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Chengyan L, Chupeng X, You W, Yinhui C, Binglong H, Dang A, Ling L, Chuan T. Identification of genetic causes in children with unexplained epilepsy based on trio-whole exome sequencing. Clin Genet 2024; 106:140-149. [PMID: 38468460 DOI: 10.1111/cge.14519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
Genotype and clinical phenotype analyses of 128 children were performed based on whole exome sequencing (WES), providing a reference for the provision of genetic counseling and the precise diagnosis and treatment of epilepsy. A total of 128 children with unexplained epilepsy were included in this study, and all their clinical data were analyzed. The children's treatments, epilepsy control, and neurodevelopmental levels were regularly followed up every 3 months. The genetic diagnostic yield of the 128 children with epilepsy is 50.8%, with an SNV diagnostic yield of 39.8% and a CNV diagnostic yield of 12.5%. Among the 128 children with epilepsy, 57.0% had onset of epilepsy in infancy, 25.8% have more than two clinical seizure forms, 62.5% require two or more anti-epileptic drug treatments, and 72.7% of the children have varying degrees of psychomotor development retardation. There are significant differences between ages of onset, neurodevelopmental levels and the presence of drug resistance in the genetic diagnostic yield (all p < 0.05). The 52 pathogenic/likely pathogenic SNVs involve 31 genes, with genes encoding ion channels having the largest number of mutations (30.8%). There were 16 cases of pathogenic/possibly pathogenic CNVs, among which the main proportions of CNVs were located in chromosome 15 and chromosome 16. Trio-WES is an essential tool for the genetic diagnosis of unexplained epilepsy, with a genetic diagnostic yield of up to 50.8%. Early genetic testing can provide an initiate appropriate therapies and accurate molecular diagnosis.
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Affiliation(s)
- Li Chengyan
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Xue Chupeng
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
- Department of Pediatrics, Shantou Central Hospital, Shantou, People's Republic of China
| | - Wang You
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Chen Yinhui
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Huang Binglong
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Ao Dang
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Liu Ling
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Tian Chuan
- Department of Pediatrics, Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
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Macdonald-Laurs E, Dzau W, Warren AEL, Coleman M, Mignone C, Stephenson SEM, Howell KB. Identification and treatment of surgically-remediable causes of infantile epileptic spasms syndrome. Expert Rev Neurother 2024; 24:661-680. [PMID: 38814860 DOI: 10.1080/14737175.2024.2360117] [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: 04/01/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
INTRODUCTION Infantile epileptic spasms syndrome (IESS) is a common developmental and epileptic encephalopathy with poor long-term outcomes. A substantial proportion of patients with IESS have a potentially surgically remediable etiology. Despite this, epilepsy surgery is underutilized in this patient group. Some surgically remediable etiologies, such as focal cortical dysplasia and malformation of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE), are under-diagnosed in infants and young children. Even when a surgically remediable etiology is recognised, for example, tuberous sclerosis or focal encephalomalacia, epilepsy surgery may be delayed or not considered due to diffuse EEG changes, unclear surgical boundaries, or concerns about operating in this age group. AREAS COVERED In this review, the authors discuss the common surgically remediable etiologies of IESS, their clinical and EEG features, and the imaging techniques that can aid in their diagnosis. They then describe the surgical approaches used in this patient group, and the beneficial impact that early epilepsy surgery can have on developing brain networks. EXPERT OPINION Epilepsy surgery remains underutilized even when a potentially surgically remediable cause is recognized. Overcoming the barriers that result in under-recognition of surgical candidates and underutilization of epilepsy surgery in IESS will improve long-term seizure and developmental outcomes.
