charcot-Marie-Tooth by targeted next-generation sequencing and functional analysis. Oncotarget 2018; 7:27655-64. [PMID: 27027447 PMCID: PMC5053678 DOI: 10.18632/oncotarget.8377] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/16/2016] [Indexed: 12/19/2022] Open
Abstract
Charcot-Marie-Tooth (CMT) disease is the most common hereditary peripheral neuropathy. More than 50 causative genes have been identified. The lack of genotype-phenotype correlations in many CMT patients make it difficult to decide which genes are affected. Recently, targeted next-generation sequencing (NGS) has been introduced as an alternative approach for diagnosis of genetic disorders. Here, we applied targeted NGS in combination with PMP22 duplication/deletion analysis to screen causative genes in 22 Chinese CMT families. The novel variants detected by targeted NGS were then further studied in cultured cells. Of the 22 unrelated patients, 8 had PMP22 duplication. The targeted NGS revealed 10 possible pathogenic variants in 11 patients, including 7 previously reported variants and 3 novel heterozygous variants (GJB1: p.Y157H; MFN2: p.G127S; YARS: p.V293M). Further classification of the novel variants according to American College of Medical Genetics and Genomics (ACMG) standards and guidelines and functional analysis in cultured cells indicated that p.Y157H in GJB1 was pathogenic, p.G127S in MFN2 was likely pathogenic, while p.V293M in YARS was likely benign. Our results suggest the potential for targeted NGS to make a more rapid and precise diagnosis in CMT patients. Moreover, the functional analysis is required when the novel variants are indistinct.
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Affiliation(s)
- Li-Xi Li
- Department of Neurology and Institute of Neurology, Huashan Hospital, Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Shao-Yun Zhao
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and The Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Zhi-Jun Liu
- Department of Neurology and Institute of Neurology, Huashan Hospital, Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Wang Ni
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and The Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Hong-Fu Li
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and The Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Bao-Guo Xiao
- Department of Neurology and Institute of Neurology, Huashan Hospital, Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, 200040, China
| | - Zhi-Ying Wu
- Department of Neurology and Institute of Neurology, Huashan Hospital, Institutes of Brain Science and State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, 200040, China.,Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and The Collaborative Innovation Center for Brain Science, Zhejiang University School of Medicine, Hangzhou, 310009, China
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25
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Hartley T, Wagner JD, Warman-Chardon J, Tétreault M, Brady L, Baker S, Tarnopolsky M, Bourque PR, Parboosingh JS, Smith C, McInnes B, Innes AM, Bernier F, Curry CJ, Yoon G, Horvath GA, Bareke E, Gillespie M, Majewski J, Bulman DE, Dyment DA, Boycott KM. Whole-exome sequencing is a valuable diagnostic tool for inherited peripheral neuropathies: Outcomes from a cohort of 50 families. Clin Genet 2017; 93:301-309. [PMID: 28708278 DOI: 10.1111/cge.13101] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/04/2017] [Accepted: 07/09/2017] [Indexed: 01/02/2023]
Abstract
The inherited peripheral neuropathies (IPNs) are characterized by marked clinical and genetic heterogeneity and include relatively frequent presentations such as Charcot-Marie-Tooth disease and hereditary motor neuropathy, as well as more rare conditions where peripheral neuropathy is associated with additional features. There are over 250 genes known to cause IPN-related disorders but it is estimated that in approximately 50% of affected individuals a molecular diagnosis is not achieved. In this study, we examine the diagnostic utility of whole-exome sequencing (WES) in a cohort of 50 families with 1 or more affected individuals with a molecularly undiagnosed IPN with or without additional features. Pathogenic or likely pathogenic variants in genes known to cause IPN were identified in 24% (12/50) of the families. A further 22% (11/50) of families carried sequence variants in IPN genes in which the significance remains unclear. An additional 12% (6/50) of families had variants in novel IPN candidate genes, 3 of which have been published thus far as novel discoveries (KIF1A, TBCK, and MCM3AP). This study highlights the use of WES in the molecular diagnostic approach of highly heterogeneous disorders, such as IPNs, places it in context of other published neuropathy cohorts, while further highlighting associated benefits for discovery.
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Affiliation(s)
- T Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - J D Wagner
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - J Warman-Chardon
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - M Tétreault
- Department of Human Genetics, McGill University, Montréal, Canada
| | - L Brady
- Department of Pediatrics, McMaster University Medical Centre, Hamilton, Canada
| | - S Baker
- Department of Medicine, McMaster University Medical Centre, Hamilton, Canada
| | - M Tarnopolsky
- Department of Pediatrics, McMaster University Medical Centre, Hamilton, Canada
| | - P R Bourque
- Department of Medicine, University of Ottawa, Ottawa, Canada
| | - J S Parboosingh
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - C Smith
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - B McInnes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - A M Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - F Bernier
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - C J Curry
- Department of Pediatrics, University of California, San Francisco, California
| | - G Yoon
- Divisions of Neurology and Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - G A Horvath
- Division of Biochemical Diseases, Department of Pediatrics, B.C. Children's Hospital, University of British Columbia, Vancouver, Canada
| | - E Bareke
- Department of Human Genetics, McGill University, Montréal, Canada
| | - M Gillespie
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | | | | | - J Majewski
- Department of Human Genetics, McGill University, Montréal, Canada
| | - D E Bulman
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - K M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
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26
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Nam DE, Yoo DH, Choi SS, Choi BO, Chung KW. Wide phenotypic spectrum in axonal Charcot-Marie-Tooth neuropathy type 2 patients with KIF5A mutations. Genes Genomics 2017; 40:77-84. [PMID: 29892902 DOI: 10.1007/s13258-017-0612-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/14/2017] [Indexed: 01/07/2023]
Abstract
The kinesin heavy chain isoform 5A (KIF5A) gene, which encodes a microtubule-based motor protein, plays an important role in the transport of organelles in the nerve cells. Mutations in the KIF5A showed a wide phenotypic spectrum from hereditary spastic paraplegia (HSP) to axonal Charcot-Marie-Tooth peripheral neuropathy type 2 (CMT2). This study identified three pathogenic KIF5A mutations in Korean CMT2 patients by whole exome sequencing. Two mutations (p.Arg204Trp and p.Arg280His) were previously reported, but p.Leu558Pro was determined to be a novel de novo mutation. All the mutations were not observed in the healthy controls and were located in highly conserved domains among vertebrate species. The p.Arg204Trp mutation was identified from a CMT2 patient with additional complex phenotypes of HSP, ataxia, fatigability and pyramidal sign, but the p.Arg280His and p.Leu588Pro mutations were identified in each axonal CMT2 patient. The p.Arg204Trp mutation was previously reported in a HSP patient with no CMT symptom. The p.Arg280His mutation was reported in a CMT2 patient, which was similarly with our case. However, it was also once reported in a HSP patient with pes cavus. As the first report in Korea, this study identified three KIF5A mutations as the underlying cause of axonal peripheral neuropathy with or without the HSP phenotype. We confirmed a wide inter- and intra-allelic phenotypic spectrum by the mutations in the KIF5A.
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Affiliation(s)
- Da Eun Nam
- Department of Biological Sciences, Kongju National University, 56 Gonjudaehak-ro, Gongju, 32588, South Korea
| | - Da Hye Yoo
- Department of Biological Sciences, Kongju National University, 56 Gonjudaehak-ro, Gongju, 32588, South Korea
| | - Sun Seong Choi
- Department of Biological Sciences, Kongju National University, 56 Gonjudaehak-ro, Gongju, 32588, South Korea
| | - Byung-Ok Choi
- Department of Neurology, and Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea. .,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Science & Technology, Sungkyunkwan University, 81 Irwon-ro, Gangnam-gu, Seoul, 06351, South Korea.
| | - Ki Wha Chung
- Department of Biological Sciences, Kongju National University, 56 Gonjudaehak-ro, Gongju, 32588, South Korea.
