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Tenorio RB, Camargo CHF, Donis KC, Almeida CCB, Teive HAG. Diagnostic Yield of NGS Tests for Hereditary Ataxia: a Systematic Review. CEREBELLUM (LONDON, ENGLAND) 2024; 23:1552-1565. [PMID: 37950147 DOI: 10.1007/s12311-023-01629-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
Next-generation sequencing (NGS), comprising targeted panels (TP), exome sequencing (ES), and genome sequencing (GS) became robust clinical tools for diagnosing hereditary ataxia (HA). Determining their diagnostic yield (DY) is crucial for optimal clinical decision-making. We conducted a comprehensive systematic literature review on the DY of NGS tests for HA. We searched PubMed and Embase databases for relevant studies between 2016 and 2022 and manually examined reference lists of relevant reviews. Eligible studies described the DY of NGS tests in patients with ataxia as a significant feature. Data from 33 eligible studies showed a median DY of 43% (IQR = 9.5-100%). The median DY for TP and ES was 46% and 41.9%, respectively. Higher DY was associated with specific phenotype selection, such as episodic ataxia at 68.35% and early and late onset of ataxia at 46.4% and 54.4%. Parental consanguinity had a DY of 52.4% (p = 0.009), and the presumed autosomal recessive (AR) inheritance pattern showed 62.5%. There was a difference between the median DY of studies that performed targeted sequencing (tandem repeat expansion, TRE) screening and those that did not (p = 0.047). A weak inverse correlation was found between DY and the extent of previous genetic investigation (rho = - 0.323; p = 0.065). The most common genes were CACNA1A and SACS. DY was higher for presumed AR inheritance pattern, positive family history, and parental consanguinity. ES appears more advantageous due to the inclusion of rare genes that might be excluded in TP.
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Affiliation(s)
- Renata Barreto Tenorio
- Postgraduate Program in Internal Medicine, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil.
| | - Carlos Henrique F Camargo
- Postgraduate Program in Internal Medicine, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil
- Movement Disorders Sector, Neurology Service, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Karina Carvalho Donis
- Medical Genetics Service, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | | | - Hélio A G Teive
- Postgraduate Program in Internal Medicine, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil
- Movement Disorders Sector, Neurology Service, Internal Medicine Department, Hospital de Clínicas, Federal University of Paraná, Curitiba, Paraná, Brazil
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Ghorbani F, Alimohamed MZ, Vilacha JF, Van Dijk KK, De Boer-Bergsma J, Fokkens MR, Lemmink H, Sijmons RH, Sikkema-Raddatz B, Groves MR, Verschuuren-Bemelmans CC, Verbeek DS, Van Diemen CC, Westers H. Feasibility of Follow-Up Studies and Reclassification in Spinocerebellar Ataxia Gene Variants of Unknown Significance. Front Genet 2022; 13:782685. [PMID: 35401678 PMCID: PMC8990126 DOI: 10.3389/fgene.2022.782685] [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: 09/24/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Spinocerebellar ataxia (SCA) is a heterogeneous group of neurodegenerative disorders with autosomal dominant inheritance. Genetic testing for SCA leads to diagnosis, prognosis and risk assessment for patients and their family members. While advances in sequencing and computing technologies have provided researchers with a rapid expansion in the genetic test content that can be used to unravel the genetic causes that underlie diseases, the large number of variants with unknown significance (VUSes) detected represent challenges. To minimize the proportion of VUSes, follow-up studies are needed to aid in their reclassification as either (likely) pathogenic or (likely) benign variants. In this study, we addressed the challenge of prioritizing VUSes for follow-up using (a combination of) variant segregation studies, 3D protein modeling, in vitro splicing assays and functional assays. Of the 39 VUSes prioritized for further analysis, 13 were eligible for follow up. We were able to reclassify 4 of these VUSes to LP, increasing the molecular diagnostic yield by 1.1%. Reclassification of VUSes remains difficult due to limited possibilities for performing variant segregation studies in the classification process and the limited availability of routine functional tests.
