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Geroldi A, Mammi A, Gaudio A, Patrone S, La Barbera A, Origone P, Ponti C, Sanguineri F, Massucco S, Marinelli L, Grandis M, Schenone A, Mandich P, Bellone E, Gotta F. Next-generation sequencing in Charcot-Marie-Tooth: a proposal for improvement of ACMG guidelines for variant evaluation. J Med Genet 2024:jmg-2024-110019. [PMID: 38871447 DOI: 10.1136/jmg-2024-110019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/04/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND The application of massive parallel sequencing technologies in the molecular analysis of Charcot-Marie-Tooth (CMT) has enabled the rapid and cost-effective identification of numerous potentially significant variants for diagnostic purposes. The objective is to reduce the number of variants, focusing only on those with pathogenic significance. The 2015 American College of Medical Genetics and Genomics (ACMG) guidelines aid in achieving this goal, but it is now evident that a pathology or gene-specific review of these rules is essential to avoid misinterpretations that may result from blindly applying the criteria. This study demonstrates how revised ACMG criteria, combined with CMT-specific literature data and expertise, can alter the final classification of a variant. METHODS We reviewed ACMG criteria based on current knowledge of CMT and provided suggestions for adapting them to the specificities of CMT. RESULTS Of the 226 index patients analysed, a diagnostic yield of 20% was obtained. It is worth noting that the 9% of cases had their final diagnosis changed with the application of the revised criteria, often resulting in the loss of the pathogenic classification of a variant. CONCLUSIONS The widespread availability of high-throughput sequencing technologies has enabled genetic testing even for laboratories without specific disease expertise. Disease-specific ACMG criteria can be a valuable tool to prevent the proliferation of variants of uncertain significance and the misinterpretation of variants.
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Affiliation(s)
- Alessandro Geroldi
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
| | - Alessia Mammi
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Andrea Gaudio
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Serena Patrone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
| | - Andrea La Barbera
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Paola Origone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Clarissa Ponti
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Francesca Sanguineri
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Sara Massucco
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Neurology Clinic, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Lucio Marinelli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Neurology Clinic, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Marina Grandis
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Neurology Clinic, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Angelo Schenone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Neurology Clinic, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Paola Mandich
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Emilia Bellone
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetic and Maternal and Infantile Sciences, University of Genoa, Genova, Italy
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Fabio Gotta
- UOC Medical Genetics, IRCCS Ospedale Policlinico San Martino, Genova, Italy
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Ghafoor S, Rafiq MA, Abbas Shah ST, Ansar M, Paton T, Ajmal M, Agha Z, Qamar R, Azam M. KIF1A novel frameshift variant p.(Ser887Profs*64) exhibits clinical heterogeneity in a Pakistani family with hereditary sensory and autonomic neuropathy type IIC. Int J Neurosci 2024; 134:665-675. [PMID: 36282036 DOI: 10.1080/00207454.2022.2140428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 10/19/2022] [Indexed: 10/31/2022]
Abstract
Background: Hereditary sensory and autonomic neuropathies (HSANs) are rare heterogeneous group of neurological disorders caused by peripheral nerve deterioration. The HSANs sub-clinical classes have clinical and genetic overlap which often lead to misdiagnosis. In the present study a Pakistani family with five affected members suffering from severe neuropathy were genetically analyzed to identify the disease causative element in the family. Methods: Genome wide high-density single nucleotide polymorphism (SNP) microarray analysis was carried out followed by whole exome sequencing of the affected proband and another affected sibling. Shared homozygous regions in all severely affected members were identified through homozygosity mapping approach. Results: The largest homozygous region of 14.1 Mb shared by the five severely affected members of the family was identified on chromosome 2. Subsequent exome sequencing identified a novel single nucleotide deletion c.2658del; p.(Ser887Profs*64) in KIF1A. Segregation analysis revealed that this mutation was homozygous in all five affected individuals of the family with severe clinical manifestation, while members of the family that were heterozygous carriers shared abnormal skin features (scaly skin) only with the homozygous affected members. Conclusions: A novel frameshift mutation p.(Ser887Profs*64) in KIF1A is the potential cause of severe HSANIIC in a Pakistani family along with incomplete penetrance in mutation carriers. We demonstrate that using a combination of different techniques not only strengthens the gene finding approach but also helps in proper sub-clinical characterization along with identification of mutated alleles exhibiting incomplete penetrance leading to intrafamilial clinical variability in HSAN group of inherited diseases.
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Affiliation(s)
- Saima Ghafoor
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
| | - Muhammad Arshad Rafiq
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Muhammad Ansar
- Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Tara Paton
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Muhammad Ajmal
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
| | - Zehra Agha
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
| | - Raheel Qamar
- Pakistan Academy of Sciences, Islamabad, Pakistan
- Science and Technology Sector, ICESCO, Rabat, Morocco
| | - Maleeha Azam
- Translational Genomics Laboratory, COMSATS University Islamabad, Pakistan
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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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Wang Y, Yin F, Chai Y, Jin J, Zhang P, Tan Q, Chen Z. Prenatal diagnosis of fetuses with ultrasound anomalies by whole-exome sequencing in Luoyang city, China. Front Genet 2024; 14:1301439. [PMID: 38318287 PMCID: PMC10838985 DOI: 10.3389/fgene.2023.1301439] [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: 09/25/2023] [Accepted: 12/20/2023] [Indexed: 02/07/2024] Open
Abstract
Background: There is a great obstacle in prenatal diagnosis of fetal anomalies due to their considerable genetic and clinical heterogeneity. Whole-exome sequencing (WES) has been confirmed as a successful option for genetic diagnosis in pediatrics, but its clinical utility for prenatal diagnosis remains to be limited. Methods: A total of 60 fetuses with abnormal ultrasound findings underwent karyotyping or chromosomal microarray analysis (CMA), and those with negative results were further subjected to WES. The identified variants were classified as pathogenic or likely pathogenic (P/LP) and the variant of uncertain significance (VUS). Pregnancy outcomes were obtained through a telephone follow-up. Results: Twelve (20%, 12/60) fetuses were diagnosed to have chromosomal abnormalities using karyotyping or CMA. Of the remaining 48 cases that underwent WES, P/LP variants were identified in 14 cases (29.2%), giving an additional diagnostic yield of 23.3% (14/60). The most frequently affected organ referred for prenatal WES was the head or neck system (40%), followed by the skeletal system (39.1%). In terms of pathogenic genes, FGFR3 was the most common diagnostic gene in this cohort. For the first time, we discovered five P/LP variants involved in SEC24D, FIG4, CTNNA3, EPG5, and PKD2. In addition, we identified three VUSes that had been reported previously. Outcomes of pregnancy were available for 54 cases, of which 24 cases were terminated. Conclusion: The results confirmed that WES is a powerful tool in prenatal diagnosis, especially for fetuses with ultrasonographic anomalies that cannot be diagnosed using conventional prenatal methods. Additionally, newly identified variants will expand the phenotypic spectrum of monogenic disorders and greatly enrich the prenatal diagnostic database.
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Affiliation(s)
- Yanan Wang
- Department of Genetics and Prenatal Diagnosis, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Fan Yin
- Puluo (Wuhan) Medical Biotechnology Co., LTD., Wuhan, China
| | - Yuqiong Chai
- Department of Genetics and Prenatal Diagnosis, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Jiapei Jin
- Department of Genetics and Prenatal Diagnosis, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Pai Zhang
- Department of Genetics and Prenatal Diagnosis, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Qianqian Tan
- Puluo (Wuhan) Medical Biotechnology Co., LTD., Wuhan, China
| | - Zhigang Chen
- Puluo (Wuhan) Medical Biotechnology Co., LTD., Wuhan, China
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Nair D, Diaz-Rosado A, Varella-Branco E, Ramos I, Black A, Angireddy R, Park J, Murali S, Yoon A, Ciesielski B, O’Brien WT, Passos-Bueno MR, Bhoj E. Heterozygous variants in TBCK cause a mild neurologic syndrome in humans and mice. Am J Med Genet A 2023; 191:2508-2517. [PMID: 37353954 PMCID: PMC10524953 DOI: 10.1002/ajmg.a.63320] [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: 12/23/2022] [Revised: 05/15/2023] [Accepted: 05/26/2023] [Indexed: 06/25/2023]
Abstract
TBCK-related encephalopathy is a rare pediatric neurodegenerative disorder caused by biallelic loss-of-function variants in the TBCK gene. After receiving anecdotal reports of neurologic phenotypes in both human and mouse TBCK heterozygotes, we quantified if TBCK haploinsufficiency causes a phenotype in mice and humans. Using the tbck+/- mouse model, we performed a battery of behavioral assays and mTOR pathway analysis to investigate potential alterations in neurophysiology. We conducted as well a phenome-wide association study (PheWAS) analysis in a large adult biobank to determine the presence of potential phenotypes associated to this variant. The tbck+/- mouse model demonstrates a reduction of exploratory behavior in animals with significant sex and genotype interactions. The concurrent PheWAS analysis of 10,900 unrelated individuals showed that patients with one copy of a TBCK loss-of-function allele had a significantly higher rate of acquired toe and foot deformities, likely indicative of a mild peripheral neuropathy phenotype. This study presents an example of what may be the underappreciated occurrence of mild neurogenic symptoms in heterozygote individuals of recessive neurogenetic syndromes.
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Affiliation(s)
- Divya Nair
- Department of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
| | - Abdias Diaz-Rosado
- Department of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Elisa Varella-Branco
- Centro de Estudos do Genoma Humano e Células-Tronco, Universidade de São Paulo, São Paulo, Brazil
| | - Igor Ramos
- Centro de Estudos do Genoma Humano e Células-Tronco, Universidade de São Paulo, São Paulo, Brazil
| | - Aaron Black
- Department of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
| | - Rajesh Angireddy
- Department of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
| | - Joseph Park
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Svathi Murali
- Department of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
- Department of Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew Yoon
- Department of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
| | - Brianna Ciesielski
- ITMAT, University of Pennsylvania, School of Medicine, Philadelphia, PA, 19104 USA
| | - W. Timothy O’Brien
- ITMAT, University of Pennsylvania, School of Medicine, Philadelphia, PA, 19104 USA
| | | | - Elizabeth Bhoj
- Department of Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 USA
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Chen PS, Chao CC, Tsai LK, Huang HY, Chien YH, Huang PH, Hwu WL, Hsieh ST, Lee NC, Hsueh HW, Yang CC. Diagnostic Challenges of Neuromuscular Disorders after Whole Exome Sequencing. J Neuromuscul Dis 2023:JND230013. [PMID: 37066920 DOI: 10.3233/jnd-230013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
BACKGROUND Whole-exome sequencing (WES) facilitates the diagnosis of hereditary neuromuscular disorders. To achieve an accurate diagnosis, physicians should interpret the genetic report carefully along with clinical information and examinations. We described our experience with (1) clinical validation in patients with variants found using WES and (2) a diagnostic approach for those with negative findings from WES. METHODS WES was performed on patients with the clinical impression of hereditary neuromuscular disorders. Information on clinical manifestations, neurological examination, electrodiagnostic studies, histopathology of muscle and nerve, and laboratory tests were collected. RESULTS Forty-one patients (Male/Female: 18/23, age of onset: 34.5±15.9) accepted WES and were categorized into four scenarios: (1) patients with a positive WES result, (2) patients with an inconclusive WES result but supporting clinical data, (3) negative findings from WES, but a final diagnosis after further work-up, and (4) undetermined etiology from WES and in further work-ups. The yield rate of the initial WES was 63.4% (26/41). Among these, seventeen patients had positive WES result, while the other nine patients had inconclusive WES result but supporting clinical data. Notably, in the fifteen patients with equivocal or negative findings from WES, four patients (26.7%) achieved a diagnosis after further workup: tumor-induced osteomalacia, metabolic myopathy with pathogenic variants in mitochondrial DNA, microsatellite expansion disease, and vasculitis-related neuropathy. The etiologies remained undetermined in eleven patients (myopathy: 7, neuropathy: 4) after WES and further workup. CONCLUSIONS It is essential to design genotype-guided molecular studies to correlate the identified variants with their clinical features. For patients who had negative findings from WES, acquired diseases, mitochondrial DNA disorders and microsatellite expansion diseases should be considered.