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27
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Hong YB, Park JM, Yu JS, Yoo DH, Nam DE, Park HJ, Lee JS, Hwang SH, Chung KW, Choi BO. Clinical characterization and genetic analysis of Korean patients with X-linked Charcot-Marie-Tooth disease type 1. J Peripher Nerv Syst 2017; 22:172-181. [PMID: 28448691 DOI: 10.1111/jns.12217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 04/17/2017] [Accepted: 04/17/2017] [Indexed: 11/30/2022]
Abstract
Mutations in the gap junction protein beta 1 gene (GJB1) cause X-linked Charcot-Marie-Tooth disease type 1 (CMTX1). CMTX1 is representative of the intermediate type of CMT, having both demyelinating and axonal neuropathic features. We analyzed the clinical and genetic characterization of 128 patients with CMTX1 from 63 unrelated families. Genetic analysis revealed a total of 43 mutations including 6 novel mutations. Ten mutations were found from two or more unrelated families. p.V95M was most frequently observed. The frequency of CMTX1 was 9.6% of total Korean CMT family and was 14.8% when calculated within genetically identified cases. Among 67 male and 61 female patients, 22 females were asymptomatic. A high-arched foot, ataxia, and tremor were observed in 87%, 41%, and 35% of the patients, respectively. In the male patients, functional disability scale, CMT neuropathy score, and compound muscle action potential of the median/ulnar nerves were more severely affected than in the female patients. This study provides a comprehensive summary of the clinical features and spectrum of GJB1 gene mutations in Korean CMTX1 patients.
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Affiliation(s)
- Young B Hong
- Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul, Korea
| | - Jin-Mo Park
- Department of Neurology, College of Medicine, Dongguk University, Gyeongju, Korea
| | - Jin S Yu
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Da H Yoo
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Da E Nam
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Hyung J Park
- Department of Neurology, Mokdong Hospital, Ewha Womans University School of Medicine, Seoul, Korea
| | - Ji-Su Lee
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sun H Hwang
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Ki W Chung
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Byung-Ok Choi
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Neuroscience Center, Samsung Medical Center, Seoul, Korea
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28
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Kim BY, Park JH, Jo HY, Koo SK, Park MH. Optimized detection of insertions/deletions (INDELs) in whole-exome sequencing data. PLoS One 2017; 12:e0182272. [PMID: 28792971 PMCID: PMC5549930 DOI: 10.1371/journal.pone.0182272] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/14/2017] [Indexed: 12/22/2022] Open
Abstract
Insertion and deletion (INDEL) mutations, the most common type of structural variance, are associated with several human diseases. The detection of INDELs through next-generation sequencing (NGS) is becoming more common due to the decrease in costs, the increase in efficiency, and sensitivity improvements demonstrated by the various sequencing platforms and analytical tools. However, there are still many errors associated with INDEL variant calling, and distinguishing INDELs from errors in NGS remains challenging. To evaluate INDEL calling from whole-exome sequencing (WES) data, we performed Sanger sequencing for all INDELs called from the several calling algorithm. We compared the performance of the four algorithms (i.e. GATK, SAMtools, Dindel, and Freebayes) for INDEL detection from the same sample. We examined the sensitivity and PPV of GATK (90.2 and 89.5%, respectively), SAMtools (75.3 and 94.4%, respectively), Dindel (90.1 and 88.6%, respectively), and Freebayes (80.1 and 94.4%, respectively). GATK had the highest sensitivity. Furthermore, we identified INDELs with high PPV (4 algorithms intersection: 98.7%, 3 algorithms intersection: 97.6%, and GATK and SAMtools intersection INDELs: 97.6%). We presented two key sources of difficulties in accurate INDEL detection: 1) the presence of repeat, and 2) heterozygous INDELs. Herein we could suggest the accessible algorithms that selectively reduce error rates and thereby facilitate INDEL detection. Our study may also serve as a basis for understanding the accuracy and completeness of INDEL detection.
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Affiliation(s)
- Bo-Young Kim
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, South Korea
| | | | - Hye-Yeong Jo
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, South Korea
| | - Soo Kyung Koo
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, South Korea
- * E-mail: (SKK); (MHP)
| | - Mi-Hyun Park
- Division of Intractable Diseases, Center for Biomedical Sciences, Korea National Institute of Health, Chungcheongbuk-do, South Korea
- * E-mail: (SKK); (MHP)
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29
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Horga A, Laurà M, Jaunmuktane Z, Jerath NU, Gonzalez MA, Polke JM, Poh R, Blake JC, Liu YT, Wiethoff S, Bettencourt C, Lunn MP, Manji H, Hanna MG, Houlden H, Brandner S, Züchner S, Shy M, Reilly MM. Genetic and clinical characteristics of NEFL-related Charcot-Marie-Tooth disease. J Neurol Neurosurg Psychiatry 2017; 88:575-585. [PMID: 28501821 PMCID: PMC5580821 DOI: 10.1136/jnnp-2016-315077] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 11/03/2022]
Abstract
OBJECTIVES To analyse and describe the clinical and genetic spectrum of Charcot-Marie-Tooth disease (CMT) caused by mutations in the neurofilament light polypeptide gene (NEFL). METHODS Combined analysis of newly identified patients with NEFL-related CMT and all previously reported cases from the literature. RESULTS Five new unrelated patients with CMT carrying the NEFL mutations P8R and N98S and the novel variant L311P were identified. Combined data from these cases and 62 kindreds from the literature revealed four common mutations (P8R, P22S, N98S and E396K) and three mutational hotspots accounting for 37 (55%) and 50 (75%) kindreds, respectively. Eight patients had de novo mutations. Loss of large-myelinated fibres was a uniform feature in a total of 21 sural nerve biopsies and 'onion bulb' formations and/or thin myelin sheaths were observed in 14 (67%) of them. The neurophysiological phenotype was broad but most patients with E90K and N98S had upper limb motor conduction velocities <38 m/s. Age of onset was ≤3 years in 25 cases. Pyramidal tract signs were described in 13 patients and 7 patients were initially diagnosed with or tested for inherited ataxia. Patients with E90K and N98S frequently presented before age 3 years and developed hearing loss or other neurological features including ataxia and/or cerebellar atrophy on brain MRI. CONCLUSIONS NEFL-related CMT is clinically and genetically heterogeneous. Based on this study, however, we propose mutational hotspots and relevant clinical-genetic associations that may be helpful in the evaluation of NEFL sequence variants and the differential diagnosis with other forms of CMT.
