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Boonsimma P, Ittiwut C, Kamolvisit W, Ittiwut R, Chetruengchai W, Phokaew C, Srichonthong C, Poonmaksatit S, Desudchit T, Suphapeetiporn K, Shotelersuk V. Exome sequencing as first-tier genetic testing in infantile-onset pharmacoresistant epilepsy: diagnostic yield and treatment impact. Eur J Hum Genet 2023; 31:179-187. [PMID: 36198807 PMCID: PMC9905506 DOI: 10.1038/s41431-022-01202-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/06/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
Abstract
Pharmacoresistant epilepsy presenting during infancy poses both diagnostic and therapeutic challenges. We aim to identify diagnostic yield and treatment implications of exome sequencing (ES) as first-tier genetic testing for infantile-onset pharmacoresistant epilepsy. From June 2016 to December 2020, we enrolled patients with infantile-onset (age ≤ 12 months) pharmacoresistant epilepsy. 103 unrelated patients underwent ES. Clinical characteristics and changes in management due to the molecular diagnosis were studied. 42% (43/103) had epilepsy onset within the first month of life. After ES as first-tier genetic testing, 62% (64/103) of the cases were solved. Two partially solved cases (2%; 2/103) with heterozygous variants identified in ALDH7A1 known to cause autosomal recessive pyridoxine dependent epilepsy underwent genome sequencing (GS). Two novel large deletions in ALDH7A1 were detected in both cases. ES identified 66 pathogenic and likely pathogenic single nucleotide variants (SNVs) in 27 genes. 19 variants have not been previously reported. GS identified two additional copy number variations (CNVs). The most common disease-causing genes are SCN1A (13%; 13/103) and KCNQ2 (8%; 8/103). Eight percent (8/103) of the patients had treatable disorders and specific treatments were provided resulting in seizure freedom. Pyridoxine dependent epilepsy was the most common treatable epilepsy (6%; 6/103). Furthermore, 35% (36/103) had genetic defects which guided gene-specific treatments. Altogether, the diagnostic yield is 64%. Molecular diagnoses change management in 43% of the cases. This study substantiates the use of next generation sequencing (NGS) as the first-tier genetic investigation in infantile-onset pharmacoresistant epilepsy.
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Affiliation(s)
- 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
| | - Chupong Ittiwut
- 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
| | - Wuttichart Kamolvisit
- 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
| | - Rungnapa Ittiwut
- 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
| | - Wanna Chetruengchai
- 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
| | - Chureerat Phokaew
- 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
| | - Chalurmpon Srichonthong
- 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
| | - Sathida Poonmaksatit
- Division of Neurology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Tayard Desudchit
- Division of Neurology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kanya Suphapeetiporn
- 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.
| | - Vorasuk Shotelersuk
- 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
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Turkdogan D, Turkyilmaz A, Sager G, Ozturk G, Unver O, Say M. Chromosomal microarray and exome sequencing in unexplained early infantile epileptic encephalopathies in a highly consanguineous population. Int J Neurosci 2021:1-18. [PMID: 34380004 DOI: 10.1080/00207454.2021.1967349] [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: 10/20/2022]
Abstract
AIM To identify genetic causes for early infantile epileptic encephalopathies (EIEE) in Turkish children with mostly consanguineous parents. METHODS In a selected EIEE group (N = 59) based on results of nongenetic and initial genetic testing with unexplained etiology, 49 patients underwent array-based comparative genomic hybridization (aCGH) and 49 patients underwent whole exome sequencing (WES) including 39 with negative aCGH results and 10 with WES-only. RESULTS Diagnostic yield of aCGH and WES for pathogenic or likely pathogenic variants was 14.3% and 38.8%, respectively. Including de novo variants of uncertain significance linked to compatible phenotypes, increased the diagnostic yield of WES to 61.2%. Out of 38 positive variants, 18 (47.4%) were novel and 16 (42.1%) were de novo. Twenty-one (56.8%) patients had recessive variants inherited from mostly consanguineous healthy parents (85.7%). Fourteen (37.8%) of patients with diagnostic results had positive variants in established EIEE genes. Seizures started during neonatal period in 32.4% patients. Posture or movement disorders were comorbid with EIEE in 40.5% of diagnosed patients. We identified treatable metabolic disorders in 8.1% of patients and pathogenic variants in genes which support using targeted medicine in 19% of patients. CONCLUSIONS Detailed electro-clinical phenotyping led to expansion of some of the known phenotypes with non-neurological and neurological findings in addition to seizures, as well as suggestion of candidate genes (SEC24B, SLC16A2 and PRICKLE2) and a copy number variant (microduplication of Xp21.1p11.4). The high ratio of recessive inheritance could be important for family counseling.