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Affiliation(s)
- Emma Macdonald-Laurs
- Department of Neurology, The Royal Children's Hospital, Parkville, VIC, Australia
- Neurosciences Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Winston Dzau
- Neurosciences Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Aaron E L Warren
- Department of Medicine (Austin Health), The University of Melbourne, Melbourne, VIC, Australia
- Brigham and Women's Hospital, Harvard Medical School, Massachusetts, USA
| | - Matthew Coleman
- Neurosciences Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Cristina Mignone
- Department of Medical Imaging, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Sarah E M Stephenson
- Neurosciences Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Katherine B Howell
- Department of Neurology, The Royal Children's Hospital, Parkville, VIC, Australia
- Neurosciences Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
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Watson S, Ngo KJ, Stevens HA, Wong DY, Kim J, Song Y, Han B, Hyun SI, Khang R, Ryu SW, Lee E, Seo G, Lee H, Lajonchere C, Fogel BL. Cross-Sectional Analysis of Exome Sequencing Diagnosis in Patients With Neurologic Phenotypes Facing Barriers to Clinical Testing. Neurol Genet 2024; 10:e200133. [PMID: 38617022 PMCID: PMC11010248 DOI: 10.1212/nxg.0000000000200133] [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: 10/25/2023] [Accepted: 01/19/2024] [Indexed: 04/16/2024]
Abstract
Background and Objectives Exome sequencing (ES) demonstrates a 20-50 percent diagnostic yield for patients with a suspected monogenic neurologic disease. Despite the proven efficacy in achieving a diagnosis for such patients, multiple barriers for obtaining exome sequencing remain. This study set out to assess the efficacy of ES in patients with primary neurologic phenotypes who were appropriate candidates for testing but had been unable to pursue clinical testing. Methods A total of 297 patients were identified from the UCLA Clinical Neurogenomics Research Center Biobank, and ES was performed, including bioinformatic assessment of copy number variation and repeat expansions. Information regarding demographics, clinical indication for ES, and reason for not pursuing ES clinically were recorded. To assess diagnostic efficacy, variants were interpreted by a multidisciplinary team of clinicians, bioinformaticians, and genetic counselors in accordance with the American College of Medical Genetics and Genomics variant classification guidelines. We next examined the specific barriers to testing for these patients, including how frequently insurance-related barriers such as coverage denials and inadequate coverage of cost were obstacles to pursuing exome sequencing. Results The cohort primarily consisted of patients with sporadic conditions (n = 126, 42.4%) of adult-onset (n = 239, 80.5%). Cerebellar ataxia (n = 225, 75.8%) was the most common presenting neurologic phenotype. Our study found that in this population of mostly adult patients with primary neurologic phenotypes that were unable to pursue exome sequencing clinically, 47 (15.8%) had diagnostic results while an additional 24 patients (8.1%) had uncertain results. Of the 297 patients, 206 were initially recommended for clinical exome but 88 (42.7%) could not pursue ES because of insurance barriers, of whom 14 (15.9%) had diagnostic findings, representing 29.8% of all patients with diagnostic findings. In addition, the incorporation of bioinformatic repeat expansion testing was valuable, identifying a total of 8 pathogenic repeat expansions (17.0% of all diagnostic findings) including 3 of the common spinocerebellar ataxias and 2 patients with Huntington disease. Discussion These findings underscore the importance and value of clinical ES as a diagnostic tool for neurogenetic disease and highlight key barriers that prevent patients from receiving important clinical information with potential treatment and psychosocial implications for patients and family members.
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Affiliation(s)
- Sonya Watson
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
| | - Kathie J Ngo
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
| | - Hannah A Stevens
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
| | - Darice Y Wong
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
| | - Jihye Kim
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
| | - Yongjun Song
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
| | - Beomman Han
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
| | - Seong-In Hyun
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
| | - Rin Khang
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
| | - Seung Woo Ryu
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
| | - Eugene Lee
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
| | - Gohun Seo
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
| | - Hane Lee
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
| | - Clara Lajonchere
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
| | - Brent L Fogel
- From the Department of Neurology (S.W., K.J.N., H.A.S., D.Y.W., C.L., B.L.F.), the Clinical Neurogenomics Research Center (S.W., H.A.S., D.Y.W., C.L., B.L.F.), the Institute for Precision Health (S.W., C.L., B.L.F.), and the Department of Human Genetics (S.W., B.L.F.), David Geffen School of Medicine, University of California at Los Angeles (UCLA); 3billion, Inc. (J.K., Y.S., B.H., S.-I.H., R.K., S.W.R., E.L., G.S., H.L.)