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Affiliation(s)
- Alejandro Horga
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, UK.,Department of Neurology, Hospital Clinico Universitario San Carlos, Madrid, Spain
| | - Matilde Laurà
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, UK.,UCL Institute of Neurology, MRC Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, London, UK
| | - Zane Jaunmuktane
- Division of Neuropathology and Department of Neurodegenerative Disease, The National Hospital for Neurology and Neurosurgery and UCL Institute of Neurology, London, UK
| | | | - Michael A Gonzalez
- Department of Human Genetics and Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, USA.,The Genesis Project Foundation, The Genesis Project Foundation, Miami, Florida, USA
| | - James M Polke
- Department of Neurogenetics, The National Hospital for Neurology and Neurosurgery and UCL Institute of Neurology, London, UK.,Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, London, UK
| | - Roy Poh
- Department of Neurogenetics, The National Hospital for Neurology and Neurosurgery and UCL Institute of Neurology, London, UK
| | - Julian C Blake
- Department of Clinical Neurophysiology, National Hospital for Neurology and Neurosurgery (and Norfolk and Norwich University Hospital), London, UK
| | - Yo-Tsen Liu
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, UK.,Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Sarah Wiethoff
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | | | - Michael Pt Lunn
- Department of Neurology, National Hospital for Neurology and Neurosurgery, London, UK
| | - Hadi Manji
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, UK
| | - Michael G Hanna
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, UK
| | - Henry Houlden
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK
| | - Sebastian Brandner
- Division of Neuropatholgoy, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK
| | | | - Michael Shy
- Department of Neurology, University of Iowa, Iowa City, Iowa, USA.,Wayne State University, Michigan, Michigan, USA
| | - Mary M Reilly
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, London, UK.,MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK
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30
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Walsh M, Bell KM, Chong B, Creed E, Brett GR, Pope K, Thorne NP, Sadedin S, Georgeson P, Phelan DG, Day T, Taylor JA, Sexton A, Lockhart PJ, Kiers L, Fahey M, Macciocca I, Gaff CL, Oshlack A, Yiu EM, James PA, Stark Z, Ryan MM. Diagnostic and cost utility of whole exome sequencing in peripheral neuropathy. Ann Clin Transl Neurol 2017; 4:318-325. [PMID: 28491899 PMCID: PMC5420808 DOI: 10.1002/acn3.409] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/07/2017] [Accepted: 03/15/2017] [Indexed: 12/15/2022] Open
Abstract
Objective To explore the diagnostic utility and cost effectiveness of whole exome sequencing (WES) in a cohort of individuals with peripheral neuropathy. Methods Singleton WES was performed in individuals recruited though one pediatric and one adult tertiary center between February 2014 and December 2015. Initial analysis was restricted to a virtual panel of 55 genes associated with peripheral neuropathies. Patients with uninformative results underwent expanded analysis of the WES data. Data on the cost of prior investigations and assessments performed for diagnostic purposes in each patient was collected. Results Fifty patients with a peripheral neuropathy were recruited (median age 18 years; range 2–68 years). The median time from initial presentation to study enrollment was 6 years 9 months (range 2 months–62 years), and the average cost of prior investigations and assessments for diagnostic purposes AU$4013 per patient. Eleven individuals received a diagnosis from the virtual panel. Eight individuals received a diagnosis following expanded analysis of the WES data, increasing the overall diagnostic yield to 38%. Two additional individuals were diagnosed with pathogenic copy number variants through SNP microarray. Conclusions This study provides evidence that WES has a high diagnostic utility and is cost effective in patients with a peripheral neuropathy. Expanded analysis of WES data significantly improves the diagnostic yield in patients in whom a diagnosis is not found on the initial targeted analysis. This is primarily due to diagnosis of conditions caused by newly discovered genes and the resolution of complex and atypical phenotypes.
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Affiliation(s)
- Maie Walsh
- Murdoch Childrens Research Institute Melbourne Australia.,Royal Melbourne Hospital Melbourne Australia
| | - Katrina M Bell
- Murdoch Childrens Research Institute Melbourne Australia
| | - Belinda Chong
- Murdoch Childrens Research Institute Melbourne Australia
| | - Emma Creed
- Royal Melbourne Hospital Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia
| | - Gemma R Brett
- Murdoch Childrens Research Institute Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia
| | - Kate Pope
- Murdoch Childrens Research Institute Melbourne Australia
| | - Natalie P Thorne
- Melbourne Genomics Health Alliance Melbourne Australia.,Murdoch Childrens Research Institute Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Simon Sadedin
- Murdoch Childrens Research Institute Melbourne Australia
| | | | - Dean G Phelan
- Murdoch Childrens Research Institute Melbourne Australia
| | - Timothy Day
- Royal Melbourne Hospital Melbourne Australia
| | | | | | - Paul J Lockhart
- Murdoch Childrens Research Institute Melbourne Australia.,Bruce Lefroy Centre Murdoch Childrens Research Institute Parkville Australia.,Department of Paediatrics The University of Melbourne Melbourne Australia
| | | | | | - Ivan Macciocca
- Murdoch Childrens Research Institute Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia
| | - Clara L Gaff
- Melbourne Genomics Health Alliance Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Alicia Oshlack
- Murdoch Childrens Research Institute Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Eppie M Yiu
- Bruce Lefroy Centre Murdoch Childrens Research Institute Parkville Australia.,Department of Paediatrics The University of Melbourne Melbourne Australia.,Royal Children's Hospital Melbourne Australia
| | - Paul A James
- Royal Melbourne Hospital Melbourne Australia.,University of Melbourne Melbourne Australia
| | - Zornitza Stark
- Murdoch Childrens Research Institute Melbourne Australia
| | - Monique M Ryan
- Murdoch Childrens Research Institute Melbourne Australia.,Melbourne Genomics Health Alliance Melbourne Australia.,Department of Paediatrics The University of Melbourne Melbourne Australia.,Royal Children's Hospital Melbourne Australia
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31
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Fattahi Z, Kalhor Z, Fadaee M, Vazehan R, Parsimehr E, Abolhassani A, Beheshtian M, Zamani G, Nafissi S, Nilipour Y, Akbari M, Kahrizi K, Kariminejad A, Najmabadi H. Improved diagnostic yield of neuromuscular disorders applying clinical exome sequencing in patients arising from a consanguineous population. Clin Genet 2016; 91:386-402. [DOI: 10.1111/cge.12810] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 04/28/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Z. Fattahi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - Z. Kalhor
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
| | - M. Fadaee
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - R. Vazehan
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - E. Parsimehr
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - A. Abolhassani
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - M. Beheshtian
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - G. Zamani
- Department of NeurologyTehran University of Medical Sciences Tehran Iran
| | - S. Nafissi
- Department of Pediatric Neurology, Pediatrics Center of Excellence, Children's Medical CenterTehran University of Medical Sciences Tehran Iran
| | - Y. Nilipour
- Pediatric Pathology Research Center, Mofid Children HospitalShahid Beheshti University of Medical Sciences Tehran Iran
| | - M.R. Akbari
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Women's College Research InstituteWomen's College Hospital Toronto Canada
- Dalla Lana School of Public HealthUniversity of Toronto Toronto Canada
| | - K. Kahrizi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
| | - A. Kariminejad
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
| | - H. Najmabadi
- Genetics Research CenterUniversity of Social Welfare and Rehabilitation Sciences Tehran Iran
- Kariminejad ‐ Najmabadi Pathology & Genetics Center Tehran Iran
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32
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Brewer MH, Chaudhry R, Qi J, Kidambi A, Drew AP, Menezes MP, Ryan MM, Farrar MA, Mowat D, Subramanian GM, Young HK, Zuchner S, Reddel SW, Nicholson GA, Kennerson ML. Whole Genome Sequencing Identifies a 78 kb Insertion from Chromosome 8 as the Cause of Charcot-Marie-Tooth Neuropathy CMTX3. PLoS Genet 2016; 12:e1006177. [PMID: 27438001 PMCID: PMC4954712 DOI: 10.1371/journal.pgen.1006177] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/15/2016] [Indexed: 11/18/2022] Open
Abstract
With the advent of whole exome sequencing, cases where no pathogenic coding mutations can be found are increasingly being observed in many diseases. In two large, distantly-related families that mapped to the Charcot-Marie-Tooth neuropathy CMTX3 locus at chromosome Xq26.3-q27.3, all coding mutations were excluded. Using whole genome sequencing we found a large DNA interchromosomal insertion within the CMTX3 locus. The 78 kb insertion originates from chromosome 8q24.3, segregates fully with the disease in the two families, and is absent from the general population as well as 627 neurologically normal chromosomes from in-house controls. Large insertions into chromosome Xq27.1 are known to cause a range of diseases and this is the first neuropathy phenotype caused by an interchromosomal insertion at this locus. The CMTX3 insertion represents an understudied pathogenic structural variation mechanism for inherited peripheral neuropathies. Our finding highlights the importance of considering all structural variation types when studying unsolved inherited peripheral neuropathy cases with no pathogenic coding mutations.