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Affiliation(s)
- Pin-Shiuan Chen
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chi-Chao Chao
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-Kai Tsai
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsin-Yi Huang
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yin-Hsiu Chien
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Hsin Huang
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Wuh-Liang Hwu
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Sung-Tsang Hsieh
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsueh-Wen Hsueh
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Anatomy and Cell Biology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chih-Chao Yang
- Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan
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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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Ceylan GG, Habiloğlu E, Çavdarlı B, Tuncez E, Bilen S, Köken ÖY, Gündüz CNS. High diagnostic yield with algorithmic molecular approach on hereditary neuropathies. REVISTA DA ASSOCIACAO MEDICA BRASILEIRA (1992) 2023; 69:233-239. [PMID: 36790232 PMCID: PMC9983476 DOI: 10.1590/1806-9282.20220929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/24/2022] [Indexed: 02/12/2023]
Abstract
OBJECTIVE Charcot-Marie-Tooth disease covers a group of inherited peripheral neuropathies. The aim of this study was to investigate the effect of targeted next-generation sequencing panels on the molecular diagnosis of Charcot-Marie-Tooth disease and its subtypes in routine clinical practice, and also to show the limitations and importance of next-generation sequencing in the diagnosis of Charcot-Marie-Tooth diseases. METHODS This is a retrospective study. Three different molecular methods (multiplex ligation probe amplification, next-generation sequencing, and whole-exome sequencing) were used to detect the mutations related to Charcot-Marie-Tooth disease. RESULTS In total, 64 patients (33 males and 31 females) with suspected Charcot-Marie-Tooth disease were analyzed for molecular etiology. In all, 25 (39%) patients were diagnosed by multiplex ligation probe amplification. With an extra 11 patients with normal PMP22 multiplex ligation probe amplification results that were consulted to our laboratory for further genetic analysis, a total of 50 patients underwent next-generation sequencing for targeted gene panels associated with Charcot-Marie-Tooth disease. Notably, 18 (36%) patients had pathogenic/likely pathogenic variants. Whole-exome sequencing was performed on five patients with normal next-generation sequencing results; the diagnostic yield by whole-exome sequencing was 80% and it was higher in the childhood group. CONCLUSION The molecular etiology in Charcot-Marie-Tooth disease patients can be determined according to pre-test evaluation, deciding the inheritance type with pedigree analysis, the clinical phenotype, and an algorithm for the genetic analysis. The presence of patients without a molecular diagnosis in all the literature suggests that there are new genes or mechanisms waiting to be discovered in the etiology of Charcot-Marie-Tooth disease.
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Affiliation(s)
- Gülay Güleç Ceylan
- Ankara City Hospital, Department of Medical Genetics - Ankara, Turkey.,Ankara Yıldırım Beyazıt Üniversitesi, Department of Medical Genetics - Ankara, Turkey
| | - Esra Habiloğlu
- Ankara City Hospital, Department of Medical Genetics - Ankara, Turkey
| | - Büşranur Çavdarlı
- Ankara City Hospital, Department of Medical Genetics - Ankara, Turkey
| | - Ebru Tuncez
- Ankara City Hospital, Department of Medical Genetics - Ankara, Turkey
| | - Sule Bilen
- Ankara City Hospital, Neurology Department - Ankara, Turkey
| | - Özlem Yayıcı Köken
- Akdeniz University, Medical Faculty, Department of Pediatrics, Division of Pediatric Neurology - Antalya, Turkey
| | - C Nur Semerci Gündüz
- Ankara City Hospital, Department of Medical Genetics - Ankara, Turkey.,Ankara Yıldırım Beyazıt Üniversitesi, Department of Medical Genetics - Ankara, Turkey
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Huang X, Wu X, Wu B, Mou J, Ma X. Identification of a rare missense mutation in GJB1 and prenatal diagnosis in a Chinese family with CMT: A case report. Medicine (Baltimore) 2022; 101:e31733. [PMID: 36397455 PMCID: PMC9666213 DOI: 10.1097/md.0000000000031733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
RATIONALE Charcot-Marie-Tooth disease (CMT) is a highly heterogeneous genetic disorder. To date, more than 90 genes have been implicated in the pathogenesis of CMT. Here, we report the identification of a rare causative mutation in a Chinese family with CMT and a pregnant patient underwent prenatal diagnosis. PATIENT CONCERNS A 33-year-old woman with 21 + 6 weeks of pregnancy presented with progressive weakness of distal extremities after 23 years of age. A total of 8 individuals in 4 generations of her family had similar muscle weakness. On proband whole-exome sequencing (WES), a rare c.121G > A variant in the GJB1 gene was identified. DIAGNOSIS Based on the clinical and genetic findings, this patient was finally diagnosed with CMT. INTERVENTIONS The prenatal diagnosis was performed on the proband fetus. OUTCOMES The fetus did not carry this rare variant, and the pregnancy continued. LESSONS Our findings provide the first clinical evidence for the causative role of GJB1 c.121G > A variant in CMT. WES is a valuable method for diagnosing patients with CMT.
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Affiliation(s)
- Xinyi Huang
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaoli Wu
- Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Bei Wu
- Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Jing Mou
- Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Xingwei Ma
- Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang, China
- *Correspondence: Xingwei Ma, Prenatal Diagnosis Center, Guizhou Provincial People’s Hospital, Guiyang 550002, China (e-mail: )
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10
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Patiyal S, Dhall A, Raghava GPS. Prediction of risk-associated genes and high-risk liver cancer patients from their mutation profile: Benchmarking of mutation calling techniques. Biol Methods Protoc 2022; 7:bpac012. [PMID: 35734767 PMCID: PMC9204470 DOI: 10.1093/biomethods/bpac012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Identification of somatic mutations with high precision is one of the major challenges in the prediction of high-risk liver-cancer patients. In the past, number of mutations calling techniques have been developed that include MuTect2, MuSE, Varscan2, and SomaticSniper. In this study, an attempt has been made to benchmark the potential of these techniques in predicting the prognostic biomarkers for liver cancer. Initially, we extracted somatic mutations in liver cancer patients using Variant Call Format (VCF) and Mutation Annotation Format (MAF) files from the cancer genome atlas. In terms of size, the MAF files are 42 times smaller than VCF files and containing only high-quality somatic mutations. Further, machine learning based models have been developed for predicting high-risk cancer patients using mutations obtained from different techniques. The performance of different techniques and data files have been compared based on their potential to discriminate high and low-risk liver-cancer patients. Based on correlation analysis, we selected 80 genes having significant negative-correlation with the overall survival of liver cancer patients. The univariate survival analysis revealed the prognostic role of highly mutated genes. Single-gene based analysis showed that MuTect2 technique based MAF file has achieved maximum hazard ratio (HRLAMC3) of 9.25 with p-value 1.78E-06. Further, we developed various prediction models using risk-associated top-10 genes for each technique. Our results indicate that MuTect2 technique based VCF files outperform all other methods with maximum Area Under the Receiver-Operating Characteristic (AUROC) curve of 0.765 and HR 4.50 (p-value 3.83E-15). Eventually, VCF file generated using MuTect2 technique performs better among other mutation calling techniques for the prediction of high-risk liver cancer patients. We hope that our findings will provide a useful and comprehensive comparison of various mutation calling techniques for the prognostic analysis of cancer patients. In order to serve the scientific community, we have provided a Python-based pipeline to develop the prediction models using mutation profiles (VCF/MAF) of cancer patients. It is available on GitHub at https://github.com/raghavagps/mutation_bench.
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Affiliation(s)
- Sumeet Patiyal
- Indraprastha Institute of Information Technology Department of Computational Biology, , Okhla Phase 3, New Delhi-110020, India
| | - Anjali Dhall
- Indraprastha Institute of Information Technology Department of Computational Biology, , Okhla Phase 3, New Delhi-110020, India
| | - Gajendra P S Raghava
- Indraprastha Institute of Information Technology Department of Computational Biology, , Okhla Phase 3, New Delhi-110020, India
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11
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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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12
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A National French Consensus on Gene List for the Diagnosis of Charcot–Marie–Tooth Disease and Related Disorders Using Next-Generation Sequencing. Genes (Basel) 2022; 13:genes13020318. [PMID: 35205364 PMCID: PMC8871532 DOI: 10.3390/genes13020318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 12/10/2022] Open
Abstract
Next generation sequencing (NGS) is strategically used for genetic diagnosis in patients with Charcot–Marie–Tooth disease (CMT) and related disorders called non-syndromic inherited peripheral neuropathies (NSIPN) in this paper. With over 100 different CMT-associated genes involved and ongoing discoveries, an important interlaboratory diversity of gene panels exists at national and international levels. Here, we present the work of the French National Network for Rare Neuromuscular Diseases (FILNEMUS) genetic diagnosis section which coordinates the seven French diagnosis laboratories using NGS for peripheral neuropathies. This work aimed to establish a unique, simple and accurate gene classification based on literature evidence. In NSIPN, three subgroups were usually distinguished: (1) HMSN, Hereditary Motor Sensory Neuropathy, (2) dHMN, distal Hereditary Motor Neuropathy, and (3) HSAN, Hereditary Sensory Autonomic Neuropathy. First, we reported ClinGen evaluation, and second, for the genes not evaluated yet by ClinGen, we classified them as “definitive” if reported in at least two clinical publications and associated with one report of functional evidence, or “limited” otherwise. In total, we report a unique consensus gene list for NSIPN including the three subgroups with 93 genes definitive and 34 limited, which is a good rate for our gene’s panel for molecular diagnostic use.
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13
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Sainio MT, Aaltio J, Hyttinen V, Kortelainen M, Ojanen S, Paetau A, Tienari P, Ylikallio E, Auranen M, Tyynismaa H. Effectiveness of clinical exome sequencing in adult patients with difficult-to-diagnose neurological disorders. Acta Neurol Scand 2022; 145:63-72. [PMID: 34418069 DOI: 10.1111/ane.13522] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/02/2021] [Accepted: 08/12/2021] [Indexed: 12/25/2022]
Abstract
OBJECTIVES Clinical diagnostics in adults with hereditary neurological diseases is complicated by clinical and genetic heterogeneity, as well as lifestyle effects. Here, we evaluate the effectiveness of exome sequencing and clinical costs in our difficult-to-diagnose adult patient cohort. Additionally, we expand the phenotypic and genetic spectrum of hereditary neurological disorders in Finland. METHODS We performed clinical exome sequencing (CES) to 100 adult patients from Finland with neurological symptoms of suspected genetic cause. The patients were classified as myopathy (n = 57), peripheral neuropathy (n = 16), ataxia (n = 15), spastic paraplegia (n = 4), Parkinsonism (n = 3), and mixed (n = 5). In addition, we gathered the costs of prior diagnostic work-up to retrospectively assess the cost-effectiveness of CES as a first-line diagnostic tool. RESULTS The overall diagnostic yield of CES was 27%. Pathogenic variants were found for 14 patients (in genes ANO5, CHCHD10, CLCN1, DES, DOK7, FKBP14, POLG, PYROXD1, SCN4A, TUBB3, and TTN) and likely pathogenic previously undescribed variants for 13 patients (in genes ABCD1, AFG3L2, ATL1, CACNA1A, COL6A1, DYSF, IRF2BPL, KCNA1, MT-ATP6, SAMD9L, SGCB, and TPM2). Age of onset below 40 years increased the probability of finding a genetic cause. Our cost evaluation of prior diagnostic work-up suggested that early CES would be cost-effective in this patient group, in which diagnostic costs increase linearly with prolonged investigations. CONCLUSIONS Based on our results, CES is a cost-effective, powerful first-line diagnostic tool in establishing the molecular diagnosis in adult neurological patients with variable symptoms. Importantly, CES can markedly shorten the diagnostic odysseys of about one third of patients.
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Affiliation(s)
- Markus T. Sainio
- Stem Cells and Metabolism Research Program Faculty of Medicine University of Helsinki Helsinki Finland
| | - Juho Aaltio
- Stem Cells and Metabolism Research Program Faculty of Medicine University of Helsinki Helsinki Finland
| | - Virva Hyttinen
- VATT Institute for Economic Research Helsinki Finland
- Department of Health and Social Management University of Eastern Finland Kuopio Finland
| | - Mika Kortelainen
- VATT Institute for Economic Research Helsinki Finland
- Department of Economics Turku School of Economics Turku Finland
| | - Simo Ojanen
- Department of Veterinary Biosciences Faculty of Veterinary Medicine University of Helsinki Helsinki Finland
| | - Anders Paetau
- Department of Pathology HUSLAB and University of Helsinki Helsinki Finland
| | - Pentti Tienari
- Clinical Neurosciences Neurology University of Helsinki and Helsinki University Hospital Helsinki Finland
- Translational Immunology Research Program Faculty of Medicine University of Helsinki Helsinki Finland
| | - Emil Ylikallio
- Stem Cells and Metabolism Research Program Faculty of Medicine University of Helsinki Helsinki Finland
- Clinical Neurosciences Neurology University of Helsinki and Helsinki University Hospital Helsinki Finland
| | - Mari Auranen
- Clinical Neurosciences Neurology University of Helsinki and Helsinki University Hospital Helsinki Finland
| | - Henna Tyynismaa
- Stem Cells and Metabolism Research Program Faculty of Medicine University of Helsinki Helsinki Finland
- Department of Medical and Clinical Genetics University of Helsinki Helsinki Finland
- Neuroscience Center Helsinki Institute of Life Science University of Helsinki Helsinki Finland
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14
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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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15
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Nagappa M, Sharma S, Govindaraj P, Chickabasaviah Y, Siram R, Shroti A, Seshagiri D, Debnath M, Bindu P, Taly A. Genetic spectrum of inherited neuropathies in India. Ann Indian Acad Neurol 2022; 25:407-416. [PMID: 35936615 PMCID: PMC9350795 DOI: 10.4103/aian.aian_269_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 11/17/2022] Open
Abstract
Background and Objectives: Charcot-Marie-Tooth (CMT) disease is the commonest inherited neuromuscular disorder and has heterogeneous manifestations. Data regarding genetic basis of CMT from India is limited. This study aims to report the variations by using high throughput sequencing in Indian CMT cohort. Methods: Fifty-five probands (M:F 29:26) with suspected inherited neuropathy underwent genetic testing (whole exome: 31, clinical exome: 17 and targeted panel: 7). Their clinical and genetic data were analysed. Results: Age at onset ranged from infancy to 54 years. Clinical features included early-onset neuropathy (n=23), skeletal deformities (n=45), impaired vision (n=8), impaired hearing (n=6), facial palsy (n=8), thickened nerves (n=4), impaired cognition (n=5), seizures (n=5), pyramidal signs (n=7), ataxia (n=8) and vocal cord palsy, slow tongue movements and psychosis in one patient each. Twenty-eight patients had demyelinating electrophysiology. Abnormal visual and auditory evoked potentials were noted in 60.60% and 37.5% respectively. Sixty two variants were identified in 37 genes including variants of uncertain significance (n=34) and novel variants (n=45). Eleven patients had additional variations in genes implicated in CMTs/ other neurological disorders. Ten patients did not have variations in neuropathy associated genes, but had variations in genes implicated in other neurological disorders. In seven patients, no variations were detected. Conclusion: In this single centre cohort study from India, genetic diagnosis could be established in 87% of patients with inherited neuropathy. The identified spectrum of genetic variations adds to the pool of existing data and provides a platform for validation studies in cell culture or animal model systems.
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16
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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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17
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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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18
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Beijer D, Baets J. The expanding genetic landscape of hereditary motor neuropathies. Brain 2021; 143:3540-3563. [PMID: 33210134 DOI: 10.1093/brain/awaa311] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
Hereditary motor neuropathies are clinically and genetically diverse disorders characterized by length-dependent axonal degeneration of lower motor neurons. Although currently as many as 26 causal genes are known, there is considerable missing heritability compared to other inherited neuropathies such as Charcot-Marie-Tooth disease. Intriguingly, this genetic landscape spans a discrete number of key biological processes within the peripheral nerve. Also, in terms of underlying pathophysiology, hereditary motor neuropathies show striking overlap with several other neuromuscular and neurological disorders. In this review, we provide a current overview of the genetic spectrum of hereditary motor neuropathies highlighting recent reports of novel genes and mutations or recent discoveries in the underlying disease mechanisms. In addition, we link hereditary motor neuropathies with various related disorders by addressing the main affected pathways of disease divided into five major processes: axonal transport, tRNA aminoacylation, RNA metabolism and DNA integrity, ion channels and transporters and endoplasmic reticulum.
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Affiliation(s)
- Danique Beijer
- Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Belgium
| | - Jonathan Baets
- Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Belgium
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19
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Hannah-Shmouni F, Al-Shahoumi R, Brady LI, Wu L, Frei J, Tarnopolsky MA. Dual molecular diagnoses in a neurometabolic specialty clinic. Am J Med Genet A 2020; 185:766-773. [PMID: 33369152 DOI: 10.1002/ajmg.a.62034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/05/2020] [Accepted: 12/06/2020] [Indexed: 11/08/2022]
Abstract
Reports of patients with concomitant diagnoses of two inherited genetic disorders, sometimes referred to as "double trouble," have appeared intermittently in the medical literature. We report eight additional cases with dual diagnoses of two genetic conditions. All cases had a phenotype atypical for their primary diagnosis, leading to the search for a second genetic diagnosis. These cases highlight the importance of the history, physical examination and continued work-up if the phenotype of the patient falls drastically outside what has been reported with their primary diagnosis. Some of the diagnoses of the patients presented here (e.g., Myotonic Dystrophy Type 1, fascioscapulohumeral muscular dystrophy) would not have been identified by genetic testing done on a next generation sequencing backbone (e.g., panel or exome sequencing). When the clinical picture is atypical or more severe than expected the possibility of a dual diagnosis (double trouble) should be considered. Identification of a second genetic condition can impact management and genetic counseling.
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Affiliation(s)
- Fady Hannah-Shmouni
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Rashid Al-Shahoumi
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Lauren I Brady
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Lily Wu
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Julia Frei
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Mark A Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
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20
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Paketci C, Karakaya M, Edem P, Bayram E, Keller N, Daimagüler HS, Cirak S, Jordanova A, Hiz S, Wirth B, Yiş U. Clinical, electrophysiological and genetic characteristics of childhood hereditary polyneuropathies. Rev Neurol (Paris) 2020; 176:846-855. [DOI: 10.1016/j.neurol.2020.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/04/2020] [Accepted: 04/07/2020] [Indexed: 12/26/2022]
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21
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Herman I, Lopez MA, Marafi D, Pehlivan D, Calame DG, Abid F, Lotze TE. Clinical exome sequencing in the diagnosis of pediatric neuromuscular disease. Muscle Nerve 2020; 63:304-310. [PMID: 33146414 DOI: 10.1002/mus.27112] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 10/29/2020] [Accepted: 10/31/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND The diagnosis of uncommon pediatric neuromuscular disease (NMD) is challenging due to genetic and phenotypic heterogeneity, yet is important to guide treatment, prognosis, and recurrence risk. Patients with diagnostically challenging presentations typically undergo extensive testing with variable molecular diagnostic yield. Given the advancement in next generation sequencing (NGS), we investigated the value of clinical whole exome sequencing (ES) in uncommon pediatric NMD. METHODS A retrospective cohort study of 106 pediatric NMD patients with a combination of ES, chromosomal microarray (CMA), and candidate gene testing was completed at a large tertiary referral center. RESULTS A molecular diagnosis was achieved in 37/79 (46%) patients with ES, 4/44 (9%) patients with CMA, and 15/74 (20%) patients with candidate gene testing. In 2/79 (3%) patients, a dual molecular diagnosis explaining the neuromuscular disease process was identified. A total of 42 patients (53%) who received ES remained without a molecular diagnosis at the conclusion of the study. CONCLUSIONS Due to NGS, molecular diagnostic yield of rare neurological diseases is at an all-time high. We show that ES has a higher diagnostic rate compared to other genetic tests in a complex pediatric neuromuscular disease cohort and should be considered early in the diagnostic journey for select NMD patients with challenging presentations in which a clinical diagnosis is not evident.