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Kim SH, Seo J, Kwon SS, Teng LY, Won D, Shin S, Lee JS, Lee ST, Choi JR, Kang HC. Common genes and recurrent causative variants in 957 Asian patients with pediatric epilepsy. Epilepsia 2024; 65:766-778. [PMID: 38073125 DOI: 10.1111/epi.17857] [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: 08/14/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVE We aimed to identify common genes and recurrent causative variants in a large group of Asian patients with different epilepsy syndromes and subgroups. METHODS Patients with unexplained pediatric-onset epilepsy were identified from the in-house Severance Neurodevelopmental Disorders and Epilepsy Database. All patients underwent either exome sequencing or multigene panels from January 2017 to December 2019, at Severance Children's Hospital in Korea. Clinical data were extracted from the medical records. RESULTS Of the 957 patients studied, 947 (99.0%) were Korean and 570 were male (59.6%). The median age at testing was 4.91 years (interquartile range, 1.53-9.39). The overall diagnostic yield was 32.4% (310/957). Clinical exome sequencing yielded a diagnostic rate of 36.9% (134/363), whereas the epilepsy panel yielded a diagnostic rate of 29.9% (170/569). Diagnostic yield differed across epilepsy syndromes. It was high in Dravet syndrome (87.2%, 41/47) and early infantile developmental epileptic encephalopathy (60.7%, 17/28), but low in West syndrome (21.8%, 34/156) and myoclonic-atonic epilepsy (4.8%, 1/21). The most frequently implicated genes were SCN1A (n = 49), STXBP1 (n = 15), SCN2A (n = 14), KCNQ2 (n = 13), CDKL5 (n = 11), CHD2 (n = 9), SLC2A1 (n = 9), PCDH19 (n = 8), MECP2 (n = 6), SCN8A (n = 6), and PRRT2 (n = 5). The recurrent genetic abnormalities included 15q11.2 deletion/duplication (n = 9), Xq28 duplication (n = 5), PRRT2 deletion (n = 4), MECP2 duplication (n = 3), SCN1A, c.2556+3A>T (n = 3), and 2q24.3 deletion (n = 3). SIGNIFICANCE Here we present the results of a large-scale study conducted in East Asia, where we identified several common genes and recurrent variants that varied depending on specific epilepsy syndromes. The overall genetic landscape of the Asian population aligns with findings from other populations of varying ethnicities.
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Affiliation(s)
- Se Hee Kim
- Division of Pediatric Neurology, Epilepsy Research Institute, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, South Korea
| | - Jieun Seo
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Soon Sung Kwon
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Lip-Yuen Teng
- Pediatric Neurology Unit, Department of Pediatrics, Hospital Tunku Azizah, Kuala Lumpur, Malaysia
| | - DongJu Won
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Joon Soo Lee
- Division of Pediatric Neurology, Epilepsy Research Institute, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, South Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Hoon-Chul Kang
- Division of Pediatric Neurology, Epilepsy Research Institute, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, South Korea
- Department of Pediatrics, Yonsei University College of Medicine, Severance Children's Hospital, Seoul, South Korea
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Fasaludeen A, McTague A, Jose M, Banerjee M, Sundaram S, Madhusoodanan UK, Radhakrishnan A, Menon RN. Genetic variant interpretation for the neurologist - A pragmatic approach in the next-generation sequencing era in childhood epilepsy. Epilepsy Res 2024; 201:107341. [PMID: 38447235 DOI: 10.1016/j.eplepsyres.2024.107341] [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: 11/27/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
Genetic advances over the past decade have enhanced our understanding of the genetic landscape of childhood epilepsy. However a major challenge for clinicians ha been understanding the rationale and systematic approach towards interpretation of the clinical significance of variant(s) detected in their patients. As the clinical paradigm evolves from gene panels to whole exome or whole genome testing including rapid genome sequencing, the number of patients tested and variants identified per patient will only increase. Each step in the process of variant interpretation has limitations and there is no single criterion which enables the clinician to draw reliable conclusions on a causal relationship between the variant and disease without robust clinical phenotyping. Although many automated online analysis software tools are available, these carry a risk of misinterpretation. This guideline provides a pragmatic, real-world approach to variant interpretation for the child neurologist. The focus will be on ascertaining aspects such as variant frequency, subtype, inheritance pattern, structural and functional consequence with regard to genotype-phenotype correlations, while refraining from mere interpretation of the classification provided in a genetic test report. It will not replace the expert advice of colleagues in clinical genetics, however as genomic investigations become a first-line test for epilepsy, it is vital that neurologists and epileptologists are equipped to navigate this landscape.
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Affiliation(s)
- Alfiya Fasaludeen
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Amy McTague
- Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Neurology, Great Ormond Street Hospital, London, United Kingdom
| | - Manna Jose
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Moinak Banerjee
- Human Molecular Genetics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Soumya Sundaram
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - U K Madhusoodanan
- Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Ashalatha Radhakrishnan
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India
| | - Ramshekhar N Menon
- Dept of Neurology, Sree Chitra Tirunal Institute for Medical Sciences & Technology (SCTIMST), Thiruvananthapuram, Kerala, India.
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Vetri L, Calì F, Saccone S, Vinci M, Chiavetta NV, Carotenuto M, Roccella M, Costanza C, Elia M. Whole Exome Sequencing as a First-Line Molecular Genetic Test in Developmental and Epileptic Encephalopathies. Int J Mol Sci 2024; 25:1146. [PMID: 38256219 PMCID: PMC10816140 DOI: 10.3390/ijms25021146] [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: 12/10/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Developmental and epileptic encephalopathies (DEE) are severe neurodevelopmental disorders characterized by recurrent, usually early-onset, epileptic seizures accompanied by developmental impairment often related to both underlying genetic etiology and abnormal epileptiform activity. Today, next-generation sequencing technologies (NGS) allow us to sequence large portions of DNA quickly and with low costs. The aim of this study is to evaluate the use of whole-exome sequencing (WES) as a first-line molecular genetic test in a sample of subjects with DEEs characterized by early-onset drug-resistant epilepsies, associated with global developmental delay and/or intellectual disability (ID). We performed 82 WESs, identifying 35 pathogenic variants with a detection rate of 43%. The identified variants were highlighted on 29 different genes including, 3 new candidate genes (KCNC2, STXBP6, DHRS9) for DEEs never identified before. In total, 23 out of 35 (66%) de novo variants were identified. The most frequently identified type of inheritance was autosomal dominant de novo (60%) followed by autosomal recessive in homozygosity (17%) and heterozygosity (11%), autosomal dominant inherited from parental mosaicism (6%) and X-linked dominant de novo (6%). The most frequent mutations identified were missense (75%) followed by frameshift deletions (16%), frameshift duplications (5%), and splicing mutations (3%). Considering the results obtained in the present study we support the use of WES as a form of first-line molecular genetic testing in DEEs.
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Affiliation(s)
- Luigi Vetri
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (L.V.); (M.V.); (N.V.C.); (M.E.)
| | - Francesco Calì
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (L.V.); (M.V.); (N.V.C.); (M.E.)
| | - Salvatore Saccone
- Department Biological, Geological and Environmental Sciences, University of Catania, Via Androne 81, 95124 Catania, Italy
| | - Mirella Vinci
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (L.V.); (M.V.); (N.V.C.); (M.E.)
| | | | - Marco Carotenuto
- Clinic of Child and Adolescent Neuropsychiatry, Department of Mental Health, Physical and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80131 Naples, Italy;
| | - Michele Roccella
- Department of Psychology, Educational Science and Human Movement, University of Palermo, 90141 Palermo, Italy; (M.R.); (C.C.)
| | - Carola Costanza
- Department of Psychology, Educational Science and Human Movement, University of Palermo, 90141 Palermo, Italy; (M.R.); (C.C.)
| | - Maurizio Elia
- Oasi Research Institute-IRCCS, 94018 Troina, Italy; (L.V.); (M.V.); (N.V.C.); (M.E.)
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7
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Koh HY, Smith L, Wiltrout KN, Podury A, Chourasia N, D’Gama AM, Park M, Knight D, Sexton EL, Koh JJ, Oby B, Pinsky R, Shao DD, French CE, Shao W, Rockowitz S, Sliz P, Zhang B, Mahida S, Moufawad El Achkar C, Yuskaitis CJ, Olson HE, Sheidley BR, Poduri AH. Utility of Exome Sequencing for Diagnosis in Unexplained Pediatric-Onset Epilepsy. JAMA Netw Open 2023; 6:e2324380. [PMID: 37471090 PMCID: PMC10359957 DOI: 10.1001/jamanetworkopen.2023.24380] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/31/2023] [Indexed: 07/21/2023] Open
Abstract
Importance Genomic advances inform our understanding of epilepsy and can be translated to patients as precision diagnoses that influence clinical treatment, prognosis, and counseling. Objective To delineate the genetic landscape of pediatric epilepsy and clinical utility of genetic diagnoses for patients with epilepsy. Design, Setting, and Participants This cohort study used phenotypic data from medical records and treating clinicians at a pediatric hospital to identify patients with unexplained pediatric-onset epilepsy. Exome sequencing was performed for 522 patients and available biological parents, and sequencing data were analyzed for single nucleotide variants (SNVs) and copy number variants (CNVs). Variant pathogenicity was assessed, patients were provided with their diagnostic results, and clinical utility was evaluated. Patients were enrolled from August 2018 to October 2021, and data were analyzed through December 2022. Exposures Phenotypic features associated with diagnostic genetic results. Main Outcomes and Measures Main outcomes included diagnostic yield and clinical utility. Diagnostic findings included variants curated as pathogenic, likely pathogenic (PLP), or diagnostic variants of uncertain significance (VUS) with clinical features consistent with the involved gene's associated phenotype. The proportion of the cohort with diagnostic findings, the genes involved, and their clinical utility, defined as impact on clinical treatment, prognosis, or surveillance, are reported. Results A total of 522 children (269 [51.5%] male; mean [SD] age at seizure onset, 1.2 [1.4] years) were enrolled, including 142 children (27%) with developmental epileptic encephalopathy and 263 children (50.4%) with intellectual disability. Of these, 100 participants (19.2%) had identifiable genetic explanations for their seizures: 89 participants had SNVs (87 germline, 2 somatic mosaic) involving 69 genes, and 11 participants had CNVs. The likelihood of identifying a genetic diagnosis was highest in patients with intellectual disability (adjusted odds ratio [aOR], 2.44; 95% CI, 1.40-4.26), early onset seizures (aOR, 0.93; 95% CI, 0.88-0.98), and motor impairment (aOR, 2.19; 95% CI 1.34-3.58). Among 43 patients with apparently de novo variants, 2 were subsequently determined to have asymptomatic parents harboring mosaic variants. Of 71 patients who received diagnostic results and were followed clinically, 29 (41%) had documented clinical utility resulting from their genetic diagnoses. Conclusions and Relevance These findings suggest that pediatric-onset epilepsy is genetically heterogeneous and that some patients with previously unexplained pediatric-onset epilepsy had genetic diagnoses with direct clinical implications.
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Affiliation(s)
- Hyun Yong Koh
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
| | - Lacey Smith
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
| | - Kimberly N. Wiltrout
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | | | - Nitish Chourasia
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- Department of Pediatrics and Neurology, University of Tennessee Health Science Center, Memphis
| | - Alissa M. D’Gama
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Division of Newborn Medicine, Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts
| | - Meredith Park
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
| | - Devon Knight
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
| | - Emma L. Sexton
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
| | - Julia J. Koh
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
| | - Brandon Oby
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
| | - Rebecca Pinsky
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
| | - Diane D. Shao
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Courtney E. French
- Research Computing, Department of Information Technology, Boston Children’s Hospital, Boston, Massachusetts
| | - Wanqing Shao
- Research Computing, Department of Information Technology, Boston Children’s Hospital, Boston, Massachusetts
| | - Shira Rockowitz
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Research Computing, Department of Information Technology, Boston Children’s Hospital, Boston, Massachusetts
| | - Piotr Sliz
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Research Computing, Department of Information Technology, Boston Children’s Hospital, Boston, Massachusetts
- Division of Molecular Medicine, Boston Children’s Hospital, Boston, Massachusetts
| | - Bo Zhang
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, Massachusetts
| | - Sonal Mahida
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
| | - Christelle Moufawad El Achkar
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
- Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, Massachusetts
| | - Christopher J. Yuskaitis
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Heather E. Olson
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Beth Rosen Sheidley
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
| | - Annapurna H. Poduri