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Affiliation(s)
- Dilsad Turkdogan
- Medical Faculty, Department of Pediatric Neurology, Marmara University, Pendik, Istanbul, Turkey
| | - Ayberk Turkyilmaz
- Medical Faculty, Department of Medical Genetics, Marmara University, Pendik, Istanbul, Turkey
| | - Gunes Sager
- Medical Faculty, Department of Pediatric Neurology, Marmara University, Pendik, Istanbul, Turkey
| | - Gulten Ozturk
- Medical Faculty, Department of Pediatric Neurology, Marmara University, Pendik, Istanbul, Turkey
| | - Olcay Unver
- Medical Faculty, Department of Pediatric Neurology, Marmara University, Pendik, Istanbul, Turkey
| | - Merve Say
- Bioinformatics, Private Practice, Kadıkoy, Istanbul, Turkey
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Chen WL, Mefford HC. Diagnostic Considerations in the Epilepsies-Testing Strategies, Test Type Advantages, and Limitations. Neurotherapeutics 2021; 18:1468-1477. [PMID: 34532824 PMCID: PMC8608977 DOI: 10.1007/s13311-021-01121-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2021] [Indexed: 02/04/2023] Open
Abstract
The role of genetics in epilepsy has been recognized for a long time. Over the past decade, genome-wide technologies have identified numerous genes and variants associated with epilepsy. In the clinical setting, a myriad of genetic testing options are available, and a subset of specific genetic diagnoses have management implications. Furthermore, genetic testing can be a dynamic process. As a result, fundamental knowledge about genetics and genomics has become essential for all specialists. Here, we review current knowledge of the genetic contribution to various types of epilepsy, provide an overview of types of genetic variants, and discuss genetic testing options and their diagnostic yield. We also consider advantages and limitations of testing approaches.
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Affiliation(s)
- Wei-Liang Chen
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, 98105, USA
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, 98105, USA.
- Current Location: Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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Keywan C, Poduri AH, Goldstein RD, Holm IA. Genetic Factors Underlying Sudden Infant Death Syndrome. APPLICATION OF CLINICAL GENETICS 2021; 14:61-76. [PMID: 33623412 PMCID: PMC7894824 DOI: 10.2147/tacg.s239478] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/24/2021] [Indexed: 12/28/2022]
Abstract
Sudden Infant Death syndrome (SIDS) is a diagnosis of exclusion. Decades of research have made steady gains in understanding plausible mechanisms of terminal events. Current evidence suggests SIDS includes heterogeneous biological conditions, such as metabolic, cardiac, neurologic, respiratory, and infectious conditions. Here we review genetic studies that address each of these areas in SIDS cases and cohorts, providing a broad view of the genetic underpinnings of this devastating phenomenon. The current literature has established a role for monogenic genetic causes of SIDS mortality in a subset of cases. To expand upon our current knowledge of disease-causing genetic variants in SIDS cohorts and their mechanisms, future genetic studies may employ functional assessments of implicated variants, broader genetic tests, and the inclusion of parental genetic data and family history information.
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Affiliation(s)
- Christine Keywan
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Annapurna H Poduri
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA.,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.,Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Richard D Goldstein
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Division of General Pediatrics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Ingrid A Holm
- Robert's Program for Sudden Unexpected Death in Pediatrics, Boston Children's Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Division of Genetics and Genomics, Department of Pediatrics, and Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, MA, USA
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5
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Uddin M, Wang Y, Woodbury-Smith M. Artificial intelligence for precision medicine in neurodevelopmental disorders. NPJ Digit Med 2019; 2:112. [PMID: 31799421 PMCID: PMC6872596 DOI: 10.1038/s41746-019-0191-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 10/29/2019] [Indexed: 12/23/2022] Open
Abstract
The ambition of precision medicine is to design and optimize the pathway for diagnosis, therapeutic intervention, and prognosis by using large multidimensional biological datasets that capture individual variability in genes, function and environment. This offers clinicians the opportunity to more carefully tailor early interventions- whether treatment or preventative in nature-to each individual patient. Taking advantage of high performance computer capabilities, artificial intelligence (AI) algorithms can now achieve reasonable success in predicting risk in certain cancers and cardiovascular disease from available multidimensional clinical and biological data. In contrast, less progress has been made with the neurodevelopmental disorders, which include intellectual disability (ID), autism spectrum disorder (ASD), epilepsy and broader neurodevelopmental disorders. Much hope is pinned on the opportunity to quantify risk from patterns of genomic variation, including the functional characterization of genes and variants, but this ambition is confounded by phenotypic and etiologic heterogeneity, along with the rare and variable penetrant nature of the underlying risk variants identified so far. Structural and functional brain imaging and neuropsychological and neurophysiological markers may provide further dimensionality, but often require more development to achieve sensitivity for diagnosis. Herein, therefore, lies a precision medicine conundrum: can artificial intelligence offer a breakthrough in predicting risks and prognosis for neurodevelopmental disorders? In this review we will examine these complexities, and consider some of the strategies whereby artificial intelligence may overcome them.
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Affiliation(s)
- Mohammed Uddin
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
- 2The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
| | - Yujiang Wang
- 3Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
- 4School of Computing, Newcastle University, Newcastle upon Tyne, UK
| | - Marc Woodbury-Smith
- 2The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON Canada
- 3Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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6
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Copy number variation analysis in 83 children with early-onset developmental and epileptic encephalopathy after targeted resequencing of a 109-epilepsy gene panel. J Hum Genet 2019; 64:1097-1106. [DOI: 10.1038/s10038-019-0661-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/23/2019] [Accepted: 08/11/2019] [Indexed: 12/13/2022]
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Coppola A, Cellini E, Stamberger H, Saarentaus E, Cetica V, Lal D, Djémié T, Bartnik‐Glaska M, Ceulemans B, Helen Cross J, Deconinck T, Masi SD, Dorn T, Guerrini R, Hoffman‐Zacharska D, Kooy F, Lagae L, Lench N, Lemke JR, Lucenteforte E, Madia F, Mefford HC, Morrogh D, Nuernberg P, Palotie A, Schoonjans A, Striano P, Szczepanik E, Tostevin A, Vermeesch JR, Van Esch H, Van Paesschen W, Waters JJ, Weckhuysen S, Zara F, Jonghe PD, Sisodiya SM, Marini C. Diagnostic implications of genetic copy number variation in epilepsy plus. Epilepsia 2019; 60:689-706. [PMID: 30866059 PMCID: PMC6488157 DOI: 10.1111/epi.14683] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 01/31/2023]
Abstract
OBJECTIVE Copy number variations (CNVs) represent a significant genetic risk for several neurodevelopmental disorders including epilepsy. As knowledge increases, reanalysis of existing data is essential. Reliable estimates of the contribution of CNVs to epilepsies from sizeable populations are not available. METHODS We assembled a cohort of 1255 patients with preexisting array comparative genomic hybridization or single nucleotide polymorphism array based CNV data. All patients had "epilepsy plus," defined as epilepsy with comorbid features, including intellectual disability, psychiatric symptoms, and other neurological and nonneurological features. CNV classification was conducted using a systematic filtering workflow adapted to epilepsy. RESULTS Of 1097 patients remaining after genetic data quality control, 120 individuals (10.9%) carried at least one autosomal CNV classified as pathogenic; 19 individuals (1.7%) carried at least one autosomal CNV classified as possibly pathogenic. Eleven patients (1%) carried more than one (possibly) pathogenic CNV. We identified CNVs covering recently reported (HNRNPU) or emerging (RORB) epilepsy genes, and further delineated the phenotype associated with mutations of these genes. Additional novel epilepsy candidate genes emerge from our study. Comparing phenotypic features of pathogenic CNV carriers to those of noncarriers of pathogenic CNVs, we show that patients with nonneurological comorbidities, especially dysmorphism, were more likely to carry pathogenic CNVs (odds ratio = 4.09, confidence interval = 2.51-6.68; P = 2.34 × 10-9 ). Meta-analysis including data from published control groups showed that the presence or absence of epilepsy did not affect the detected frequency of CNVs. SIGNIFICANCE The use of a specifically adapted workflow enabled identification of pathogenic autosomal CNVs in 10.9% of patients with epilepsy plus, which rose to 12.7% when we also considered possibly pathogenic CNVs. Our data indicate that epilepsy with comorbid features should be considered an indication for patients to be selected for a diagnostic algorithm including CNV detection. Collaborative large-scale CNV reanalysis leads to novel declaration of pathogenicity in unexplained cases and can promote discovery of promising candidate epilepsy genes.
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Affiliation(s)
- Antonietta Coppola
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyWC1N3BGUK
- The Chalfont Centre for EpilepsyChesham Lane, Chalfont St PeterBucksUK
- Epilepsy CentreDepartment of Neuroscience, Reproductive and Odontostomatological SciencesFederico II UniversityNaplesItaly
| | - Elena Cellini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and LaboratoriesNeuroscience DepartmentA Meyer Children‘s HospitalUniversity of FlorenceFlorenceItaly
| | - Hannah Stamberger
- Neurogenetics GroupCenter for Molecular NeurologyVIB2650AntwerpBelgium
- Laboratory of NeurogeneticsInstitute Born‐BungeUniversity of AntwerpAntwerpBelgium
- Department of NeurologyAntwerp University HospitalAntwerpBelgium
| | - Elmo Saarentaus
- Analytic and Translational Genetics UnitMassachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Institute of Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - Valentina Cetica
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and LaboratoriesNeuroscience DepartmentA Meyer Children‘s HospitalUniversity of FlorenceFlorenceItaly
| | - Dennis Lal
- Analytic and Translational Genetics UnitMassachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Epilepsy CenterNeurological InstituteCleveland ClinicClevelandOH44195US
- Genomic Medicine InstituteLerner Research Institute Cleveland ClinicClevelandOH44195US
- Cologne Center for GenomicsUniversity of CologneGermany
| | - Tania Djémié
- Neurogenetics GroupCenter for Molecular NeurologyVIB2650AntwerpBelgium
- Laboratory of NeurogeneticsInstitute Born‐BungeUniversity of AntwerpAntwerpBelgium
| | | | - Berten Ceulemans
- Department of Neurology‐Pediatric NeurologyUniversity and University Hospital AntwerpAntwerpBelgium
| | - J. Helen Cross
- Neurology DepartmentGreat Ormond Street HospitalNHS Foundation TrustLondonUK
- Clinical NeuroscienceUCL GOSH Institute of Child HealthLondonUK
- Young EpilepsyLingfieldUK
| | - Tine Deconinck
- Neurogenetics GroupCenter for Molecular NeurologyVIB2650AntwerpBelgium
- Laboratory of NeurogeneticsInstitute Born‐BungeUniversity of AntwerpAntwerpBelgium
| | | | - Thomas Dorn
- Swiss Epilepsy CenterBleulerstrasse 60CH‐8008Switzerland
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and LaboratoriesNeuroscience DepartmentA Meyer Children‘s HospitalUniversity of FlorenceFlorenceItaly
| | | | - Frank Kooy
- Department of Medical GeneticsUniversity of AntwerpAntwerpBelgium
| | - Lieven Lagae
- Department of Development and RegenerationSection Pediatric NeurologyUniversity Hospital KU Leuven3000LeuvenBelgium
| | - Nicholas Lench
- North East Thames Regional Genetics ServiceGreat Ormond Street Hospital for ChildrenNHS Foundation TrustLondonUK
| | - Johannes R. Lemke
- Institute of Human GeneticsUniversity of Leipzig Hospitals and ClinicsLeipzigGermany
| | - Ersilia Lucenteforte
- Department of Clinical and Experimental MedicineUniversity of Pisa, ItalyClinical Trial OfficeMeyer Children‘s HospitalFlorenceItaly
| | - Francesca Madia
- Neurogenetic LaboratoryScientific Institute for Research, Hospitalisation and Health Care (IRCCS) G. Gaslini InstituteGenovaItaly
| | - Heather C. Mefford
- Department of PediatricsDivision of Genetic MedicineUniversity of WashingtonSeattleUSA
| | - Deborah Morrogh
- North East Thames Regional Genetics ServiceGreat Ormond Street Hospital for ChildrenNHS Foundation TrustLondonUK
| | | | - Aarno Palotie
- Analytic and Translational Genetics UnitMassachusetts General HospitalHarvard Medical SchoolBostonMassachusettsUSA
- Stanley Center for Psychiatric ResearchBroad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Institute of Molecular Medicine Finland FIMMUniversity of HelsinkiHelsinkiFinland
| | - An‐Sofie Schoonjans
- Department of Neurology‐Pediatric NeurologyUniversity and University Hospital AntwerpAntwerpBelgium
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases UnitDINOGMI‐Department of Neurosciences, Rehabilitation, Ophthalmology Genetics, Maternal and Child HealthUniversity of Genoa, ‘G. Gaslini’ InstituteGenovaItaly
| | - Elzbieta Szczepanik
- Clinic of Neurology of Children and AdolescentsInstitute of Mother and ChildWarsawPoland
| | - Anna Tostevin
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyWC1N3BGUK
- The Chalfont Centre for EpilepsyChesham Lane, Chalfont St PeterBucksUK
| | - Joris R. Vermeesch
- Center for Human GeneticsUniversity Hospitals LeuvenHerestraat 493000LeuvenBelgium
| | - Hilde Van Esch
- Center for Human GeneticsUniversity Hospitals LeuvenHerestraat 493000LeuvenBelgium
| | - Wim Van Paesschen
- Department of NeurologyUniversity Hospitals LeuvenHerestraat 493000LeuvenBelgium
| | - Jonathan J Waters
- North East Thames Regional Genetics ServiceGreat Ormond Street Hospital for ChildrenNHS Foundation TrustLondonUK
| | - Sarah Weckhuysen
- Neurogenetics GroupCenter for Molecular NeurologyVIB2650AntwerpBelgium
- Laboratory of NeurogeneticsInstitute Born‐BungeUniversity of AntwerpAntwerpBelgium
- Department of NeurologyAntwerp University HospitalAntwerpBelgium
| | - Federico Zara
- Neurogenetic LaboratoryScientific Institute for Research, Hospitalisation and Health Care (IRCCS) G. Gaslini InstituteGenovaItaly
| | - Peter De Jonghe
- Neurogenetics GroupCenter for Molecular NeurologyVIB2650AntwerpBelgium
- Laboratory of NeurogeneticsInstitute Born‐BungeUniversity of AntwerpAntwerpBelgium
- Department of NeurologyAntwerp University HospitalAntwerpBelgium
| | - Sanjay M. Sisodiya
- Department of Clinical and Experimental EpilepsyUCL Queen Square Institute of NeurologyWC1N3BGUK
- The Chalfont Centre for EpilepsyChesham Lane, Chalfont St PeterBucksUK
| | - Carla Marini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and LaboratoriesNeuroscience DepartmentA Meyer Children‘s HospitalUniversity of FlorenceFlorenceItaly
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Kessi M, Xiong J, Wu L, Yang L, He F, Chen C, Pang N, Duan H, Zhang W, Arafat A, Yin F, Peng J. Rare Copy Number Variations and Predictors in Children With Intellectual Disability and Epilepsy. Front Neurol 2018; 9:947. [PMID: 30510536 PMCID: PMC6252327 DOI: 10.3389/fneur.2018.00947] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/23/2018] [Indexed: 11/19/2022] Open
Abstract
Introduction: The concurrence of intellectual disability/global developmental delay and epilepsy (ID/GDD-EP) is very common in the pediatric population. The etiologies for both conditions are complex and largely unknown. The predictors of significant copy number variations (CNVs) are known for the cases with ID/GDD, but unknown for those with exclusive ID/GDD-EP. Importantly, the known predictors are largely from the same ethnic group; hence, they lack replication. Purpose: We aimed to determine and investigate the diagnostic yield of CNV tests, new causative CNVs, and the independent predictors of significant CNVs in Chinese children with unexplained ID/GDD-EP. Materials and methods: A total of 100 pediatric patients with unexplained ID/GDD-EP and 1,000 healthy controls were recruited. The American College of Medical Genetics guideline was used to classify the CNVs. Additionally, clinical information was collected and compared between those with significant and non-significant CNVs. Results: Twenty-eight percent of the patients had significant CNVs, 16% had variants of unknown significance, and 56% had non-significant CNVs. In total, 31 CNVs were identified in 28% (28/100) of cases: 25 pathogenic and 6 likely pathogenic. Eighteen known syndromes were diagnosed in 17 cases. Thirteen rare CNVs (8 novel and 5 reported in literature) were identified, of which three spanned dosage-sensitive genes: 19q13.2 deletion (ATP1A3), Xp11.4-p11.3 deletion (CASK), and 6q25.3-q25.3 deletion (ARID1B). By comparing clinical features in patients with significant CNVs against those with non-significant CNVs, a statistically significant association was found between the presence of significant CNVs and speech and language delay for those aged above 2 years and for those with facial malformations, microcephaly, congenital heart disease, fair skin, eye malformations, and mega cisterna magna. Multivariate logistic regression analysis allowed the identification of two independent significant CNV predictors, which are eye malformations and facial malformations. Conclusion: Our study supports the performance of CNV tests in pediatric patients with unexplained ID/GDD-EP, as there is high diagnostic yield, which informs genetic counseling. It adds 13 rare CNVs (8 novel), which can be accountable for both conditions. Moreover, congenital eye and facial malformations are clinical markers that can aid clinicians to understand which patients can benefit from the CNV testing and which will not, thus helping patients to avoid unnecessary and expensive tests.
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Affiliation(s)
- Miriam Kessi
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Juan Xiong
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Liwen Wu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Lifen Yang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fang He
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Chen Chen
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Nan Pang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Haolin Duan
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Wen Zhang
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Ahmed Arafat
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
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9
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Ostrander BEP, Butterfield RJ, Pedersen BS, Farrell AJ, Layer RM, Ward A, Miller C, DiSera T, Filloux FM, Candee MS, Newcomb T, Bonkowsky JL, Marth GT, Quinlan AR. Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy. NPJ Genom Med 2018; 3:22. [PMID: 30109124 PMCID: PMC6089881 DOI: 10.1038/s41525-018-0061-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 07/14/2018] [Accepted: 07/18/2018] [Indexed: 12/12/2022] Open
Abstract
Early infantile epileptic encephalopathy (EIEE) is a devastating epilepsy syndrome with onset in the first months of life. Although mutations in more than 50 different genes are known to cause EIEE, current diagnostic yields with gene panel tests or whole-exome sequencing are below 60%. We applied whole-genome analysis (WGA) consisting of whole-genome sequencing and comprehensive variant discovery approaches to a cohort of 14 EIEE subjects for whom prior genetic tests had not yielded a diagnosis. We identified both de novo point and INDEL mutations and de novo structural rearrangements in known EIEE genes, as well as mutations in genes not previously associated with EIEE. The detection of a pathogenic or likely pathogenic mutation in all 14 subjects demonstrates the utility of WGA to reduce the time and costs of clinical diagnosis of EIEE. While exome sequencing may have detected 12 of the 14 causal mutations, 3 of the 12 patients received non-diagnostic exome panel tests prior to genome sequencing. Thus, given the continued decline of sequencing costs, our results support the use of WGA with comprehensive variant discovery as an efficient strategy for the clinical diagnosis of EIEE and other genetic conditions.
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Affiliation(s)
- Betsy E. P. Ostrander
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Russell J. Butterfield
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Brent S. Pedersen
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Andrew J. Farrell
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Ryan M. Layer
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Alistair Ward
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Chase Miller
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Tonya DiSera
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Francis M. Filloux
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Meghan S. Candee
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Tara Newcomb
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Joshua L. Bonkowsky
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Gabor T. Marth
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Aaron R. Quinlan
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT USA
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT USA
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10
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Peycheva V, Kamenarova K, Ivanova N, Stamatov D, Avdjieva-Tzavella D, Alexandrova I, Zhelyazkova S, Pacheva I, Dimova P, Ivanov I, Litvinenko I, Bozhinova V, Tournev I, Simeonov E, Mitev V, Jordanova A, Kaneva R. Chromosomal microarray analysis of Bulgarian patients with epilepsy and intellectual disability. Gene 2018; 667:45-55. [DOI: 10.1016/j.gene.2018.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/13/2018] [Accepted: 05/03/2018] [Indexed: 12/08/2022]
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Howell KB, Eggers S, Dalziel K, Riseley J, Mandelstam S, Myers CT, McMahon JM, Schneider A, Carvill GL, Mefford HC, Scheffer IE, Harvey AS. A population-based cost-effectiveness study of early genetic testing in severe epilepsies of infancy. Epilepsia 2018; 59:1177-1187. [PMID: 29750358 DOI: 10.1111/epi.14087] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2018] [Indexed: 01/12/2023]
Abstract
OBJECTIVE The severe epilepsies of infancy (SEI) are a devastating group of disorders that pose a major care and economic burden on society; early diagnosis is critical for optimal management. This study sought to determine the incidence and etiologies of SEI, and model the yield and cost-effectiveness of early genetic testing. METHODS A population-based study was undertaken of the incidence, etiologies, and cost-effectiveness of a whole exome sequencing-based gene panel (targeted WES) in infants with SEI born during 2011-2013, identified through electroencephalography (EEG) and neonatal databases. SEI was defined as seizure onset before age 18 months, frequent seizures, epileptiform EEG, and failure of ≥2 antiepileptic drugs. Medical records, investigations, MRIs, and EEGs were analyzed, and genetic testing was performed if no etiology was identified. Economic modeling was performed to determine yield and cost-effectiveness of investigation of infants with unknown etiology at epilepsy onset, incorporating targeted WES at different stages of the diagnostic pathway. RESULTS Of 114 infants with SEI (incidence = 54/100 000 live births/y), the etiology was determined in 76 (67%): acquired brain injuries (n = 14), focal cortical dysplasias (n = 14), other brain malformations (n = 17), channelopathies (n = 11), chromosomal (n = 9), metabolic (n = 6), and other genetic (n = 5) disorders. Modeling showed that incorporating targeted WES increased diagnostic yield compared to investigation without targeted WES (48/86 vs 39/86). Early targeted WES had lower total cost ($677 081 U.S. dollars [USD] vs $738 136 USD) than late targeted WES. A pathway with early targeted WES and limited metabolic testing yielded 7 additional diagnoses compared to investigation without targeted WES (46/86 vs 39/86), with lower total cost ($455 597 USD vs $661 103 USD), lower cost per diagnosis ($9904 USD vs $16 951 USD), and a dominant cost-effectiveness ratio. SIGNIFICANCE Severe epilepsies occur in 1 in 2000 infants, with the etiology identified in two-thirds, most commonly malformative. Early use of targeted WES yields more diagnoses at lower cost. Early genetic diagnosis will enable timely administration of precision medicines, once developed, with the potential to improve long-term outcome.
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Affiliation(s)
- Katherine B Howell
- Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Stefanie Eggers
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Kim Dalziel
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Melbourne School of Global and Population Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Jessica Riseley
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simone Mandelstam
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Medical Imaging, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Radiology, University of Melbourne, Melbourne, Victoria, Australia.,Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia
| | - Candace T Myers
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Jacinta M McMahon
- Department of Medicine, Epilepsy Research Centre, Austin Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Amy Schneider
- Department of Medicine, Epilepsy Research Centre, Austin Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Ingrid E Scheffer
- Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia.,Department of Medicine, Epilepsy Research Centre, Austin Health, University of Melbourne, Melbourne, Victoria, Australia
| | - A Simon Harvey
- Department of Neurology, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
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Patel J, Mercimek-Mahmutoglu S. Epileptic Encephalopathy in Childhood: A Stepwise Approach for Identification of Underlying Genetic Causes. Indian J Pediatr 2016; 83:1164-74. [PMID: 26821542 DOI: 10.1007/s12098-015-1979-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/02/2015] [Indexed: 01/29/2023]
Abstract
Epilepsy is one of the most common neurological disorders in childhood. Epilepsy associated with global developmental delay and cognitive dysfunction is defined as epileptic encephalopathy. Certain inherited metabolic disorders presenting with epileptic encephalopathy can be treated with disease specific diet, vitamin, amino acid or cofactor supplementations. In those disorders, disease specific therapy is successful to achieve good seizure control and improve long-term neurodevelopmental outcome. For this reason, intractable epilepsy with global developmental delay or history of developmental regression warrants detailed metabolic investigations for the possibility of an underlying treatable inherited metabolic disorder, which should be undertaken as first line investigations. An underlying genetic etiology in epileptic encephalopathy has been supported by recent studies such as array comparative genomic hybridization, targeted next generation sequencing panels, whole exome and whole genome sequencing. These studies report a diagnostic yield up to 70%, depending on the applied genetic testing as well as number of patients enrolled. In patients with epileptic encephalopathy, a stepwise approach for diagnostic work-up will help to diagnose treatable inherited metabolic disorders quickly. Application of detailed genetic investigations such as targeted next generation sequencing as second line and whole exome sequencing as third line testing will diagnose underlying genetic disease which will help for genetic counseling as well as guide for prenatal diagnosis. Knowledge of underlying genetic cause will provide novel insights into the pathogenesis of epileptic encephalopathy and pave the ground towards the development of targeted neuroprotective treatment strategies to improve the health outcome of children with epileptic encephalopathy.
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Affiliation(s)
- Jaina Patel
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, M5G 1X8, Canada
| | - Saadet Mercimek-Mahmutoglu
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, M5G 1X8, Canada. .,Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada.
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13
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Zuberi SM. Editorial note. Eur J Paediatr Neurol 2015; 19:389. [PMID: 26043359 DOI: 10.1016/j.ejpn.2015.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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