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Affiliation(s)
- Isabella Herman
- Department of Pediatrics, Section of Pediatric Neurology and Developmental Neuroscience, Baylor College of Medicine & Texas Children's Hospital, Houston, Texas, USA
| | - Michael A Lopez
- Department of Pediatrics, Division of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Davut Pehlivan
- Department of Pediatrics, Section of Pediatric Neurology and Developmental Neuroscience, Baylor College of Medicine & Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Daniel G Calame
- Department of Pediatrics, Section of Pediatric Neurology and Developmental Neuroscience, Baylor College of Medicine & Texas Children's Hospital, Houston, Texas, USA
| | - Farida Abid
- Department of Pediatrics, Section of Pediatric Neurology and Developmental Neuroscience, Baylor College of Medicine & Texas Children's Hospital, Houston, Texas, USA
| | - Timothy E Lotze
- Department of Pediatrics, Section of Pediatric Neurology and Developmental Neuroscience, Baylor College of Medicine & Texas Children's Hospital, Houston, Texas, USA
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22
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Wu J, Lu G. Multiple functions of TBCK protein in neurodevelopment disorders and tumors. Oncol Lett 2020; 21:17. [PMID: 33240423 PMCID: PMC7681195 DOI: 10.3892/ol.2020.12278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022] Open
Abstract
TBC1 domain containing kinase (TBCK) protein is composed of three conserved domains, including N-terminal Serine/Threonine kinase domain, central TBC domain and C-terminal rhodanese homology domain (RHOD). A total of 9 different transcripts (classified as long and short TBCK) generated by alternative splicing have been reported in different cell lines. Exogenous expression of long TBCK has been identified to function as a suppressor of cell growth in certain cell types. On the contrary, TBCK has also been reported to serve a tumor-promoting role in other cell lines, indicating that TBCK might function differentially, depending on the context in different cellular environments. Furthermore, deleterious homozygous or compound heterozygous mutations identified by whole-exome sequencing in the TBCK gene could ablate the function of TBCK, further impacting the mTOR signaling pathway and leading to neurogenetic disorders, such as hypotonia, global developmental delay, facial dysmorphic features and brain abnormalities. However, as a poorly explored protein, there are a lot of studies associated with the functions of TBCK that need to be performed in the future. The present review summarizes data regarding the structural features and potential roles of TBCK in developmental and neurological diseases and tumorigenesis. Future prospects of TBCK research lie in revealing numerous biological functions of TBCK.
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Affiliation(s)
- Jin Wu
- Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14203, USA
| | - Guanting Lu
- Department of Pathology, People's Hospital of Deyang City, Deyang, Sichuan 618000, P.R. China
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23
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Abstract
Abstract
Inherited peripheral neuropathy is the most common hereditary neuromuscular disease with a prevalence of about 1:2,500. The most frequent form is Charcot-Marie-Tooth disease (CMT, or hereditary motor and sensory neuropathy [HMSN]). Other clinical entities are hereditary neuropathy with liability to pressure palsies (HNPP), distal hereditary motor neuropathies (dHMN), and hereditary sensory and autonomic neuropathies (HSAN). With the exception of HNPP, which is almost always caused by defects of the PMP22 gene, all other forms show genetic heterogeneity with altogether more than 100 genes involved. Mutation detection rates vary considerably, reaching up to 80 % in demyelinating CMT (CMT1) but are still as low as 10–30 % in axonal CMT (CMT2), dHMN, and HSAN. Based on current information, analysis of only four genes (PMP22, GJB1, MPZ, MFN2) identifies 80–90 % of CMT-causing mutations that can be detected in all known disease genes. For the remaining patients, parallel analysis of multiple neuropathy genes using next-generation sequencing is now replacing phenotype-oriented multistep gene-by-gene sequencing. Such approaches tend to generate a wealth of genetic information that requires comprehensive evaluation of the pathogenic relevance of identified variants. In this review, we present current classification systems, specific phenotypic clues, and diagnostic yields in the different subgroups of hereditary CMT and motor neuropathies.
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24
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Nicita F, Ginevrino M, Travaglini L, D'Arrigo S, Zorzi G, Borgatti R, Terrone G, Catteruccia M, Vasco G, Brankovic V, Siliquini S, Romano S, Veredice C, Pedemonte M, Armando M, Lettori D, Stregapede F, Bosco L, Sferra A, Tessarollo V, Romaniello R, Ristori G, Bertini E, Valente EM, Zanni G. Heterozygous KIF1A variants underlie a wide spectrum of neurodevelopmental and neurodegenerative disorders. J Med Genet 2020; 58:475-483. [PMID: 32737135 DOI: 10.1136/jmedgenet-2020-107007] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/22/2020] [Accepted: 05/30/2020] [Indexed: 01/02/2023]
Abstract
BACKGROUND Dominant and recessive variants in the KIF1A gene on chromosome 2q37.3 are associated with several phenotypes, although only three syndromes are currently listed in the OMIM classification: hereditary sensory and autonomic neuropathy type 2 and spastic paraplegia type 30, both recessively inherited, and mental retardation type 9 with dominant inheritance. METHODS In this retrospective multicentre study, we describe the clinical, neuroradiological and genetic features of 19 Caucasian patients (aged 3-65 years) harbouring heterozygous KIF1A variants, and extensively review the available literature to improve current classification of KIF1A-related disorders. RESULTS Patients were divided into two groups. Group 1 comprised patients with a complex phenotype with prominent pyramidal signs, variably associated in all but one case with additional features (ie, epilepsy, ataxia, peripheral neuropathy, optic nerve atrophy); conversely, patients in group 2 presented an early onset or congenital ataxic phenotype. Fourteen different heterozygous missense variants were detected by next-generation sequencing screening, including three novel variants, most falling within the kinesin motor domain. CONCLUSION The present study further enlarges the clinical and mutational spectrum of KIF1A-related disorders by describing a large series of patients with dominantly inherited KIF1A pathogenic variants ranging from pure to complex forms of hereditary spastic paraparesis/paraplegias (HSP) and ataxic phenotypes in a lower proportion of cases. A comprehensive review of the literature indicates that KIF1A screening should be implemented in HSP regardless of its mode of inheritance or presentations as well as in other complex neurodegenerative or neurodevelopmental disorders showing congenital or early onset ataxia.
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Affiliation(s)
- Francesco Nicita
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neuroscience and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Roma, Italy
| | - Monia Ginevrino
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Roma, Italy.,Laboratory of Medical Genetics, IRCCS, Bambino Gesù Children's Hospital, Roma, Italy
| | - Lorena Travaglini
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neuroscience and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Roma, Italy
| | - Stefano D'Arrigo
- Department of Developmental Neurology, Fondazione IRCCS, Istituto Neurologico Carlo Besta, Milano, Italy
| | - Giovanna Zorzi
- Child Neuropsychiatry Unit, Fondazione IRCCS, Istituto Neurologico Carlo Besta, Milano, Italy
| | - Renato Borgatti
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.,IRCCS Mondino Foundation, Pavia, Italy
| | - Gaetano Terrone
- Department of Translational Medicine, Section of Pediatrics, Child Neurology Unit, Universita degli Studi di Napoli Federico II, Napoli, Campania, Italy
| | - Michela Catteruccia
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neuroscience and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Roma, Italy
| | - Gessica Vasco
- Unit of Neurorehabilitation, Department of Neuroscience and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Roma, Italy
| | - Vesna Brankovic
- Clinic for Child Neurology and Psychiatry, University of Belgrade, Belgrade, Serbia
| | - Sabrina Siliquini
- Child Neuropsychiatry Unit, Pediatric Hospital G. Salesi, Ospedali Riuniti, Ancona, Italy
| | - Silvia Romano
- Neurosciences, Mental Health, and Sensory Organs (NESMOS) Department, Center for Experimental Neurological Therapies, S. Andrea Hospital Site, Sapienza University of Rome, Rome, Italy
| | - Chiara Veredice
- Child Neurology and Psychiatry, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rom, Italy
| | - Marina Pedemonte
- Unit of Pediatric Neurology and Muscle Diseases, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Michelina Armando
- Unit of Neurorehabilitation, Department of Neuroscience and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Roma, Italy
| | - Donatella Lettori
- Unit of Neurorehabilitation, Department of Neuroscience and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Roma, Italy
| | - Fabrizia Stregapede
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neuroscience and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Roma, Italy.,Department of Sciences, Roma Tre University, Rom, Italy
| | - Luca Bosco
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neuroscience and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Roma, Italy
| | - Antonella Sferra
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neuroscience and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Roma, Italy
| | - Valeria Tessarollo
- Department of Developmental Neurology, Fondazione IRCCS, Istituto Neurologico Carlo Besta, Milano, Italy
| | - Romina Romaniello
- Neuropsychiatry and Neurorehabilitation Unit, Scientific Institute, IRCCS Eugenio Medea, Lecco, Italy
| | - Giovanni Ristori
- Neurosciences, Mental Health, and Sensory Organs (NESMOS) Department, Center for Experimental Neurological Therapies, S. Andrea Hospital Site, Sapienza University of Rome, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neuroscience and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Roma, Italy
| | - Enza Maria Valente
- IRCCS Mondino Foundation, Pavia, Italy.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Ginevra Zanni
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neuroscience and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Roma, Italy
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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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26
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Michaelidou K, Tsiverdis I, Erimaki S, Papadimitriou D, Amoiridis G, Papadimitriou A, Mitsias P, Zaganas I. Whole exome sequencing establishes diagnosis of Charcot-Marie-Tooth 4J, 1C, and X1 subtypes. Mol Genet Genomic Med 2020; 8:e1141. [PMID: 32022442 PMCID: PMC7196464 DOI: 10.1002/mgg3.1141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 01/01/2020] [Accepted: 01/03/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Charcot-Marie-Tooth (CMT) hereditary polyneuropathies pose a diagnostic challenge. Our aim here is to describe CMT patients diagnosed by whole exome sequencing (WES) following years of fruitless testing. METHODS/RESULTS Three patients with polyneuropathy suspected to be genetic in origin, but not harboring PMP22 gene deletion/duplication, were offered WES. The first patient, a 66-year-old man, had been suffering from progressive weakness and atrophies in the lower and upper extremities for 20 years. Due to ambiguous electrophysiological findings, immune therapies were administered to no avail. Twelve years after PMP22 deletion/duplication testing, WES revealed two pathogenic variants in the FIG4 gene (p.Ile41Thr and p.Phe598fs, respectively), as a cause of CMT 4J. The second patient, a 19-year-old man, had been suffering from hearing and gait impairment since at least his infancy, and recently presented with weakness and dystonia of the lower extremities. In this patient, WES identified the p.Leu122Val LITAF gene variant in heterozygous state, suggesting the diagnosis of CMT 1C, several years after initial genetic analyses. The third patient, a 44-year-old man, presented with progressive weakness and atrophies of the lower and upper extremities since the age of 17 years old. In this patient, WES identified the hemizygous p.Arg164Gln pathogenic variant in the GJB1 gene, establishing the diagnosis of CMT X1, 8 years after testing for PMP22 deletion/duplication. CONCLUSION Novel diagnostic techniques, such as WES, offer the possibility to decipher the cause of CMT subtypes, ending the diagnostic Odyssey of the patients and sparing them from unnecessary and potentially harmful treatments.
