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Lin ZJ, Li B, Lin PX, Song W, Yan LM, Meng H, He N. Clinical application of trio-based whole-exome sequencing in idiopathic generalized epilepsy. Seizure 2024; 116:24-29. [PMID: 36842888 DOI: 10.1016/j.seizure.2023.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023] Open
Abstract
PURPOSE Idiopathic generalized epilepsies (IGEs) are a common group of genetic generalized epilepsies with high genetic heterogeneity and complex inheritance. However, the genetic basis is still largely unknown. This study aimed to explore the genetic etiologies in IGEs. METHODS Trio-based whole-exome sequencing was performed in 60 cases with IGEs. The pathogenicity of candidate genetic variants was evaluated by the criteria of the American College of Medical Genetics and Genomics (ACMG), and the clinical causality was assessed by concordance between the observed phenotype and the reported phenotype. RESULTS Seven candidate variants were detected in seven unrelated cases with IGE (11.7%, 7/60). According to ACMG, a de novo SLC2A1 (c.376C>T/p.Arg126Cys) variant identified in childhood absence epilepsy was evaluated as pathogenic with clinical concordance. Six variants were assessed to be uncertain significance by ACMG, but then considered causative after evaluation of clinical concordance. These variants included CLCN4 hemizygous variant (c.2044G>A/p.Glu682Lys) and IQSEC2 heterozygous variant (c.4315C>T/p.Pro1439Ser) in juvenile absence epilepsy, EFHC1 variant (c.1504C>T/p.Arg502Trp) and CACNA1H (c.589G>T/p.Ala197Ser) both with incomplete penetrance in juvenile myoclonic epilepsy, and GRIN2A variant (c.2011C>G/p.Gln671Glu) and GABRB1 variant (c.1075G>A/p.Val359Ile) both co-segregated with juvenile myoclonic epilepsy. Among them, GABRB1 was for the first time identified as potential novel causative gene for IGE. SIGNIFICANCE Considering the genetic heterogeneity and complex inheritance of IGEs, a comprehensive evaluation combined the ACMG scoring and assessment of clinical concordance is suggested for the pathogenicity analysis of variants identified in clinical screening. GABRB1 is probably a novel causative gene for IGE, which warrants further studies.
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Affiliation(s)
- Zhi-Jian Lin
- