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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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NGS in Hereditary Ataxia: When Rare Becomes Frequent. Int J Mol Sci 2021; 22:ijms22168490. [PMID: 34445196 PMCID: PMC8395181 DOI: 10.3390/ijms22168490] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 12/17/2022] Open
Abstract
The term hereditary ataxia (HA) refers to a heterogeneous group of neurological disorders with multiple genetic etiologies and a wide spectrum of ataxia-dominated phenotypes. Massive gene analysis in next-generation sequencing has entered the HA scenario, broadening our genetic and clinical knowledge of these conditions. In this study, we employed a targeted resequencing panel (TRP) in a large and highly heterogeneous cohort of 377 patients with a clinical diagnosis of HA, but no molecular diagnosis on routine genetic tests. We obtained a positive result (genetic diagnosis) in 33.2% of the patients, a rate significantly higher than those reported in similar studies employing TRP (average 19.4%), and in line with those performed using exome sequencing (ES, average 34.6%). Moreover, 15.6% of the patients had an uncertain molecular diagnosis. STUB1, PRKCG, and SPG7 were the most common causative genes. A comparison with published literature data showed that our panel would have identified 97% of the positive cases reported in previous TRP-based studies and 92% of those diagnosed by ES. Proper use of multigene panels, when combined with detailed phenotypic data, seems to be even more efficient than ES in clinical practice.
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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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Cheng HL, Dong HL, Liu DS, Ni W, Ma Y, Yang L, Du YC, Chen DF, Dong Y, Wu ZY. TGM6 might not be a specific causative gene for spinocerebellar ataxia resulting from genetic analysis and functional study. Gene 2021; 779:145495. [PMID: 33588035 DOI: 10.1016/j.gene.2021.145495] [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: 12/10/2020] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
OBJECTIVE To investigate whether TGM6 is a specific causative gene for spinocerebellar ataxia type 35 (SCA35). MATERIALS AND METHODS The next-generation sequencing (NGS) data consisted of 47 SCA, 762 non-SCA patients and 2827 normal controls were analyzed. The allele frequencies of low frequent and deleterious TGM6 variants were compared. Functional studies were performed in five widely distributed variants (V314M, R342Q, P347L, V391M, L517W). RESULTS Two TGM6 detrimental variants were identified in one SCA patient, 14 in non-SCA patients and 43 in normal controls, the allele frequencies of TGM6 variants did not differ among the SCA and other controls. Seven reported pathogenic variants (c.7 + 1G > T, c.331C > T, c.1171G > A, c.1478C > T, c.1528G > C, c.1550 T > G and c.1722_1724delAGA) were identified in patients with various neurologic diseases or normal controls. All the 5 widely distributed variants led to destabilization and significantly reduction of enzymatic activity of TG6 as the reported pathogenic mutations. CONCLUSIONS TGM6 might not be a specific causative gene for SCA35, the relevant clinical consult or diagnostic should be pay more attention.
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Affiliation(s)
- Hao-Ling Cheng
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China; Department of Neurology, First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Hai-Lin Dong
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - De-Shan Liu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Wang Ni
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yin Ma
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Lu Yang
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi-Chu Du
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Dian-Fu Chen
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Dong
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China.
| | - Zhi-Ying Wu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China.
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Giunti P, Mantuano E, Frontali M. Episodic Ataxias: Faux or Real? Int J Mol Sci 2020; 21:ijms21186472. [PMID: 32899446 PMCID: PMC7555854 DOI: 10.3390/ijms21186472] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 11/22/2022] Open
Abstract
The term Episodic Ataxias (EA) was originally used for a few autosomal dominant diseases, characterized by attacks of cerebellar dysfunction of variable duration and frequency, often accompanied by other ictal and interictal signs. The original group subsequently grew to include other very rare EAs, frequently reported in single families, for some of which no responsible gene was found. The clinical spectrum of these diseases has been enormously amplified over time. In addition, episodes of ataxia have been described as phenotypic variants in the context of several different disorders. The whole group is somewhat confused, since a strong evidence linking the mutation to a given phenotype has not always been established. In this review we will collect and examine all instances of ataxia episodes reported so far, emphasizing those for which the pathophysiology and the clinical spectrum is best defined.
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Affiliation(s)
- Paola Giunti
- Laboratory of Neurogenetics, Department of Molecular Neuroscience, UCL Institute of Neurology, London WC2N 5DU, UK
- Correspondence: (P.G.); (M.F.)
| | - Elide Mantuano
- Laboratory of Neurogenetics, Institute of Translational Pharmacology, National Research Council of Italy, 00133 Rome, Italy;
| | - Marina Frontali
- Laboratory of Neurogenetics, Institute of Translational Pharmacology, National Research Council of Italy, 00133 Rome, Italy;
- Correspondence: (P.G.); (M.F.)