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Affiliation(s)
- Kleita Michaelidou
- Neurogenetics LaboratoryMedical SchoolUniversity of CreteHeraklion, CreteGreece
| | - Ioannis Tsiverdis
- Neurology DepartmentUniversity Hospital of CreteHeraklion, CreteGreece
| | - Sophia Erimaki
- Neurophysiology UnitUniversity Hospital of CreteHeraklion, CreteGreece
| | | | | | | | - Panayiotis Mitsias
- Neurogenetics LaboratoryMedical SchoolUniversity of CreteHeraklion, CreteGreece
- Neurology DepartmentUniversity Hospital of CreteHeraklion, CreteGreece
- Neurophysiology UnitUniversity Hospital of CreteHeraklion, CreteGreece
- Department of NeurologyHenry Ford Hospital/Wayne State UniversityDetroitMIUSA
| | - Ioannis Zaganas
- Neurogenetics LaboratoryMedical SchoolUniversity of CreteHeraklion, CreteGreece
- Neurology DepartmentUniversity Hospital of CreteHeraklion, CreteGreece
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27
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Kurihara M, Ishiura H, Bannai T, Mitsui J, Yoshimura J, Morishita S, Hayashi T, Shimizu J, Toda T, Tsuji S. A Novel de novo KIF1A Mutation in a Patient with Autism, Hyperactivity, Epilepsy, Sensory Disturbance, and Spastic Paraplegia. Intern Med 2020; 59:839-842. [PMID: 31813911 PMCID: PMC7118386 DOI: 10.2169/internalmedicine.3661-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Heterozygous mutations in KIF1A have been reported to cause syndromic intellectual disability or pure spastic paraplegia. However, their genotype-phenotype correlations have not been fully elucidated. We herein report a man with autism and hyperactivity along with sensory disturbance and spastic paraplegia, carrying a novel de novo mutation in KIF1A [c.37C>T (p.R13C)]. Autism and hyperactivity have only previously been reported in a patient with c.38 G>A (R13H) mutation. This case suggests that alterations in this arginine at codon 13 might lead to a common clinical spectrum and further expand the genetic and clinical spectra associated with KIF1A mutations.
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Affiliation(s)
- Masanori Kurihara
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
| | - Taro Bannai
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
- Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Japan
| | - Toshihiro Hayashi
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
- Department of Physiology, Teikyo University School of Medicine, Japan
| | - Jun Shimizu
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
- Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Japan
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28
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Beecroft SJ, Yau KS, Allcock RJN, Mina K, Gooding R, Faiz F, Atkinson VJ, Wise C, Sivadorai P, Trajanoski D, Kresoje N, Ong R, Duff RM, Cabrera-Serrano M, Nowak KJ, Pachter N, Ravenscroft G, Lamont PJ, Davis MR, Laing NG. Targeted gene panel use in 2249 neuromuscular patients: the Australasian referral center experience. Ann Clin Transl Neurol 2020; 7:353-362. [PMID: 32153140 PMCID: PMC7086001 DOI: 10.1002/acn3.51002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/28/2020] [Accepted: 02/06/2020] [Indexed: 12/12/2022] Open
Abstract
Objective To develop, test, and iterate a comprehensive neuromuscular targeted gene panel in a national referral center. Methods We designed two iterations of a comprehensive targeted gene panel for neuromuscular disorders. Version 1 included 336 genes, which was increased to 464 genes in Version 2. Both panels used TargetSeqTM probe‐based hybridization for target enrichment followed by Ion Torrent sequencing. Targeted high‐coverage sequencing and analysis was performed on 2249 neurology patients from Australia and New Zealand (1054 Version 1, 1195 Version 2) from 2012 to 2015. No selection criteria were used other than referral from a suitable medical specialist (e.g., neurologist or clinical geneticist). Patients were classified into 15 clinical categories based on the clinical diagnosis from the referring clinician. Results Six hundred and sixty‐five patients received a genetic diagnosis (30%). Diagnosed patients were significantly younger that undiagnosed patients (26.4 and 32.5 years, respectively; P = 4.6326E‐9). The diagnostic success varied markedly between disease categories. Pathogenic variants in 10 genes explained 38% of the disease burden. Unexpected phenotypic expansions were discovered in multiple cases. Triage of unsolved cases for research exome testing led to the discovery of six new disease genes. Interpretation A comprehensive targeted diagnostic panel was an effective method for neuromuscular disease diagnosis within the context of an Australasian referral center. Use of smaller disease‐specific panels would have precluded diagnosis in many patients and increased cost. Analysis through a centralized laboratory facilitated detection of recurrent, but under‐recognized pathogenic variants.
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Affiliation(s)
- Sarah J Beecroft
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Kyle S Yau
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Richard J N Allcock
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Kym Mina
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Rebecca Gooding
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Fathimath Faiz
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Vanessa J Atkinson
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia.,Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Cheryl Wise
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Padma Sivadorai
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Daniel Trajanoski
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Nina Kresoje
- School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Royston Ong
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Rachael M Duff
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Macarena Cabrera-Serrano
- Department of Neurology, Hospital Universitario Virgen del Rocio, Instituto de Biomedicina de Sevilla, CSIC, Universidad de Sevilla, Sevilla, Spain
| | - Kristen J Nowak
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia.,Public and Aboriginal Health Division, Department of Health, Office of Population Health Genomics, Perth, Western Australia, Australia
| | - Nicholas Pachter
- Genetic Services of Western Australia, Department of Health, Government of Western Australia, Perth, Western Australia, Australia.,School of Paediatrics and Child Health, University of Western Australia, Perth, Western Australia, Australia
| | - Gianina Ravenscroft
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Phillipa J Lamont
- Neurogenetic Unit, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Mark R Davis
- Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Nigel G Laing
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia.,Department of Diagnostic Genomics, Department of Health, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia
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29
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Systematic comparison of somatic variant calling performance among different sequencing depth and mutation frequency. Sci Rep 2020; 10:3501. [PMID: 32103116 PMCID: PMC7044309 DOI: 10.1038/s41598-020-60559-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 01/29/2020] [Indexed: 12/09/2022] Open
Abstract
In the past decade, treatments for tumors have made remarkable progress, such as the successful clinical application of targeted therapies. Nowadays, targeted therapies are based primarily on the detection of mutations, and next-generation sequencing (NGS) plays an important role in relevant clinical research. The mutation frequency is a major problem in tumor mutation detection and increasing sequencing depth is a widely used method to improve mutation calling performance. Therefore, it is necessary to evaluate the effect of different sequencing depth and mutation frequency as well as mutation calling tools. In this study, Strelka2 and Mutect2 tools were used in detecting the performance of 30 combinations of sequencing depth and mutation frequency. Results showed that the precision rate kept greater than 95% in most of the samples. Generally, for higher mutation frequency (≥20%), sequencing depth ≥200X is sufficient for calling 95% mutations; for lower mutation frequency (≤10%), we recommend improving experimental method rather than increasing sequencing depth. Besides, according to our results, although Strelka2 and Mutect2 performed similarly, the former performed slightly better than the latter one at higher mutation frequency (≥20%), while Mutect2 performed better when the mutation frequency was lower than 10%. Besides, Strelka2 was 17 to 22 times faster than Mutect2 on average. Our research will provide a useful and comprehensive guideline for clinical genomic researches on somatic mutation identification through systematic performance comparison among different sequencing depths and mutation frequency.
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30
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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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31
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Gabrych DR, Lau VZ, Niwa S, Silverman MA. Going Too Far Is the Same as Falling Short †: Kinesin-3 Family Members in Hereditary Spastic Paraplegia. Front Cell Neurosci 2019; 13:419. [PMID: 31616253 PMCID: PMC6775250 DOI: 10.3389/fncel.2019.00419] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/02/2019] [Indexed: 01/18/2023] Open
Abstract
Proper intracellular trafficking is essential for neuronal development and function, and when any aspect of this process is dysregulated, the resulting "transportopathy" causes neurological disorders. Hereditary spastic paraplegias (HSPs) are a family of such diseases attributed to over 80 spastic gait genes (SPG), specifically characterized by lower extremity spasticity and weakness. Multiple genes in the trafficking pathway such as those relating to microtubule structure and function and organelle biogenesis are representative disease loci. Microtubule motor proteins, or kinesins, are also causal in HSP, specifically mutations in Kinesin-I/KIF5A (SPG10) and two kinesin-3 family members; KIF1A (SPG30) and KIF1C (SPG58). KIF1A is a motor enriched in neurons, and involved in the anterograde transport of a variety of vesicles that contribute to pre- and post-synaptic assembly, autophagic processes, and neuron survival. KIF1C is ubiquitously expressed and, in addition to anterograde cargo transport, also functions in retrograde transport between the Golgi and the endoplasmic reticulum. Only a handful of KIF1C cargos have been identified; however, many have crucial roles such as neuronal differentiation, outgrowth, plasticity and survival. HSP-related kinesin-3 mutants are characterized mainly as loss-of-function resulting in deficits in motility, regulation, and cargo binding. Gain-of-function mutants are also seen, and are characterized by increased microtubule-on rates and hypermotility. Both sets of mutations ultimately result in misdelivery of critical cargos within the neuron. This likely leads to deleterious cell biological cascades that likely underlie or contribute to HSP clinical pathology and ultimately, symptomology. Due to the paucity of histopathological or cell biological data assessing perturbations in cargo localization, it has been difficult to positively link these mutations to the outcomes seen in HSPs. Ultimately, the goal of this review is to encourage future academic and clinical efforts to focus on "transportopathies" through a cargo-centric lens.
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Affiliation(s)
- Dominik R Gabrych
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Victor Z Lau
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Shinsuke Niwa
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
| | - Michael A Silverman
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada.,Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC, Canada
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32
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Gustavsson EK, Follett J, Farrer MJ, Aasly JO. Family with primary periodic paralysis and a mutation in MCM3AP, a gene implicated in mRNA transport. Muscle Nerve 2019; 60:311-314. [PMID: 31241196 DOI: 10.1002/mus.26622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 06/21/2019] [Accepted: 06/23/2019] [Indexed: 11/07/2022]
Abstract
INTRODUCTION Primary periodic paralyses (PPs) are rare genetic neuromuscular disorders commonly caused by mutations in genes related to ion channel function. However, 10%-20% of cases remain as genetically unexplained. Herein we present a family with PP with paralytic episodes generally lasting for 1-7 days at a time, associated with a drop in K+ levels. METHODS Screening for mutations in known disease-causing genes was negative, hence we performed whole-exome sequencing of 5 family members. RESULTS Minichromosome maintenance 3-associated protein (MCM3AP) c.2615G>A (p.C872Y) was found to cosegregate with disease in the family and was not present in control subjects. The mutation is novel, highly conserved across multiple species, and predicted to be damaging. DISCUSSION MCM3AP encodes germinal center-associated nuclear protein (GANP), a protein involved in the export of certain messenger RNAs from the nucleus to the cytoplasm. Our findings suggest that a novel mutation in MCM3AP is associated with hypokalemic PP. Muscle Nerve, 2019.
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Affiliation(s)
- Emil K Gustavsson
- Djavad Mowafaghian Centre for Brain Health, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada.,Department of Neurology, St. Olav's Hospital, Trondheim, Norway.,Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jordan Follett
- Djavad Mowafaghian Centre for Brain Health, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Matthew J Farrer
- Djavad Mowafaghian Centre for Brain Health, 2215 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jan O Aasly
- Department of Neurology, St. Olav's Hospital, Trondheim, Norway.,Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, Trondheim, Norway
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Almutawa W, Smith C, Sabouny R, Smit RB, Zhao T, Wong R, Lee-Glover L, Desrochers-Goyette J, Ilamathi HS, Suchowersky O, Germain M, Mains PE, Parboosingh JS, Pfeffer G, Innes AM, Shutt TE. The R941L mutation in MYH14 disrupts mitochondrial fission and associates with peripheral neuropathy. EBioMedicine 2019; 45:379-392. [PMID: 31231018 PMCID: PMC6642256 DOI: 10.1016/j.ebiom.2019.06.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 11/25/2022] Open
Abstract
Background Peripheral neuropathies are often caused by disruption of genes responsible for myelination or axonal transport. In particular, impairment in mitochondrial fission and fusion are known causes of peripheral neuropathies. However, the causal mechanisms for peripheral neuropathy gene mutations are not always known. While loss of function mutations in MYH14 typically cause non-syndromic hearing loss, the recently described R941L mutation in MYH14, encoding the non-muscle myosin protein isoform NMIIC, leads to a complex clinical presentation with an unexplained peripheral neuropathy phenotype. Methods Confocal microscopy was used to examine mitochondrial dynamics in MYH14 patient fibroblast cells, as well as U2OS and M17 cells overexpressing NMIIC. The consequence of the R941L mutation on myosin activity was modeled in C. elegans. Findings We describe the third family carrying the R941L mutation in MYH14, and demonstrate that the R941L mutation impairs non-muscle myosin protein function. To better understand the molecular basis of the peripheral neuropathy phenotype associated with the R941L mutation, which has been hindered by the fact that NMIIC is largely uncharacterized, we have established a previously unrecognized biological role for NMIIC in mediating mitochondrial fission in human cells. Notably, the R941L mutation acts in a dominant-negative fashion to inhibit mitochondrial fission, especially in the cell periphery. In addition, we observed alterations to the organization of the mitochondrial genome. Interpretation As impairments in mitochondrial fission cause peripheral neuropathy, this insight into the function of NMIIC likely explains the peripheral neuropathy phenotype associated with the R941L mutation. Fund This study was supported by the Alberta Children's Hospital Research Institute, the Canadian Institutes of Health Research and the Care4Rare Canada Consortium.
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Affiliation(s)
- Walaa Almutawa
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Christopher Smith
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Rasha Sabouny
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ryan B Smit
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Tian Zhao
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Rachel Wong
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Laurie Lee-Glover
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Justine Desrochers-Goyette
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada; Centre de Recherche Biomed, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Hema Saranya Ilamathi
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada; Centre de Recherche Biomed, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Oksana Suchowersky
- Departments of Medicine (Neurology), Medical Genetics and Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Marc Germain
- Groupe de Recherche en Signalisation Cellulaire and Département de Biologie Médicale, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada; Centre de Recherche Biomed, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada
| | - Paul E Mains
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jillian S Parboosingh
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Gerald Pfeffer
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - A Micheil Innes
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| | - Timothy E Shutt
- Alberta Children's Hospital Research Institute, Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, Department of Clinical Neurosciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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A. Mahler E, Johannsen J, Tsiakas K, Kloth K, Lüttgen S, Mühlhausen C, Alhaddad B, B. Haack T, M. Strom T, Kortüm F, Meitinger T, C. Muntau A, Santer R, Kubisch C, Lessel D, Denecke* J, Hempel* M. Exome Sequencing in Children. DEUTSCHES ARZTEBLATT INTERNATIONAL 2019; 116:197-204. [PMID: 31056085 PMCID: PMC6514384 DOI: 10.3238/arztebl.2019.0197] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 07/27/2018] [Accepted: 01/17/2019] [Indexed: 01/26/2023]
Abstract
BACKGROUND In developed countries, global developmental disorders are encounter- ed in approximately 1% of all children. The causes are manifold, and no exogenous cause can be identified in about half of the affected children. The parallel investi- gation of the coding sequences of all genes of the affected individual (whole exome sequencing, WES) has developed into a successful diagnostic method for identify- ing the cause of the problem. It is not yet clear, however, when WES should best be used in routine clinical practice in order to exploit the potential of this method to the fullest. METHODS In an interdisciplinary study, we carried out standardized clinical pheno- typing and a systematic genetic analysis (WES of the index patient and his or her parents, so-called trio WES) in 50 children with developmental disturbances of unclear etiology and with nonspecific neurological manifestations. RESULTS In 21 children (42% of the collective), we were able to identify the cause of the disorder by demonstrating a mutation in a gene known to be associated with disease. Three of these children subsequently underwent specific treatment. In 22 other children (44%), we detected possibly etiological changes in candidate genes not currently known to be associated with human disease. CONCLUSION Our detection rate of at least 42% is high in comparison with the results obtained in other studies from Germany and other countries to date and implies that WES can be used to good effect as a differential diagnostic tool in pediatric neurol- ogy. WES should be carried out in both the index patient and his or her parents (trio- WES) and accompanied by close interdisciplinary collaboration of human geneti- cists and pediatricians, by comprehensive and targeted phenotyping (also after the diagnosis is established), and by the meticulous evaluation of all gene variants.
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Affiliation(s)
- Elisa A. Mahler
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf
| | - Jessika Johannsen
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf
| | | | - Katja Kloth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf
| | - Sabine Lüttgen
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf
| | - Chris Mühlhausen
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf
| | - Bader Alhaddad
- Institute of Human Genetics, Klinikum Rechts der Isar, TUM, Munich
| | - Tobias B. Haack
- Institute of Human Genetics, Klinikum Rechts der Isar, TUM, Munich
- Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
| | - Tim M. Strom
- Institute of Human Genetics, Klinikum Rechts der Isar, TUM, Munich
- Institute of Human Genetics, Helmholtz Center Munich
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum Rechts der Isar, TUM, Munich
- Institute of Human Genetics, Helmholtz Center Munich
| | - Ania C. Muntau
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf
| | - René Santer
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf
- Undiagnosed Disease Program at the University Medical Center Hamburg-Eppendorf (UDP-UKE)
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf
| | - Jonas Denecke*
- *Joint last authors
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf
| | - Maja Hempel*
- *Joint last authors
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf
- Undiagnosed Disease Program at the University Medical Center Hamburg-Eppendorf (UDP-UKE)
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35
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Ortiz-González XR, Tintos-Hernández JA, Keller K, Li X, Foley AR, Bharucha-Goebel DX, Kessler SK, Yum SW, Crino PB, He M, Wallace DC, Bönnemann CG. Homozygous boricua TBCK mutation causes neurodegeneration and aberrant autophagy. Ann Neurol 2019; 83:153-165. [PMID: 29283439 DOI: 10.1002/ana.25130] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 12/26/2017] [Accepted: 12/26/2017] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Autosomal-recessive mutations in TBCK cause intellectual disability of variable severity. Although the physiological function of TBCK remains unclear, loss-of-function mutations are associated with inhibition of mechanistic target of rapamycin complex 1 (mTORC1) signaling. Given that mTORC1 signaling is known to regulate autophagy, we hypothesized that TBCK-encephalopathy patients with a neurodegenerative course have defects in autophagic-lysosomal dysfunction. METHODS Children (n = 8) of Puerto Rican (Boricua) descent affected with homozygous TBCK p.R126X mutations underwent extensive neurological phenotyping and neurophysiological studies. We quantified autophagosome content in TBCK-/- patient-derived fibroblasts by immunostaining and assayed autophagic markers by western assay. Free sialylated oligosaccharide profiles were assayed in patient's urine and fibroblasts. RESULTS The neurological phenotype of children with TBCK p.R126X mutations, which we call TBCK-encephaloneuronopathy (TBCKE), include congenital hypotonia, progressive motor neuronopathy, leukoencephalopathy, and epilepsy. Systemic features include coarse facies, dyslipidemia, and osteoporosis. TBCK-/- fibroblasts in vitro exhibit increased numbers of LC3+ autophagosomes and increased autophagic flux by immunoblots. Free oligosaccharide profiles in fibroblasts and urine of TBCKE patients differ from control fibroblasts and are ameliorated by treatment with the mTORC1 activator leucine. INTERPRETATION TBCKE is a clinically distinguishable syndrome with progressive central and peripheral nervous system dysfunction, consistently observed in patients with the p.R126X mutation. We provide evidence that inappropriate autophagy in the absence of cellular stressors may play a role in this disorder, and that mTORC1 activation may ameliorate the autophagic-lysosomal system dysfunction. Free oligosaccharide profiles could serve as a novel biomarker for this disorder as well as a tool to evaluate potential therapeutic interventions. Ann Neurol 2018;83:153-165.
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Affiliation(s)
- Xilma R Ortiz-González
- Department of Pediatrics, Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jesus A Tintos-Hernández
- Department of Pediatrics, Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA.,Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kierstin Keller
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Xueli Li
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Diana X Bharucha-Goebel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD.,Division of Neurology, Children's National Health System, Washington, DC
| | - Sudha K Kessler
- Department of Pediatrics, Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Sabrina W Yum
- Department of Pediatrics, Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Peter B Crino
- Department of Neurology, University of Maryland School of Medicine, Baltimore, MD
| | - Miao He
- Department of Pathology and Laboratory Medicine, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
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Biallelic sequence variants in INTS1 in patients with developmental delays, cataracts, and craniofacial anomalies. Eur J Hum Genet 2019; 27:582-593. [PMID: 30622326 DOI: 10.1038/s41431-018-0298-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 10/25/2018] [Indexed: 12/24/2022] Open
Abstract
The Integrator complex subunit 1 (INTS1) is a component of the integrator complex that comprises 14 subunits and associates with RPB1 to catalyze endonucleolytic cleavage of nascent snRNAs and assist RNA polymerase II in promoter-proximal pause-release on protein-coding genes. We present five patients, including two sib pairs, with biallelic sequence variants in INTS1. The patients manifested absent or severely limited speech, an abnormal gait, hypotonia and cataracts. Exome sequencing revealed biallelic variants in INTS1 in all patients. One sib pair demonstrated a missense variant, p.(Arg77Cys), and a frameshift variant, p.(Arg1800Profs*20), another sib pair had a homozygous missense variant, p.(Pro1874Leu), and the fifth patient had a frameshift variant, p.(Leu1764Cysfs*16) and a missense variant, p.(Leu2164Pro). We also report additional clinical data on three previously described individuals with a homozygous, loss of function variant, p.(Ser1784*) in INTS1 that shared cognitive delays, cataracts and dysmorphic features with these patients. Several of the variants affected the protein C-terminus and preliminary modeling showed that the p.(Pro1874Leu) and p.(Leu2164Pro) variants may interfere with INTS1 helix folding. In view of the cataracts observed, we performed in-situ hybridization and demonstrated expression of ints1 in the zebrafish eye. We used Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 to make larvae with biallelic insertion/deletion (indel) variants in ints1. The mutant larvae developed typically through gastrulation, but sections of the eye showed abnormal lens development. The distinctive phenotype associated with biallelic variants in INTS1 points to dysfunction of the integrator complex as a mechanism for intellectual disability, eye defects and craniofacial anomalies.
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Beck-Wödl S, Harzer K, Sturm M, Buchert R, Rieß O, Mennel HD, Latta E, Pagenstecher A, Keber U. Homozygous TBC1 domain-containing kinase (TBCK) mutation causes a novel lysosomal storage disease - a new type of neuronal ceroid lipofuscinosis (CLN15)? Acta Neuropathol Commun 2018; 6:145. [PMID: 30591081 PMCID: PMC6307319 DOI: 10.1186/s40478-018-0646-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 12/03/2018] [Indexed: 02/07/2023] Open
Abstract
Homozygous mutation of TBC1 domain-containing kinase (TBCK) is the cause of a very recently defined severe childhood disorder, which is characterized by severe hypotonia, global developmental delay, intellectual disability, epilepsy, characteristic facies and premature death. The link between TBCK loss of function and symptoms in patients with TBCK deficiency disorder (TBCK-DD) remains elusive. Here we demonstrate for the first time the histopathological characteristics of TBCK deficiency consisting of 1) a widespread and massive accumulation of lipofuscin storage material in neurons of the central nervous system without notable neuronal degeneration, 2) storage deposits in few astrocytes, 3) carbohydrate-rich deposits in brain, spleen and liver and 4) vacuolated lymphocytes. Biochemical examinations ruled out more than 20 known lysosomal storage diseases. These investigations strikingly uncover TBCK-DD as a novel type of lysosomal storage disease which is characterized by different storage products rather than one specific type of accumulated material. Due to the clear predominance of intraneuronal lipofuscin storage material and the characteristic clinical presentation we propose to classify this disease as a new subtype of neuronal ceroid lipofuscinosis (CLN15). Our results and previous reports suggest an autophagosomal-lysosomal dysfunction caused by enhanced mTORC1-mediated autophagosome formation and reduced Rab-mediated autophagosome-lysosome fusion, thus disclosing potential novel targets for therapeutic approaches in TBCK-DD.
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Bacquet J, Stojkovic T, Boyer A, Martini N, Audic F, Chabrol B, Salort-Campana E, Delmont E, Desvignes JP, Verschueren A, Attarian S, Chaussenot A, Delague V, Levy N, Bonello-Palot N. Molecular diagnosis of inherited peripheral neuropathies by targeted next-generation sequencing: molecular spectrum delineation. BMJ Open 2018; 8:e021632. [PMID: 30373780 PMCID: PMC6224714 DOI: 10.1136/bmjopen-2018-021632] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
PURPOSE Inherited peripheral neuropathies (IPN) represent a large heterogenous group of hereditary diseases with more than 100 causative genes reported to date. In this context, targeted next-generation sequencing (NGS) offers the opportunity to screen all these genes with high efficiency in order to unravel the genetic basis of the disease. Here, we compare the diagnostic yield of targeted NGS with our previous gene by gene Sanger sequencing strategy. We also describe several novel likely pathogenic variants. DESIGN AND PARTICIPANTS We have completed the targeted NGS of 81 IPN genes in a cohort of 123 unrelated patients affected with diverse forms of IPNs, mostly Charcot-Marie-Tooth disease (CMT): 23% CMT1, 52% CMT2, 9% distal hereditary motor neuropathy, 7% hereditary sensory and autonomic neuropathy and 6.5% intermediate CMT. RESULTS We have solved the molecular diagnosis in 49 of 123 patients (~40%). Among the identified variants, 26 variants were already reported in the literature. In our cohort, the most frequently mutated genes are respectively: MFN2, SH3TC2, GDAP1, NEFL, GAN, KIF5A and AARS. Panel-based NGS was more efficient in familial cases than in sporadic cases (diagnostic yield 49%vs19%, respectively). NGS-based search for copy number variations, allowed the identification of three duplications in three patients and raised the diagnostic yield to 41%. This yield is two times higher than the one obtained previously by gene Sanger sequencing screening. The impact of panel-based NGS screening is particularly important for demyelinating CMT (CMT1) subtypes, for which the success rate reached 87% (36% only for axonal CMT2). CONCLUSION NGS allowed to identify causal mutations in a shorter and cost-effective time. Actually, targeted NGS is a well-suited strategy for efficient molecular diagnosis of IPNs. However, NGS leads to the identification of numerous variants of unknown significance, which interpretation requires interdisciplinary collaborations between molecular geneticists, clinicians and (neuro)pathologists.
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Affiliation(s)
- Juliette Bacquet
- Département de génétique médicale, Hôpital Timone enfants, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Tanya Stojkovic
- Centre de référence des maladies neuromusculaires, Hôpital Pitié-Salpétrière, Assistance-Publique Hôpitaux de Paris, Paris, France
| | - Amandine Boyer
- Département de génétique médicale, Hôpital Timone enfants, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Nathalie Martini
- Département de génétique médicale, Hôpital Timone enfants, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Frédérique Audic
- Centre de référence des maladies neuromusculaires, Hôpital Timone enfants, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Brigitte Chabrol
- Centre de référence des maladies neuromusculaires, Hôpital Timone enfants, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Emmanuelle Salort-Campana
- Centre de référence des maladies neuromusculaires, Hôpital Timone Adultes, Assistance Publique Hôpitaux de Marseille, Marseille, France
- INSERM, MMG, UMR 1251, Aix Marseille Univ, Marseille, France
| | - Emilien Delmont
- Centre de référence des maladies neuromusculaires, Hôpital Timone Adultes, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | | | - Annie Verschueren
- Centre de référence des maladies neuromusculaires, Hôpital Timone Adultes, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Shahram Attarian
- Centre de référence des maladies neuromusculaires, Hôpital Timone Adultes, Assistance Publique Hôpitaux de Marseille, Marseille, France
- INSERM, MMG, UMR 1251, Aix Marseille Univ, Marseille, France
| | | | - Valérie Delague
- INSERM, MMG, UMR 1251, Aix Marseille Univ, Marseille, France
| | - Nicolas Levy
- Département de génétique médicale, Hôpital Timone enfants, Assistance Publique Hôpitaux de Marseille, Marseille, France
- INSERM, MMG, UMR 1251, Aix Marseille Univ, Marseille, France
| | - Nathalie Bonello-Palot
- Département de génétique médicale, Hôpital Timone enfants, Assistance Publique Hôpitaux de Marseille, Marseille, France
- INSERM, MMG, UMR 1251, Aix Marseille Univ, Marseille, France
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Is PNPT1
-related hearing loss ever non-syndromic? Whole exome sequencing of adult siblings expands the natural history of PNPT1
-related disorders. Am J Med Genet A 2018; 176:2487-2493. [DOI: 10.1002/ajmg.a.40516] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/27/2018] [Accepted: 07/27/2018] [Indexed: 11/07/2022]
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Further delineation of TBCK - Infantile hypotonia with psychomotor retardation and characteristic facies type 3. Eur J Med Genet 2018; 62:273-277. [PMID: 30103036 DOI: 10.1016/j.ejmg.2018.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 07/23/2018] [Accepted: 08/09/2018] [Indexed: 01/19/2023]
Abstract
Deleterious homozygous or compound heterozygous mutations in the TBCK (TBC1-domain-containing kinase) gene (implicated in the MTOR pathway) produce profound hypotonia, global developmental delay, facial dysmorphic features, and brain abnormalities. The disorder has been named "infantile hypotonia with psychomotor retardation and characteristic facies-3" (IHPRF3). Here we present two sisters with a novel mutation in TBCK (NM_001163435.2: c.753dup; p.(Lys252*)) who have this ultrarare disorder. We have reviewed the literature on the 33 previously reported cases to provide a characterization of this emerging phenotype. Pathogenic mutations in TBCK have a predominant involvement of the Central Nervous System with a progressive pattern, leading to the conclusion where pathogenic mutations of the said gene lead to a progressive neurodegenerative disease. This report adds novel mutation and features to this complex phenotype. Further investigation is required to understand the pathogenesis of TBCK.
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Bertier G, Joly Y. Clinical exome sequencing in France and Quebec: what are the challenges? What does the future hold? LIFE SCIENCES, SOCIETY AND POLICY 2018; 14:17. [PMID: 30066179 PMCID: PMC6068066 DOI: 10.1186/s40504-018-0081-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND The decreasing cost of next-generation sequencing technologies (NGS) has resulted in their increased use in research, and in the clinic. However, France and Quebec have not yet implemented nation-wide personalized medicine programs using NGS. To produce policies on the large-scale implementation of NGS, decision makers could benefit from a detailed understanding of how these technologies are currently used, their limitations, and the benefits they could bring to patients. OBJECTIVES We aimed at answering two research questions: How are patients' NGS data currently managed in healthcare institutions in Quebec and in France? What issues do technology users identify which should be solved in order to implement clinical genomics at the national level? METHOD Through a multiple case study method, we analysed interviews and documentation from four teams that use whole-exome sequencing in hybrid clinical research projects focusing on cancer and rare diseases. RESULTS Interviewees detailed numerous challenges linked with managing the complexity of the process of collecting and interpreting data in a relevant manner for patients, and described how obtaining buy-in from multiple stakeholders was necessary. CONCLUSION A strong political will is essential for personalized medicine to be implemented efficiently in France and Quebec.
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Affiliation(s)
- Gabrielle Bertier
- Department of Human Genetics, Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1 Canada
- Université Toulouse III Paul Sabatier and Inserm UMR 1027, 37 allées Jules Guesde, F-31000 Toulouse, France
| | - Yann Joly
- Department of Human Genetics, Center of Genomics and Policy, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec H3A 0G1 Canada
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Karakaya M, Storbeck M, Strathmann EA, Delle Vedove A, Hölker I, Altmueller J, Naghiyeva L, Schmitz-Steinkrüger L, Vezyroglou K, Motameny S, Alawbathani S, Thiele H, Polat AI, Okur D, Boostani R, Karimiani EG, Wunderlich G, Ardicli D, Topaloglu H, Kirschner J, Schrank B, Maroofian R, Magnusson O, Yis U, Nürnberg P, Heller R, Wirth B. Targeted sequencing with expanded gene profile enables high diagnostic yield in non-5q-spinal muscular atrophies. Hum Mutat 2018; 39:1284-1298. [PMID: 29858556 DOI: 10.1002/humu.23560] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/14/2018] [Accepted: 05/30/2018] [Indexed: 11/08/2022]
Abstract
Spinal muscular atrophies (SMAs) are a heterogeneous group of disorders characterized by muscular atrophy, weakness, and hypotonia due to suspected lower motor neuron degeneration (LMND). In a large cohort of 3,465 individuals suspected with SMA submitted for SMN1 testing to our routine diagnostic laboratory, 48.8% carried a homozygous SMN1 deletion, 2.8% a subtle mutation, and an SMN1 deletion, whereas 48.4% remained undiagnosed. Recently, several other genes implicated in SMA/LMND have been reported. Despite several efforts to establish a diagnostic algorithm for non-5q-SMA (SMA without deletion or point mutations in SMN1 [5q13.2]), data from large-scale studies are not available. We tested the clinical utility of targeted sequencing in non-5q-SMA by developing two different gene panels. We first analyzed 30 individuals with a small panel including 62 genes associated with LMND using IonTorrent-AmpliSeq target enrichment. Then, additional 65 individuals were tested with a broader panel encompassing up to 479 genes implicated in neuromuscular diseases (NMDs) with Agilent-SureSelect target enrichment. The NMD panel provided a higher diagnostic yield (33%) than the restricted LMND panel (13%). Nondiagnosed cases were further subjected to exome or genome sequencing. Our experience supports the use of gene panels covering a broad disease spectrum for diseases that are highly heterogeneous and clinically difficult to differentiate.
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Affiliation(s)
- Mert Karakaya
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Markus Storbeck
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Eike A Strathmann
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Andrea Delle Vedove
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Irmgard Hölker
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Janine Altmueller
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Leyla Naghiyeva
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Lea Schmitz-Steinkrüger
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Katharina Vezyroglou
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Susanne Motameny
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Salem Alawbathani
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Ayse Ipek Polat
- Dokuz Eylül University, Department of Pediatric Neurology, Izmir, Turkey
| | - Derya Okur
- Dokuz Eylül University, Department of Pediatric Neurology, Izmir, Turkey
| | - Reza Boostani
- Mashhad University of Medical Sciences, Department of Neurology, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Next Generation Genetic Polyclinic, Mashhad, Iran.,Razavi Cancer Research Center, Razavi Hospital, Imam Reza International University, Mashhad, Iran
| | | | - Didem Ardicli
- Hacettepe University, Department of Pediatric Neurology, Ankara, Turkey
| | - Haluk Topaloglu
- Hacettepe University, Department of Pediatric Neurology, Ankara, Turkey
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Bertold Schrank
- DKD HELIOS Kliniken, Department of Neurology, Wiesbaden, Germany
| | - Reza Maroofian
- Genetics and Molecular Cell Sciences Research Centre, St George's University of London, London, UK
| | | | - Uluc Yis
- Dokuz Eylül University, Department of Pediatric Neurology, Izmir, Turkey
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Raoul Heller
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute of Genetics, and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
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Cutrupi AN, Brewer MH, Nicholson GA, Kennerson M. Structural variations causing inherited peripheral neuropathies: A paradigm for understanding genomic organization, chromatin interactions, and gene dysregulation. Mol Genet Genomic Med 2018; 6:422-433. [PMID: 29573232 PMCID: PMC6014456 DOI: 10.1002/mgg3.390] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/09/2018] [Accepted: 03/01/2018] [Indexed: 11/16/2022] Open
Abstract
Inherited peripheral neuropathies (IPNs) are a clinically and genetically heterogeneous group of diseases affecting the motor and sensory peripheral nerves. IPNs have benefited from gene discovery and genetic diagnosis using next-generation sequencing with over 80 causative genes available for testing. Despite this success, up to 50% of cases remain genetically unsolved. In the absence of protein coding mutations, noncoding DNA or structural variation (SV) mutations are a possible explanation. The most common IPN, Charcot-Marie-Tooth neuropathy type 1A (CMT1A), is caused by a 1.5 Mb duplication causing trisomy of the dosage sensitive gene PMP22. Using genome sequencing, we recently identified two large genomic rearrangements causing IPN subtypes X-linked CMT (CMTX3) and distal hereditary motor neuropathy (DHMN1), thereby expanding the spectrum of SV mutations causing IPN. Understanding how newly discovered SVs can cause IPN may serve as a useful paradigm to examine the role of topologically associated domains (TADs), chromatin interactions, and gene dysregulation in disease. This review will describe the growing role of SV in the pathogenesis of IPN and the importance of considering this type of mutation in Mendelian diseases where protein coding mutations cannot be identified.
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Affiliation(s)
- Anthony N. Cutrupi
- Northcott Neuroscience LaboratoryANZAC Research InstituteSydneyNSWAustralia
- Sydney Medical SchoolUniversity of SydneySydneyNSWAustralia
| | - Megan H. Brewer
- Northcott Neuroscience LaboratoryANZAC Research InstituteSydneyNSWAustralia
- Sydney Medical SchoolUniversity of SydneySydneyNSWAustralia
| | - Garth A. Nicholson
- Northcott Neuroscience LaboratoryANZAC Research InstituteSydneyNSWAustralia
- Sydney Medical SchoolUniversity of SydneySydneyNSWAustralia
- Molecular Medicine LaboratoryConcord HospitalSydneyNSWAustralia
| | - Marina L. Kennerson
- Northcott Neuroscience LaboratoryANZAC Research InstituteSydneyNSWAustralia
- Sydney Medical SchoolUniversity of SydneySydneyNSWAustralia
- Molecular Medicine LaboratoryConcord HospitalSydneyNSWAustralia
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Del Pino M, Andrés A, Bernabéu AÁ, de Juan-Rivera J, Fernández E, de Dios García Díaz J, Hernández D, Luño J, Fernández IM, Paniagua J, Posada de la Paz M, Rodríguez-Pérez JC, Santamaría R, Torra R, Ambros JT, Vidau P, Torregrosa JV. Fabry Nephropathy: An Evidence-Based Narrative Review. Kidney Blood Press Res 2018; 43:406-421. [PMID: 29558749 DOI: 10.1159/000488121] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 03/09/2018] [Indexed: 11/19/2022] Open
Abstract
Fabry disease (FD) is a rare, X-linked disorder caused by mutations in the GLA gene encoding the enzyme α-galactosidase A. Complete or partial deficiency in this enzyme leads to intracellular accumulation of globotriaosylceramide (Gb3) and other glycosphingolipids in many cell types throughout the body, including the kidney. Progressive accumulation of Gb3 in podocytes, endothelial cells, epithelial cells, and tubular cells contribute to the renal symptoms of FD, which manifest as proteinuria and reduced glomerular filtration rate leading to renal insufficiency. A correct diagnosis of FD, although challenging, has considerable implications regarding treatment, management, and counseling. The diagnosis may be confirmed by demonstrating the enzyme deficiency in males and by identifying the specific GLA gene mutation in male and female patients. Treatment with enzyme replacement therapy, as part of the therapeutic strategy to prevent complications of the disease, may be beneficial in stabilizing renal function or slowing its decline, particularly in the early stages of the disease. Emergent treatments for FD include the recently approved chaperone molecule migalastat for patients with amenable mutations. The objective of this report is to provide an updated overview on Fabry nephropathy, with a focus on the most relevant aspects of its epidemiology, diagnosis, pathophysiology, and treatment options.
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Affiliation(s)
- María Del Pino
- Nephrology Service, Hospital Torrecardenas, Almeria, Spain
| | - Amado Andrés
- Division of Nephrology, Instituto de Investigación Hospital 12 de Octubre, Universidad Complutense de Madrid, Madrid, Spain
| | | | | | - Elvira Fernández
- Unit for the Detection and Treatment of Atherothrombotic Diseases (UDETMA), Nephrology Department, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, Lleida, Spain
| | - Juan de Dios García Díaz
- Clinical Genetics Unit, Department of Internal Medicine University Hospital Príncipe de Asturias Alcalá de Henares, Madrid, Spain
| | - Domingo Hernández
- Nephrology Department, Carlos Haya Regional University Hospital and University of Málaga, IBIMA, REDinREN (RD16/0009/0006), Málaga, Spain
| | - José Luño
- Nephrology Service, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | | | - José Paniagua
- Nephrology Service, Hospital El Bierzo, Ponferrada, Spain
| | - Manuel Posada de la Paz
- Institute of Rare Diseases Research, SpainRDR and CIBERER, Institute of Health Carlos III, Madrid, Spain
| | - José Carlos Rodríguez-Pérez
- University Hospital of Gran Canaria Dr. Negrin, Universidad de Las Palmas de Gran Canaria (Las Palmas), Las Palmas, Spain
| | - Rafael Santamaría
- Nephrology Department, Reina Sofia University Hospital, Maimonides Institute for Research in Biomedicine of Cordoba and University of Cordoba, Red de Investigación Renal (RedinRen), Cordoba, Spain
| | - Roser Torra
- Inherited Kidney Disorders, Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, REDinREN, Instituto de Investigación Carlos III, Barcelona, Spain
| | - Joan Torras Ambros
- Nephrology Service, Experimental Nephrology Laboratory, Hospital de Bellvitge, IDIBELL, Barcelona, Spain
| | - Pedro Vidau
- Nephrology Service, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Josep-Vicent Torregrosa
- Nephrology and Renal Transplant Department, Hospital Clinic, University of Barcelona, RedInRen, Barcelona, Spain
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Abstract
The majority of rare diseases affect children, most of whom have an underlying genetic cause for their condition. However, making a molecular diagnosis with current technologies and knowledge is often still a challenge. Paediatric genomics is an immature but rapidly evolving field that tackles this issue by incorporating next-generation sequencing technologies, especially whole-exome sequencing and whole-genome sequencing, into research and clinical workflows. This complex multidisciplinary approach, coupled with the increasing availability of population genetic variation data, has already resulted in an increased discovery rate of causative genes and in improved diagnosis of rare paediatric disease. Importantly, for affected families, a better understanding of the genetic basis of rare disease translates to more accurate prognosis, management, surveillance and genetic advice; stimulates research into new therapies; and enables provision of better support.
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46
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Pang SYY, Teo KC, Hsu JS, Chang RSK, Li M, Sham PC, Ho SL. The role of gene variants in the pathogenesis of neurodegenerative disorders as revealed by next generation sequencing studies: a review. Transl Neurodegener 2017; 6:27. [PMID: 29046784 PMCID: PMC5639582 DOI: 10.1186/s40035-017-0098-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/02/2017] [Indexed: 12/13/2022] Open
Abstract
The clinical diagnosis of neurodegenerative disorders based on phenotype is difficult in heterogeneous conditions with overlapping symptoms. It does not take into account the disease etiology or the highly variable clinical course even amongst patients diagnosed with the same disorder. The advent of next generation sequencing (NGS) has allowed for a system-wide, unbiased approach to identify all gene variants in the genome simultaneously. With the plethora of new genes being identified, genetic rather than phenotype-based classification of Mendelian diseases such as spinocerebellar ataxia (SCA), hereditary spastic paraplegia (HSP) and Charcot-Marie-Tooth disease (CMT) has become widely accepted. It has also become clear that gene variants play a role in common and predominantly sporadic neurodegenerative diseases such as Parkinson’s disease (PD) and amyotrophic lateral sclerosis (ALS). The observation of pleiotropy has emerged, with mutations in the same gene giving rise to diverse phenotypes, which further increases the complexity of phenotype-genotype correlation. Possible mechanisms of pleiotropy include different downstream effects of different mutations in the same gene, presence of modifier genes, and oligogenic inheritance. Future directions include development of bioinformatics tools and establishment of more extensive public genotype/phenotype databases to better distinguish deleterious gene variants from benign polymorphisms, translation of genetic findings into pathogenic mechanisms through in-vitro and in-vivo studies, and ultimately finding disease-modifying therapies for neurodegenerative disorders.
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Affiliation(s)
- Shirley Yin-Yu Pang
- Division of Neurology, Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, People's Republic of China
| | - Kay-Cheong Teo
- Division of Neurology, Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, People's Republic of China
| | - Jacob Shujui Hsu
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, People's Republic of China
| | - Richard Shek-Kwan Chang
- Division of Neurology, Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, People's Republic of China
| | - Miaoxin Li
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, People's Republic of China.,Department of Medical Genetics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People's Republic of China.,Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou, People's Republic of China
| | - Pak-Chung Sham
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong, People's Republic of China
| | - Shu-Leong Ho
- Division of Neurology, Department of Medicine, Queen Mary Hospital, University of Hong Kong, Hong Kong, People's Republic of China
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