- Epilepsy Genetics Program, Boston Children’s Hospital, Boston, Massachusetts
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts
- F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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Chokvithaya S, Caengprasath N, Buasong A, Jantasuwan S, Santawong K, Leela-adisorn N, Tongkobpetch S, Ittiwut C, Saengow VE, Kamolvisit W, Boonsimma P, Bongsebandhu-phubhakdi S, Shotelersuk V. Nine patients with KCNQ2-related neonatal seizures and functional studies of two missense variants. Sci Rep 2023; 13:3328. [PMID: 36849527 PMCID: PMC9971330 DOI: 10.1038/s41598-023-29924-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 02/13/2023] [Indexed: 03/01/2023] Open
Abstract
Mutations in KCNQ2 encoding for voltage-gated K channel subunits underlying the neuronal M-current have been associated with infantile-onset epileptic disorders. The clinical spectrum ranges from self-limited neonatal seizures to epileptic encephalopathy and delayed development. Mutations in KCNQ2 could be either gain- or loss-of-function which require different therapeutic approaches. To better understand genotype-phenotype correlation, more reports of patients and their mutations with elucidated molecular mechanism are needed. We studied 104 patients with infantile-onset pharmacoresistant epilepsy who underwent exome or genome sequencing. Nine patients with neonatal-onset seizures from unrelated families were found to harbor pathogenic or likely pathogenic variants in the KCNQ2 gene. The p.(N258K) was recently reported, and p. (G279D) has never been previously reported. Functional effect of p.(N258K) and p.(G279D) has never been previously studied. The cellular localization study demonstrated that the surface membrane expression of Kv7.2 carrying either variant was decreased. Whole-cell patch-clamp analyses revealed that both variants significantly impaired Kv7.2 M-current amplitude and density, conductance depolarizing shift in voltage dependence of activation, membrane resistance, and membrane time constant (Tau), indicating a loss-of-function in both the homotetrameric and heterotetrameric with Kv7.3 channels. In addition, both variants exerted dominant-negative effects in heterotetrameric with Kv7.3 channels. This study expands the mutational spectrum of KCNQ2- related epilepsy and their functional consequences provide insights into their pathomechanism.
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Affiliation(s)
- Suphalak Chokvithaya
- grid.7922.e0000 0001 0244 7875Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand ,grid.419934.20000 0001 1018 2627Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330 Thailand ,grid.415584.90000 0004 0576 1386Department of Clinical Pathology and Medical Technology Laboratory, Queen Sirikit National Institute of Child Health, Ministry of Public Health, Bangkok, Thailand
| | - Natarin Caengprasath
- grid.7922.e0000 0001 0244 7875Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand ,grid.419934.20000 0001 1018 2627Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330 Thailand
| | - Aayalida Buasong
- grid.7922.e0000 0001 0244 7875Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand ,grid.419934.20000 0001 1018 2627Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330 Thailand
| | - Supavadee Jantasuwan
- grid.7922.e0000 0001 0244 7875Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand ,grid.419934.20000 0001 1018 2627Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330 Thailand
| | - Kanokwan Santawong
- grid.7922.e0000 0001 0244 7875Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand ,grid.419934.20000 0001 1018 2627Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330 Thailand
| | - Netchanok Leela-adisorn
- grid.7922.e0000 0001 0244 7875Department of Stem Cell and Cell, Therapy Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Siraprapa Tongkobpetch
- grid.7922.e0000 0001 0244 7875Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand ,grid.419934.20000 0001 1018 2627Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330 Thailand
| | - Chupong Ittiwut
- grid.7922.e0000 0001 0244 7875Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand ,grid.419934.20000 0001 1018 2627Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330 Thailand
| | - Vitchayaporn Emarach Saengow
- grid.416297.f0000 0004 0388 8201Department of Pediatrics, Maharat Nakhon Ratchasima Hospital, Nakhon Ratchasima, Thailand
| | - Wuttichart Kamolvisit
- grid.7922.e0000 0001 0244 7875Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand ,grid.419934.20000 0001 1018 2627Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330 Thailand
| | - Ponghatai Boonsimma
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand. .,Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330, Thailand.
| | - Saknan Bongsebandhu-phubhakdi
- grid.7922.e0000 0001 0244 7875Department of Physiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand ,grid.419934.20000 0001 1018 2627Chula Neuroscience Center, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- grid.7922.e0000 0001 0244 7875Center of Excellence for Medical Genomics, Medical Genomics Cluster, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand ,grid.419934.20000 0001 1018 2627Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, 10330 Thailand
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9
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McNeill A. The value of exomes across the ages. Eur J Hum Genet 2023; 31:129-130. [PMID: 36750729 PMCID: PMC9905505 DOI: 10.1038/s41431-023-01281-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience, The University of Sheffield, Sheffield, UK.
- Sheffield Clinical Genetics Department, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
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