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Chen C, Dong H, Wei Q, Li L, Yu H, Li J, Liu G, Li H, Bai G, Ma H, Wu Z. Genetic spectrum and clinical profiles in a southeast Chinese cohort of Charcot‐Marie‐Tooth disease. Clin Genet 2019; 96:439-448. [PMID: 31372974 DOI: 10.1111/cge.13616] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/19/2019] [Accepted: 07/23/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Cong‐Xin Chen
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang ProvinceZhejiang University School of Medicine Hangzhou China
- Department of Neurology and Institute of NeurologyFirst Affiliated Hospital, Fujian Medical University Fuzhou China
| | - Hai‐Lin Dong
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang ProvinceZhejiang University School of Medicine Hangzhou China
| | - Qiao Wei
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang ProvinceZhejiang University School of Medicine Hangzhou China
| | - Li‐Xi Li
- Department of Neurology and Institute of NeurologyHuashan Hospital, Shanghai Medical College, Fudan University Shanghai China
| | - Hao Yu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang ProvinceZhejiang University School of Medicine Hangzhou China
| | - Jia‐Qi Li
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang ProvinceZhejiang University School of Medicine Hangzhou China
| | - Gong‐Lu Liu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang ProvinceZhejiang University School of Medicine Hangzhou China
| | - Hong‐Fu Li
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang ProvinceZhejiang University School of Medicine Hangzhou China
| | - Ge Bai
- Institute of Neuroscience and Key Laboratory of Medical Neurobiology of Zhejiang ProvinceZhejiang University School of Medicine Hangzhou China
| | - Huan Ma
- Institute of Neuroscience and Key Laboratory of Medical Neurobiology of Zhejiang ProvinceZhejiang University School of Medicine Hangzhou China
| | - Zhi‐Ying Wu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, and Key Laboratory of Medical Neurobiology of Zhejiang ProvinceZhejiang University School of Medicine Hangzhou China
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Finsterer J, Zarrouk‐Mahjoub S. Mitochondrial ataxia is genetically and phenotypically heterogeneous. CNS Neurosci Ther 2018; 24:1301-1302. [PMID: 29998495 PMCID: PMC6490036 DOI: 10.1111/cns.13031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
| | - Sinda Zarrouk‐Mahjoub
- Pasteur Institute of TunisUniversity of Tunis El Manar and Genomics PlatformTunisTunisia
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Dong HL, Ma Y, Li QF, Du YC, Yang L, Chen S, Wu ZY. Genetic and clinical features of Chinese patients with mitochondrial ataxia identified by targeted next-generation sequencing. CNS Neurosci Ther 2018; 25:21-29. [PMID: 29756269 DOI: 10.1111/cns.12972] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 12/17/2022] Open
Abstract
AIM To characterize the mutations in mitochondrial DNA (mtDNA) and mitochondrion-related nuclear genes (nDNA), and clinical features in Chinese patients with mitochondrial ataxia. METHODS Targeted next-generation sequencing (NGS) technology was performed to screen the whole mtDNA sequence and nDNA genes in a cohort of 33 unrelated ataxia patients. RESULTS A total of 5 pedigrees were finally genetically diagnosed as mitochondrial ataxia, with 3 pathogenic mutations (m.8344A>G, m.9176T>C, and m.9185T>C), one likely pathogenic mutation (m.3995A>G) in mtDNA, and one pathogenic mutation (c.1159_1162dupAAGT, p.Ser388Terfs) in PDHA1. The prevalence of mitochondrial ataxia in our patient cohort is 15.2%. In addition, all 4 patients with mtDNA mutations experienced symptoms of ataxia with age at onset ranging from 12 to 39 years (21 ± 12.2) and developed extrapyramidal symptoms during the disease course. One male patient with pyruvate dehydrogenase deficiency showed an acute intermittent ataxia phenotype. CONCLUSIONS Our results implicate that mitochondrial ataxia might not be as rare in Chinese as previously assumed. This study firstly defines the mutations of mitochondrial ataxia in a Chinese population by targeted NGS, which broadens the clinical spectrum of mtDNA mutations and highlights the importance of screening mtDNA and nDNA mutations among undefined ataxia patients.
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Affiliation(s)
- Hai-Lin Dong
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yin Ma
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Quan-Fu Li
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi-Chu Du
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Lu Yang
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Sheng Chen
- Department of Neurology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhi-Ying Wu
- Department of Neurology and Research Center of Neurology in Second Affiliated Hospital, Key Laboratory of Medical Neurobiology of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
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