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Affiliation(s)
- Megan H. Brewer
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- * E-mail:
| | - Rabia Chaudhry
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
| | - Jessica Qi
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Discipline of Pathology, University of Sydney, Camperdown, New South Wales, Australia
| | - Aditi Kidambi
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
| | - Alexander P. Drew
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
| | - Manoj P. Menezes
- The Institute for Neuroscience and Muscle Research, The Children’s Hospital at Westmead, Westmead, New South Wales, Australia
- T.Y. Nelson Department of Neurology and Neurosurgery, The Children’s Hospital at Westmead, Westmead, New South Wales, Australia
- Paediatrics and Child Health, University of Sydney, Camperdown, New South Wales, Australia
| | - Monique M. Ryan
- Department of Neurology, Royal Children’s Hospital, Parkville, Victoria, Australia
- Murdoch Childrens Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Michelle A. Farrar
- Department of Neurology, Sydney Children’s Hospital, Randwick, New South Wales, Australia
- School of Women’s and Children’s Health, UNSW Medicine, University of New South Wales, Kensington, New South Wales, Australia
| | - David Mowat
- School of Women’s and Children’s Health, UNSW Medicine, University of New South Wales, Kensington, New South Wales, Australia
- Department of Medical Genetics, Sydney Children’s Hospital, Randwick, New South Wales, Australia
| | - Gopinath M. Subramanian
- Department of Paediatrics, John Hunter Children’s Hospital, Newcastle, New South Wales, Australia
| | - Helen K. Young
- Department of Paediatrics, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Northern Clinical School, Sydney Medical School, University of Sydney, St Leonards, New South Wales, Australia
- Department of Neurogenetics, The Children’s Hospital at Westmead, Westmead, New South Wales, Australia
| | - Stephan Zuchner
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
- Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Stephen W. Reddel
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales, Australia
| | - Garth A. Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine, Concord Repatriation General Hospital, Concord, New South Wales, Australia
| | - Marina L. Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Sydney Medical School, University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine, Concord Repatriation General Hospital, Concord, New South Wales, Australia
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33
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Nam SH, Hong YB, Hyun YS, Nam DE, Kwak G, Hwang SH, Choi BO, Chung KW. Identification of Genetic Causes of Inherited Peripheral Neuropathies by Targeted Gene Panel Sequencing. Mol Cells 2016; 39:382-8. [PMID: 27025386 PMCID: PMC4870185 DOI: 10.14348/molcells.2016.2288] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 02/11/2016] [Accepted: 02/22/2016] [Indexed: 12/19/2022] Open
Abstract
Inherited peripheral neuropathies (IPN), which are a group of clinically and genetically heterogeneous peripheral nerve disorders including Charcot-Marie-Tooth disease (CMT), exhibit progressive degeneration of muscles in the extremities and loss of sensory function. Over 70 genes have been reported as genetic causatives and the number is still growing. We prepared a targeted gene panel for IPN diagnosis based on next generation sequencing (NGS). The gene panel was designed to detect mutations in 73 genes reported to be genetic causes of IPN or related peripheral neuropathies, and to detect duplication of the chromosome 17p12 region, the major genetic cause of CMT1A. We applied the gene panel to 115 samples from 63 non-CMT1A families, and isolated 15 pathogenic or likely-pathogenic mutations in eight genes from 25 patients (17 families). Of them, eight mutations were unreported variants. Of particular interest, this study revealed several very rare mutations in the SPTLC2, DCTN1, and MARS genes. In addition, the effectiveness of the detection of CMT1A was confirmed by comparing five 17p12-nonduplicated controls and 15 CMT1A cases. In conclusion, we developed a gene panel for one step genetic diagnosis of IPN. It seems that its time- and cost-effectiveness are superior to previous tiered-genetic diagnosis algorithms, and it could be applied as a genetic diagnostic system for inherited peripheral neuropathies.
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Affiliation(s)
- Soo Hyun Nam
- Department of Biological Sciences, Kongju National University, Gongju 32588,
Korea
| | - Young Bin Hong
- Stem Cell & Regenerative Medicine Center and Neuroscience Center, Samsung Medical Center, Seoul 06351,
Korea
| | - Young Se Hyun
- Department of Biological Sciences, Kongju National University, Gongju 32588,
Korea
| | - Da Eun Nam
- Department of Biological Sciences, Kongju National University, Gongju 32588,
Korea
| | - Geon Kwak
- Department of Neurology, Sungkyunkwan University School of Medicine, Seoul 06351,
Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Science & Tech., Sungkyunkwan University, Seoul 06351,
Korea
| | - Sun Hee Hwang
- Department of Neurology, Sungkyunkwan University School of Medicine, Seoul 06351,
Korea
| | - Byung-Ok Choi
- Stem Cell & Regenerative Medicine Center and Neuroscience Center, Samsung Medical Center, Seoul 06351,
Korea
- Department of Neurology, Sungkyunkwan University School of Medicine, Seoul 06351,
Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Science & Tech., Sungkyunkwan University, Seoul 06351,
Korea
| | - Ki Wha Chung
- Department of Biological Sciences, Kongju National University, Gongju 32588,
Korea
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34
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Chen H, Zhou X, Wang J, Wang X, Liu L, Wu S, Li T, Chen S, Yang J, Sham PC, Zhu G, Zhang X, Wang B. Exome Sequencing and Gene Prioritization Correct Misdiagnosis in a Chinese Kindred with Familial Amyloid Polyneuropathy. Sci Rep 2016; 6:26362. [PMID: 27212199 PMCID: PMC4876459 DOI: 10.1038/srep26362] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/26/2016] [Indexed: 11/09/2022] Open
Abstract
Inherited neuropathies show considerable heterogeneity in clinical manifestations and genetic etiologies, and are therefore often difficult to diagnose. Whole-exome sequencing (WES) has been widely adopted to make definite diagnosis of unclear conditions, with proven efficacy in optimizing patients' management. In this study, a large Chinese kindred segregating autosomal dominant polyneuropathy with incomplete penetrance was ascertained through a patient who was initially diagnosed as Charcot-Marie-Tooth disease. To investigate the genetic cause, forty-six living family members were genotyped by SNP microarrays, and one confirmed patient was subject to WES. Through systematic computational prioritization, we identified a missense mutation c.G148T in TTR gene which results in a p.V50L substitution known to cause transthyretin-related familial amyloid polyneuropathy. Co-segregation analysis and clinical follow-up confirmed the new diagnosis, which suggested new therapeutic options to the patients and informed high risk family members. This study confirms WES as a powerful tool in translational medicine, and further demostrates the practical utility of gene prioritization in narrowing the scope of causative mutation.
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Affiliation(s)
- Hui Chen
- Department of Neurology, Military General Hospital of Beijing PLA, Beijing, China
| | - Xueya Zhou
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China.,Department of Psychiatry and Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jing Wang
- Department of Medical Genetics, The Capital Medical University, Beijing, China
| | - Xi Wang
- National Research Institute of Family Planning, Beijing, China
| | - Liyang Liu
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China
| | - Shinan Wu
- National Research Institute of Family Planning, Beijing, China
| | - Tengyan Li
- National Research Institute of Family Planning, Beijing, China
| | - Si Chen
- National Research Institute of Family Planning, Beijing, China
| | - Jingwen Yang
- National Research Institute of Family Planning, Beijing, China
| | - Pak Chung Sham
- Department of Psychiatry and Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Guangming Zhu
- Department of Neurology, Military General Hospital of Beijing PLA, Beijing, China
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, TNLIST/Department of Automation, Tsinghua University, Beijing, China
| | - Binbin Wang
- National Research Institute of Family Planning, Beijing, China
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35
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Genotype–phenotype correlation of Charcot-Marie-Tooth type 1E patients with PMP22 mutations. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0423-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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36
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Lee J, Jung SC, Hong YB, Yoo JH, Koo H, Lee JH, Hong HD, Kim SB, Chung KW, Choi BO. Recessive optic atrophy, sensorimotor neuropathy and cataract associated with novel compound heterozygous mutations in OPA1. Mol Med Rep 2016; 14:33-40. [PMID: 27150940 PMCID: PMC4918608 DOI: 10.3892/mmr.2016.5209] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 11/30/2015] [Indexed: 01/05/2023] Open
Abstract
Mutations in the optic atrophy 1 gene (OPA1) are associated with autosomal dominant optic atrophy and 20% of patients demonstrate extra-ocular manifestations. In addition to these autosomal dominant cases, only a few syndromic cases have been reported thus far with compound heterozygous OPA1 mutations, suggestive of either recessive or semi‑dominant patterns of inheritance. The majority of these patients were diagnosed with Behr syndrome, characterized by optic atrophy, ataxia and peripheral neuropathy. The present study describes a 10-year-old boy with Behr syndrome presenting with early‑onset severe optic atrophy, sensorimotor neuropathy, ataxia and congenital cataracts. He had optic atrophy and was declared legally blind at six years old. Electrophysiological, radiological, and histopathological findings were compatible with axonal sensorimotor polyneuropathy. At birth, he presented with a congenital cataract, which has not been previously described in patients with OPA1 mutations. Whole exome sequencing indicated a pair of novel compound heterozygous mutations: p.L620fs*13 (c.1857‑1858delinsT) and p.R905Q (c.G2714A). Neither mutation was observed in controls (n=300), and thus, they were predicted to be pathogenic by multiple in silico analyses. The mutation sites were highly conserved throughout different vertebrate species. The patients parents did not have any ophthalmic or neurologic symptoms and the results of electrophysiological studies were normal, suggestive of an autosomal recessive pattern of inheritance. The present study identified novel compound heterozygous OPA1 mutations in a patient with recessive optic atrophy, sensorimotor neuropathy and congenital cataracts, indicating an expansion of the clinical spectrum of pathologies associated with OPA1 mutations. Thus, OPA1 gene screening is advisable in the workup of patients with recessive optic atrophy, particularly with Behr syndrome and cataracts.
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Affiliation(s)
- Jinho Lee
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135‑710, Republic of Korea
| | - Sung-Chul Jung
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul 120‑750, Republic of Korea
| | - Young Bin Hong
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135‑710, Republic of Korea
| | - Jeong Hyun Yoo
- Department of Radiology, Ewha Womans University School of Medicine, Seoul 120‑750, Republic of Korea
| | - Heasoo Koo
- Department of Pathology, Ewha Womans University School of Medicine, Seoul 120‑750, Republic of Korea
| | - Ja Hyun Lee
- Department of Biological Science, Kongju National University, Konju, Chungnam 314‑701, Republic of Korea
| | - Hyun Dae Hong
- Department of Biological Science, Kongju National University, Konju, Chungnam 314‑701, Republic of Korea
| | - Sang-Beom Kim
- Department of Neurology, Kyung Hee University College of Medicine, Seoul 143‑601, Republic of Korea
| | - Ki Wha Chung
- Department of Biological Science, Kongju National University, Konju, Chungnam 314‑701, Republic of Korea
| | - Byung-Ok Choi
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135‑710, Republic of Korea
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37
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Jo H, Park M, Woo H, Han M, Kim B, Choi B, Chung K, Koo S. Application of whole‐exome sequencing for detecting copy number variants in CMT1A/HNPP. Clin Genet 2016; 90:177-81. [DOI: 10.1111/cge.12714] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/30/2015] [Accepted: 12/08/2015] [Indexed: 11/26/2022]
Affiliation(s)
- H.‐Y. Jo
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - M.‐H. Park
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - H.‐M. Woo
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - M.H. Han
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - B.‐Y. Kim
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
| | - B.‐O. Choi
- Department of Neurology, Samsung Medical Center Sungkyunkwan University School of Medicine Seoul South Korea
| | - K.W. Chung
- Department of Biological Sciences Kongju National University Gongju South Korea
| | - S.K. Koo
- Division of Intractable Diseases, Center for Biomedical Sciences Korea National Institute of Health Cheongju South Korea
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38
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Hong YB, Kang J, Kim JH, Lee J, Kwak G, Hyun YS, Nam SH, Hong HD, Choi YR, Jung SC, Koo H, Lee JE, Choi BO, Chung KW. DGAT2 Mutation in a Family with Autosomal-Dominant Early-Onset Axonal Charcot-Marie-Tooth Disease. Hum Mutat 2016; 37:473-80. [PMID: 26786738 DOI: 10.1002/humu.22959] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/12/2016] [Indexed: 01/08/2023]
Abstract
Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy and is a genetically and clinically heterogeneous disorder. We examined a Korean family in which two individuals had an autosomal-dominant axonal CMT with early-onset, sensory ataxia, tremor, and slow disease progression. Pedigree analysis and exome sequencing identified a de novo missense mutation (p.Y223H) in the diacylglycerol O-acyltransferase 2 (DGAT2) gene. DGAT2 encodes an endoplasmic reticulum-mitochondrial-associated membrane protein, acyl-CoA:diacylglycerol acyltransferase, which catalyzes the final step of the triglyceride (TG) biosynthesis pathway. The patient showed consistently decreased serum TG levels, and overexpression of the mutant DGAT2 significantly inhibited the proliferation of mouse motor neuron cells. Moreover, the variant form of human DGAT2 inhibited the axonal branching in the peripheral nervous system of zebrafish. We suggest that mutation of DGAT2 is the novel underlying cause of an autosomal-dominant axonal CMT2 neuropathy. This study will help provide a better understanding of the pathophysiology of axonal CMT and contribute to the molecular diagnostics of peripheral neuropathies.
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Affiliation(s)
- Young Bin Hong
- Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul, South Korea
| | - Junghee Kang
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, South Korea
| | - Ji Hyun Kim
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, South Korea
| | - Jinho Lee
- Neuroscience center, Samsung Medical Center, Seoul, South Korea
| | - Geon Kwak
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, South Korea.,Neuroscience center, Samsung Medical Center, Seoul, South Korea
| | - Young Se Hyun
- Department of Biological Sciences, Kongju National University, Gongju, South Korea
| | - Soo Hyun Nam
- Department of Biological Sciences, Kongju National University, Gongju, South Korea
| | - Hyun Dae Hong
- Department of Biological Sciences, Kongju National University, Gongju, South Korea
| | - Yu-Ri Choi
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, South Korea
| | - Sung-Chul Jung
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, South Korea
| | - Heasoo Koo
- Department of Pathology, Ewha Womans University School of Medicine, Mokdong Hospital, Seoul, South Korea
| | - Ji Eun Lee
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, South Korea.,SGI, Samsung Medical Center, Seoul, South Korea
| | - Byung-Ok Choi
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, South Korea.,Neuroscience center, Samsung Medical Center, Seoul, South Korea.,Department of Neurology, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Ki Wha Chung
- Department of Biological Sciences, Kongju National University, Gongju, South Korea
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39
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Identification of Korean-specific SNP markers from whole-exome sequencing data. Int J Legal Med 2016; 130:669-77. [DOI: 10.1007/s00414-015-1313-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/30/2015] [Indexed: 10/22/2022]
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40
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De Leeneer K, Hellemans J, Steyaert W, Lefever S, Vereecke I, Debals E, Crombez B, Baetens M, Van Heetvelde M, Coppieters F, Vandesompele J, De Jaegher A, De Baere E, Coucke P, Claes K. Flexible, scalable, and efficient targeted resequencing on a benchtop sequencer for variant detection in clinical practice. Hum Mutat 2015; 36:379-87. [PMID: 25504618 DOI: 10.1002/humu.22739] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 12/02/2014] [Indexed: 12/30/2022]
Abstract
The release of benchtop next-generation sequencing (NGS) instruments has paved the way to implement the technology in clinical setting. The need for flexible, qualitative, and cost-efficient workflows is high. We used singleplex-PCR for highly efficient target enrichment, allowing us to reach the quality standards set in Sanger sequencing-based diagnostics. For the library preparation, a modified NexteraXT protocol was used, followed by sequencing on a MiSeq instrument. With an innovative pooling strategy, high flexibility, scalability, and cost-efficiency were obtained, independent of the availability of commercial kits. The approach was validated for ∼250 genes associated with monogenic disorders. An overall sensitivity (>99%) similar to Sanger sequencing was observed in combination with a positive predictive value of >98%. The distribution of coverage was highly uniform, guaranteeing a minimal number of gaps to be filled with alternative methods. ISO15189-accreditation was obtained for the workflow. A major asset of the singleplex PCR-based enrichment is that new targets can be easily implemented. Diagnostic laboratories have validated assays available ensuring that the proposed workflow can easily be adopted. Although our platform was optimized for constitutional variant detection of monogenic disease genes, it is now also used as a model for somatic mutation detection in acquired diseases.
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Affiliation(s)
- Kim De Leeneer
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
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Hoyle JC, Isfort MC, Roggenbuck J, Arnold WD. The genetics of Charcot-Marie-Tooth disease: current trends and future implications for diagnosis and management. APPLICATION OF CLINICAL GENETICS 2015; 8:235-43. [PMID: 26527893 PMCID: PMC4621202 DOI: 10.2147/tacg.s69969] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Charcot–Marie–Tooth (CMT) disease is the most common hereditary polyneuropathy and is classically associated with an insidious onset of distal predominant motor and sensory loss, muscle wasting, and pes cavus. Other forms of hereditary neuropathy, including sensory predominant or motor predominant forms, are sometimes included in the general classification of CMT, but for the purpose of this review, we will focus primarily on the forms associated with both sensory and motor deficits. CMT has a great deal of genetic heterogeneity, leading to diagnostic considerations that are still rapidly evolving for this disorder. Clinical features, inheritance pattern, gene mutation frequencies, and electrodiagnostic features all are helpful in formulating targeted testing algorithms in practical clinical settings, but these still have shortcomings. Next-generation sequencing (NGS), combined with multigene testing panels, is increasing the sensitivity and efficiency of genetic testing and is quickly overtaking targeted testing strategies. Currently, multigene panel testing and NGS can be considered first-line in many circumstances, although obtaining initial targeted testing for the PMP22 duplication in CMT patients with demyelinating conduction velocities is still a reasonable strategy. As technology improves and cost continues to fall, targeted testing will be completely replaced by multigene NGS panels that can detect the full spectrum of CMT mutations. Nevertheless, clinical acumen is still necessary given the variants of uncertain significance encountered with NGS. Despite the current limitations, the genetic diagnosis of CMT is critical for accurate prognostication, genetic counseling, and in the future, specific targeted therapies. Although whole exome and whole genome sequencing strategies have the power to further elucidate the genetics of CMT, continued technological advances are needed.
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Affiliation(s)
- J Chad Hoyle
- Department of Neurology, Division of Neuromuscular Disorders, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Michael C Isfort
- Department of Neurology, Division of Neuromuscular Disorders, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Jennifer Roggenbuck
- Department of Neurology, Division of Neuromuscular Disorders, The Ohio State University Wexner Medical Center, Columbus, OH, USA ; Department of Internal Medicine, Division of Human Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - W David Arnold
- Department of Neurology, Division of Neuromuscular Disorders, The Ohio State University Wexner Medical Center, Columbus, OH, USA ; Department of Physical Medicine and Rehabilitation, The Ohio State University Wexner Medical Center, Columbus, OH, USA ; Department of Neuroscience, The Ohio State University Wexner Medical Center, Columbus, OH, USA
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Choi YR, Hong YB, Jung SC, Lee JH, Kim YJ, Park HJ, Lee J, Koo H, Lee JS, Jwa DH, Jung N, Woo SY, Kim SB, Chung KW, Choi BO. A novel homozygous MPV17 mutation in two families with axonal sensorimotor polyneuropathy. BMC Neurol 2015; 15:179. [PMID: 26437932 PMCID: PMC4595119 DOI: 10.1186/s12883-015-0430-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 09/14/2015] [Indexed: 12/12/2022] Open
Abstract
Background Mutations in MPV17 cause the autosomal recessive disorder mitochondrial DNA depletion syndrome 6 (MTDPS6), also called Navajo neurohepatopathy (NNH). Clinical features of MTDPS6 is infantile onset of progressive liver failure with seldom development of progressive neurologic involvement. Methods Whole exome sequencing (WES) was performed to isolate the causative gene of two unrelated neuropathy patients (9 and 13 years of age) with onset of the syndrome. Clinical assessments and biochemical analysis were performed. Results A novel homozygous mutation (p.R41Q) in MPV17 was found by WES in both patients. Both showed axonal sensorimotor polyneuropathy without liver and brain involvement, which is neurophysiologically similar to axonal Charcot-Marie-Tooth disease (CMT). A distal sural nerve biopsy showed an almost complete loss of the large and medium-sized myelinated fibers compatible with axonal neuropathy. An in vitro assay using mouse motor neuronal cells demonstrated that the abrogation of MPV17 significantly affected cell integrity. In addition, the expression of the mutant protein affected cell proliferation. These results imply that both the loss of normal function of MPV17 and the gain of detrimental effects of the mutant protein might affect neuronal function. Conclusion We report a novel homozygous mutation in MPV17 from two unrelated patients harboring axonal sensorimotor polyneuropathy without hepatoencephalopathy. This report expands the clinical spectrum of diseases caused by mutations of MPV17, and we recommend MPV17 gene screening for axonal peripheral neuropathies. Electronic supplementary material The online version of this article (doi:10.1186/s12883-015-0430-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu-Ri Choi
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, Korea.
| | - Young Bin Hong
- Stem Cell & Regenerative Medicine Center, Samsung Medical Center, Seoul, Korea.
| | - Sung-Chul Jung
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, Korea.
| | - Ja Hyun Lee
- Department of Biological Science, Kongju National University, 56 Gonjudaehak-ro, Gongju, Chungnam, 314-701, Korea.
| | - Ye Jin Kim
- Department of Biological Science, Kongju National University, 56 Gonjudaehak-ro, Gongju, Chungnam, 314-701, Korea.
| | - Hyung Jun Park
- Department of Neurology, Ewha Womans University School of Medicine, Seoul, Korea.
| | - Jinho Lee
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-Gu, Seoul, 135-710, Korea.
| | - Heasoo Koo
- Department of Pathology, Ewha Womans University School of Medicine, Seoul, Korea.
| | - Ji-Su Lee
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-Gu, Seoul, 135-710, Korea.
| | - Dong Hwan Jwa
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-Gu, Seoul, 135-710, Korea.
| | - Namhee Jung
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, Korea.
| | - So-Youn Woo
- Department of Microbiology, Ewha Womans University School of Medicine, Seoul, Korea.
| | - Sang-Beom Kim
- Department of Neurology, Kyung Hee University, College of Medicine, Seoul, Korea.
| | - Ki Wha Chung
- Department of Biological Science, Kongju National University, 56 Gonjudaehak-ro, Gongju, Chungnam, 314-701, Korea.
| | - Byung-Ok Choi
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-Gu, Seoul, 135-710, Korea. .,Neuroscience center, Samsung Medical Center, Seoul, Korea.
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43
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Hyun YS, Lee J, Kim HJ, Hong YB, Koo H, Smith AST, Kim DH, Choi BO, Chung KW. Charcot-Marie-Tooth Disease Type 4H Resulting from Compound Heterozygous Mutations in FGD4 from Nonconsanguineous Korean Families. Ann Hum Genet 2015; 79:460-9. [PMID: 26400421 DOI: 10.1111/ahg.12134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 07/03/2015] [Indexed: 01/06/2023]
Abstract
Charcot-Marie-Tooth disease type 4H (CMT4H) is an autosomal recessive demyelinating subtype of peripheral enuropathies caused by mutations in the FGD4 gene. Most CMT4H patients are in consanguineous Mediterranean families characterized by early onset and slow progression. We identified two CMT4H patients from a Korean CMT cohort, and performed a detailed genetic and clinical analysis in both cases. Both patients from nonconsanguineous families showed characteristic clinical manifestations of CMT4H including early onset, scoliosis, areflexia, and slow disease progression. Exome sequencing revealed novel compound heterozygous mutations in FGD4 as the underlying cause in both families (p.Arg468Gln and c.1512-2A>C in FC73, p.Met345Thr and c.2043+1G>A (p.Trp663Trpfs*30) in FC646). The missense mutations were located in highly conserved RhoGEF and PH domains which were predicted to be pathogenic in nature by in silico modeling. The CMT4H occurrence frequency was calculated to 0.7% in the Korean demyelinating CMT patients. This study is the first report of CMT4H in Korea. FGD4 assay could be considered as a means of molecular diagnosis for sporadic cases of demyelinating CMT with slow progression.
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Affiliation(s)
- Young Se Hyun
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Jinho Lee
- Department of Neurology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hye Jin Kim
- Department of Biological Sciences, Kongju National University, Gongju, Korea
| | - Young Bin Hong
- Department of Neurology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Heasoo Koo
- Department of Pathology, Ewha Womans University School of Medicine, Seoul, Korea
| | - Alec S T Smith
- Department of Bioengineering, University of Washington, WA, USA
| | - Deok-Ho Kim
- Department of Bioengineering, University of Washington, WA, USA
| | - Byung-Ok Choi
- Department of Neurology, Sungkyunkwan University School of Medicine, Seoul, Korea.,Neuroscience Center, Samsung Medical Center, Seoul, Korea
| | - Ki Wha Chung
- Department of Biological Sciences, Kongju National University, Gongju, Korea
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Antoniadi T, Buxton C, Dennis G, Forrester N, Smith D, Lunt P, Burton-Jones S. Application of targeted multi-gene panel testing for the diagnosis of inherited peripheral neuropathy provides a high diagnostic yield with unexpected phenotype-genotype variability. BMC MEDICAL GENETICS 2015; 16:84. [PMID: 26392352 PMCID: PMC4578331 DOI: 10.1186/s12881-015-0224-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/21/2015] [Indexed: 01/01/2023]
Abstract
Background Inherited peripheral neuropathy (IPN) is a clinically and genetically heterogeneous group of disorders with more than 90 genes associated with the different subtypes. Sequential gene screening is gradually being replaced by next generation sequencing (NGS) applications. Methods We designed and validated a targeted NGS panel assay including 56 genes associated with known causes of IPN. We report our findings following NGS panel testing of 448 patients with different types of clinically-suspected IPN. Results Genetic diagnosis was achieved in 137 patients (31 %) and involved 195 pathogenic variants in 31 genes. 93 patients had pathogenic variants in genes where a resulting phenotype follows dominant inheritance, 32 in genes where this would follow recessive inheritance, and 12 presented with X-linked disease. Almost half of the diagnosed patients (64) had a pathogenic variant either in genes not previously available for routine diagnostic testing in a UK laboratory (50 patients) or in genes whose primary clinical association was not IPN (14). Seven patients had a pathogenic variant in a gene not hitherto indicated from their phenotype and three patients had more than one pathogenic variant, explaining their complex phenotype and providing information essential for accurate prediction of recurrence risks. Conclusions Our results demonstrate that targeted gene panel testing is an unbiased approach which overcomes the limitations imposed by limited existing knowledge for rare genes, reveals high heterogeneity, and provides high diagnostic yield. It is therefore a highly efficient and cost effective tool for achieving a genetic diagnosis for IPN. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0224-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thalia Antoniadi
- Bristol Genetics Laboratory, North Bristol NHS Trust, Southmead Hospital, Bristol, BS10 5NB, UK.
| | - Chris Buxton
- Bristol Genetics Laboratory, North Bristol NHS Trust, Southmead Hospital, Bristol, BS10 5NB, UK.
| | - Gemma Dennis
- Bristol Genetics Laboratory, North Bristol NHS Trust, Southmead Hospital, Bristol, BS10 5NB, UK.
| | - Natalie Forrester
- Bristol Genetics Laboratory, North Bristol NHS Trust, Southmead Hospital, Bristol, BS10 5NB, UK.
| | - Debbie Smith
- Bristol Genetics Laboratory, North Bristol NHS Trust, Southmead Hospital, Bristol, BS10 5NB, UK.
| | - Peter Lunt
- Department of Social & Community Medicine, University of Bristol, Oakfield House, Bristol, BS8 2BN, UK.
| | - Sarah Burton-Jones
- Bristol Genetics Laboratory, North Bristol NHS Trust, Southmead Hospital, Bristol, BS10 5NB, UK.
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45
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Biancalana V, Laporte J. Diagnostic use of Massively Parallel Sequencing in Neuromuscular Diseases: Towards an Integrated Diagnosis. J Neuromuscul Dis 2015; 2:193-203. [PMID: 27858740 PMCID: PMC5240547 DOI: 10.3233/jnd-150092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Massively parallel sequencing is revolutionizing the genetic testing in diagnosis laboratories, replacing gene-by-gene investigations with a "gene panel" strategy. This new approach is particularly promising for the diagnosis of neuromuscular disorders affecting children as well as adults, which is constrained by strong clinical and genetic heterogeneity. While it leads to a strong improvement in molecular diagnosis, this new approach is dramatically changing the whole diagnosis process, establishing new decision trees and requiring integrated strategies between clinicians and laboratories. To have an overview of the implementation and benefit of these novel sequencing strategies for the diagnosis of neuromuscular disorders, we surveyed the current literature on the application of targeted genes panel sequencing, exome sequencing and genome sequencing. We highlight advantages and disadvantages of these different strategies in a diagnosis setting, discuss about unresolved cases, and point potential validation approaches and outcomes of massively parallel sequencing. It appears important to integrate such novel strategies with clinical, histopathological and imaging investigations, for a faster and more accurate diagnosis and patient care, and to foster research projects and clinical trials.
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Affiliation(s)
- Valérie Biancalana
- Faculté de Médecine, Laboratoire de Diagnostic Génétique, Nouvel Hôpital Civil, Strasbourg, France
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Collège de France, Illkirch, France
| | - Jocelyn Laporte
- Department of Translational Medicine and Neurogenetics, IGBMC, INSERM U964, CNRS UMR7104, University of Strasbourg, Collège de France, Illkirch, France
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46
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Tian X, Liang WC, Feng Y, Wang J, Zhang VW, Chou CH, Huang HD, Lam CW, Hsu YY, Lin TS, Chen WT, Wong LJ, Jong YJ. Expanding genotype/phenotype of neuromuscular diseases by comprehensive target capture/NGS. NEUROLOGY-GENETICS 2015; 1:e14. [PMID: 27066551 PMCID: PMC4807910 DOI: 10.1212/nxg.0000000000000015] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 06/15/2015] [Indexed: 12/31/2022]
Abstract
Objective: To establish and evaluate the effectiveness of a comprehensive next-generation sequencing (NGS) approach to simultaneously analyze all genes known to be responsible for the most clinically and genetically heterogeneous neuromuscular diseases (NMDs) involving spinal motoneurons, neuromuscular junctions, nerves, and muscles. Methods: All coding exons and at least 20 bp of flanking intronic sequences of 236 genes causing NMDs were enriched by using SeqCap EZ solution-based capture and enrichment method followed by massively parallel sequencing on Illumina HiSeq2000. Results: The target gene capture/deep sequencing provides an average coverage of ∼1,000× per nucleotide. Thirty-five unrelated NMD families (38 patients) with clinical and/or muscle pathologic diagnoses but without identified causative genetic defects were analyzed. Deleterious mutations were found in 29 families (83%). Definitive causative mutations were identified in 21 families (60%) and likely diagnoses were established in 8 families (23%). Six families were left without diagnosis due to uncertainty in phenotype/genotype correlation and/or unidentified causative genes. Using this comprehensive panel, we not only identified mutations in expected genes but also expanded phenotype/genotype among different subcategories of NMDs. Conclusions: Target gene capture/deep sequencing approach can greatly improve the genetic diagnosis of NMDs. This study demonstrated the power of NGS in confirming and expanding clinical phenotypes/genotypes of the extremely heterogeneous NMDs. Confirmed molecular diagnoses of NMDs can assist in genetic counseling and carrier detection as well as guide therapeutic options for treatable disorders.
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Affiliation(s)
- Xia Tian
- Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Wen-Chen Liang
- Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Yanming Feng
- Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Jing Wang
- Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Victor Wei Zhang
- Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Chih-Hung Chou
- Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Hsien-Da Huang
- Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Ching Wan Lam
- Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Ya-Yun Hsu
- Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Thy-Sheng Lin
- Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Wan-Tzu Chen
- Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Lee-Jun Wong
- Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Yuh-Jyh Jong
- Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
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Exome Sequence Analysis Suggests that Genetic Burden Contributes to Phenotypic Variability and Complex Neuropathy. Cell Rep 2015; 12:1169-83. [PMID: 26257172 DOI: 10.1016/j.celrep.2015.07.023] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 05/27/2015] [Accepted: 07/09/2015] [Indexed: 02/08/2023] Open
Abstract
Charcot-Marie-Tooth (CMT) disease is a clinically and genetically heterogeneous distal symmetric polyneuropathy. Whole-exome sequencing (WES) of 40 individuals from 37 unrelated families with CMT-like peripheral neuropathy refractory to molecular diagnosis identified apparent causal mutations in ∼ 45% (17/37) of families. Three candidate disease genes are proposed, supported by a combination of genetic and in vivo studies. Aggregate analysis of mutation data revealed a significantly increased number of rare variants across 58 neuropathy-associated genes in subjects versus controls, confirmed in a second ethnically discrete neuropathy cohort, suggesting that mutation burden potentially contributes to phenotypic variability. Neuropathy genes shown to have highly penetrant Mendelizing variants (HPMVs) and implicated by burden in families were shown to interact genetically in a zebrafish assay exacerbating the phenotype established by the suppression of single genes. Our findings suggest that the combinatorial effect of rare variants contributes to disease burden and variable expressivity.
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48
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Introduzione sugli aspetti genetici delle neuropatie. Neurologia 2015. [DOI: 10.1016/s1634-7072(15)72178-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Chardon JW, Smith A, Woulfe J, Pena E, Rakhra K, Dennie C, Beaulieu C, Huang L, Schwartzentruber J, Hawkins C, Harms M, Dojeiji S, Zhang M, Majewski J, Bulman D, Boycott K, Dyment D. LIMS2 mutations are associated with a novel muscular dystrophy, severe cardiomyopathy and triangular tongues. Clin Genet 2015; 88:558-64. [DOI: 10.1111/cge.12561] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/07/2015] [Accepted: 01/09/2015] [Indexed: 02/03/2023]
Affiliation(s)
- Jodi Warman Chardon
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
- Ottawa Hospital Research Institute; Ottawa Ontario Canada
| | - A.C. Smith
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Ontario Canada
| | - J. Woulfe
- Department of Pathology; The Ottawa Hospital; Ottawa Ontario Canada
- Ottawa Hospital Research Institute; Ottawa Ontario Canada
| | - E. Pena
- Department of Medical Imaging; The Ottawa Hospital; Ottawa Ontario Canada
| | - K. Rakhra
- Ottawa Hospital Research Institute; Ottawa Ontario Canada
- Department of Medical Imaging; The Ottawa Hospital; Ottawa Ontario Canada
| | - C. Dennie
- Ottawa Hospital Research Institute; Ottawa Ontario Canada
- Department of Medical Imaging; The Ottawa Hospital; Ottawa Ontario Canada
- University of Ottawa Heart Institute; Ottawa Ontario Canada
| | - C. Beaulieu
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Ontario Canada
| | - Lijia Huang
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Ontario Canada
| | - J. Schwartzentruber
- McGill University and Genome Quebec Innovation Center; Montreal Quebec Canada
| | - C. Hawkins
- Department of Laboratory Medicine & Pathobiology; The Hospital for Sick Children; Toronto Ontario Canada
| | - M.B. Harms
- Department of Neurology and Hope Center for Neurological Disorders; Washington University; Saint Louis MO USA
| | - S. Dojeiji
- The Ottawa Hospital Rehabilitation Center; Ottawa Ontario Canada
| | - M. Zhang
- Ottawa Hospital Research Institute; Ottawa Ontario Canada
| | - J. Majewski
- Department of Human Genetics; McGill University; Montreal Quebec Canada
| | - D.E. Bulman
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Ontario Canada
- Department of Pediatrics; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
| | - K.M. Boycott
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Ontario Canada
| | - D.A. Dyment
- Department of Genetics; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
- Children's Hospital of Eastern Ontario Research Institute; University of Ottawa; Ottawa Ontario Canada
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Gerek NZ, Liu L, Gerold K, Biparva P, Thomas ED, Kumar S. Evolutionary Diagnosis of non-synonymous variants involved in differential drug response. BMC Med Genomics 2015; 8 Suppl 1:S6. [PMID: 25952014 PMCID: PMC4315320 DOI: 10.1186/1755-8794-8-s1-s6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Many pharmaceutical drugs are known to be ineffective or have negative side effects in a substantial proportion of patients. Genomic advances are revealing that some non-synonymous single nucleotide variants (nsSNVs) may cause differences in drug efficacy and side effects. Therefore, it is desirable to evaluate nsSNVs of interest in their ability to modulate the drug response. Results We found that the available data on the link between drug response and nsSNV is rather modest. There were only 31 distinct drug response-altering (DR-altering) and 43 distinct drug response-neutral (DR-neutral) nsSNVs in the whole Pharmacogenomics Knowledge Base (PharmGKB). However, even with this modest dataset, it was clear that existing bioinformatics tools have difficulties in correctly predicting the known DR-altering and DR-neutral nsSNVs. They exhibited an overall accuracy of less than 50%, which was not better than random diagnosis. We found that the underlying problem is the markedly different evolutionary properties between positions harboring nsSNVs linked to drug responses and those observed for inherited diseases. To solve this problem, we developed a new diagnosis method, Drug-EvoD, which was trained on the evolutionary properties of nsSNVs associated with drug responses in a sparse learning framework. Drug-EvoD achieves a TPR of 84% and a TNR of 53%, with a balanced accuracy of 69%, which improves upon other methods significantly. Conclusions The new tool will enable researchers to computationally identify nsSNVs that may affect drug responses. However, much larger training and testing datasets are needed to develop more reliable and accurate tools.
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