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Affiliation(s)
- Fatemeh Ghorbani
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Mohamed Z. Alimohamed
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Shree Hindu Mandal Hospital, Dar es Salaam, Tanzania
| | - Juliana F. Vilacha
- Groningen Biomolecular Sciences and Biotechnology Institute, Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Krista K. Van Dijk
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Jelkje De Boer-Bergsma
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Michiel R. Fokkens
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Henny Lemmink
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Rolf H. Sijmons
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Matthew R. Groves
- Structural Biology in Drug Design, Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | | | - Dineke S. Verbeek
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- *Correspondence: Dineke S. Verbeek,
| | - Cleo C. Van Diemen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Helga Westers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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Wan N, Chen Z, Wan L, Yuan H, Tang Z, Liu M, Peng Y, Peng L, Lei L, Xie Y, Deng Q, Wang S, Wang C, Peng H, Hou X, Shi Y, Long Z, Qiu R, Xia K, Tang B, Jiang H. Genetic etiology of a Chinese ataxia cohort: Expanding the mutational spectrum of hereditary ataxias. Parkinsonism Relat Disord 2021; 89:120-127. [PMID: 34284285 DOI: 10.1016/j.parkreldis.2021.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 06/02/2021] [Accepted: 07/08/2021] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Hereditary ataxias demonstrate a high degree of clinical and genetic heterogeneity. Understanding the genetic etiology of hereditary ataxias is crucial for genetic counseling and clinical management. METHODS The clinical and genetic data of patients with familial or sporadic ataxias who referred to our tertiary medical center were retrospectively analyzed. Probands in this study underwent SCA repeat expansion panel firstly to screen for repeat expansion SCAs; those with negative results had NGS-targeted panels or WES testing to detect conventional mutations. RESULTS A total of 223 patients were enrolled from 206 families. 5 kinds of coexisting SCA repeat expansions were observed (SCA3/SCA17, SCA3/SCA8, SCA2/SCA8, SCA3/SCA12 and SCA8/SCA12) in 12 patients from 8 families, among which SCA2/SCA8, SCA8/SCA12 and SCA3/SCA12 were reported for the first time. The coexistence of expanded SCA3 with SCA17 alleles was the most common in our study. NGS identified pathogenic/likely pathogenic variants in 12 ataxia causative genes in 13 probands. Spastic paraplegia ataxia was the most common diagnosis. Six novel mutations were detected in five ataxia-related genes. CONCLUSION Coexistence may not specific to a certain SCA subtype and the frequency might have been underestimated before. SCA repeat expansion panel should be considered in patients with overlapping SCA features. In addition, our study broadened the conventional mutation spectrum in ataxia-related genes. These results facilitate a better understanding of the genetic basis for hereditary ataxias.
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Affiliation(s)
- Na Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Linlin Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongyu Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhichao Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Mingjie Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yun Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Linliu Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lijing Lei
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yue Xie
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qi Deng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Shang Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Chunrong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Huirong Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xuan Hou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuting Shi
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhe Long
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Rong Qiu
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Kun Xia
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China; Hunan Key Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China; Laboratory of Medical Genetics, Central South University, Changsha, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China; Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China; Laboratory of Medical Genetics, Central South University, Changsha, China; School of Basic Medical Science, Central South University, Changsha, China.
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4
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da Graça FF, Peluzzo TM, Bonadia LC, Martinez ARM, Diniz de Lima F, Pedroso JL, Barsottini OGP, Gama MTD, Akçimen F, Dion PA, Rouleau GA, Marques W, França MC. Diagnostic Yield of Whole Exome Sequencing for Adults with Ataxia: a Brazilian Perspective. THE CEREBELLUM 2021; 21:49-54. [PMID: 33956305 DOI: 10.1007/s12311-021-01268-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/07/2021] [Indexed: 12/14/2022]
Abstract
Previous studies using whole exome sequencing (WES) have shown that a significant proportion of adult patients with undiagnosed ataxia in European and North American cohorts have a known genetic cause. Little is known about the diagnostic yield of WES in non-Caucasian ataxic populations. Herein, we used WES to investigate a Brazilian cohort of 76 adult patients with idiopathic ataxia previously screened for trinucleotide expansions in known ataxia genes. We collected clinical and radiological data from each patient. WES was performed following standard procedures. Only variants labeled as pathogenic or likely pathogenic according to American college of medical genetics and genomics (ACMG) criteria were retrieved. We determined the diagnostic yield of WES for the whole cohort and also for subgroups defined according to presence or not of pyramidal signs, peripheral neuropathy, and cerebellar atrophy. There were 41 women and 35 men. Mean age at testing was 48 years. Pyramidal signs, peripheral neuropathy, tremor, and cerebellar atrophy were found in 38.1%, 13.1%, 10.5%, and 68.3% of all subjects, respectively. Diagnostic yield of WES was 35.5%. Thirty-six distinct mutations were found in 20 different genes, determining the diagnosis of 18 autosomal recessive and 9 autosomal dominant ataxias. SACS and SPG7 were the most frequently found underlying genes. WES performed better in the subgroup with vs the subgroup without spasticity (p = 0.005). WES was diagnostic in 35.5% of cases of the Brazilian cohort of ataxia cases. These results have implications for diagnosis, genetic counseling and eventually treatment.
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Affiliation(s)
- Felipe Franco da Graça
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Rua Tessália Vieira de Camargo, 126. Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil
| | - Thiago M Peluzzo
- Department of Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Luciana Cardoso Bonadia
- Department of Medical Genetics, School of Medical Sciences, University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Alberto Rolim Muro Martinez
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Rua Tessália Vieira de Camargo, 126. Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil
| | - Fabricio Diniz de Lima
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Rua Tessália Vieira de Camargo, 126. Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil
| | - José Luiz Pedroso
- Ataxia Unit, Department of Neurology, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Orlando G P Barsottini
- Ataxia Unit, Department of Neurology, Federal University of São Paulo (UNIFESP), São Paulo, SP, Brazil
| | | | - Fulya Akçimen
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada
| | - Patrick A Dion
- Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, QC, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada
| | - Wilson Marques
- Department of Neuroscience and Behavioural Science, School of Medicine, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Marcondes Cavalcante França
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), Rua Tessália Vieira de Camargo, 126. Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-887, Brazil.
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5
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Salinas V, Vega P, Marsili L, Pérez‐Maturo J, Martínez N, Zavala L, González‐Morón D, Medina N, Rodriguez‐Quiroga SA, Amartino H, Maxit C, Sturchio A, Grimberg B, Duque K, Comas B, Silva W, Consalvo D, Sfaello I, Espay AJ, Kauffman MA. The odyssey of complex neurogenetic disorders: From undetermined to positive. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:876-884. [DOI: 10.1002/ajmg.c.31848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/14/2020] [Accepted: 09/27/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Valeria Salinas
- Neurogenetics Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
- Faculty of Biomedical Sciences, Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute‐CONICET Universidad Austral Buenos Aires Argentina
| | - Patricia Vega
- Neurogenetics Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
| | - Luca Marsili
- UC Gardner Neuroscience Institute, Department of Neurology, Gardner Center for Parkinson's disease and Movement Disorders University of Cincinnati Ohio
| | - Josefina Pérez‐Maturo
- Neurogenetics Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
- Faculty of Biomedical Sciences, Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute‐CONICET Universidad Austral Buenos Aires Argentina
| | - Nerina Martínez
- Neurogenetics Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
| | - Lucia Zavala
- Neurogenetics Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
| | | | - Nancy Medina
- Neurogenetics Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
| | | | - Hernán Amartino
- Pediatric Neurology Unit Hospital Universitario Austral Buenos Aires Argentina
| | - Clarisa Maxit
- Pediatric Neurology Unit, Hospital Italiano de Buenos Aires Buenos Aires Argentina
| | - Andrea Sturchio
- UC Gardner Neuroscience Institute, Department of Neurology, Gardner Center for Parkinson's disease and Movement Disorders University of Cincinnati Ohio
| | - Barbara Grimberg
- UC Gardner Neuroscience Institute, Department of Neurology, Gardner Center for Parkinson's disease and Movement Disorders University of Cincinnati Ohio
| | - Kevin Duque
- UC Gardner Neuroscience Institute, Department of Neurology, Gardner Center for Parkinson's disease and Movement Disorders University of Cincinnati Ohio
| | - Betiana Comas
- Neurology Unit, Hospital de la Baxada “Dra. Teresa Ratto” Paraná Entre Ríos Argentina
| | - Walter Silva
- Pediatric Neurology Unit, Hospital Italiano de Buenos Aires Buenos Aires Argentina
| | - Damián Consalvo
- Neurology Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
| | - Ignacio Sfaello
- CETES, Instituto de Neurología Infanto‐Juvenil Córdoba Argentina
| | - Alberto J. Espay
- UC Gardner Neuroscience Institute, Department of Neurology, Gardner Center for Parkinson's disease and Movement Disorders University of Cincinnati Ohio
| | - Marcelo A. Kauffman
- Neurogenetics Unit, Hospital JM Ramos Mejía Buenos Aires Argentina
- Faculty of Biomedical Sciences, Precision Medicine and Clinical Genomics Group, Translational Medicine Research Institute‐CONICET Universidad Austral Buenos Aires Argentina
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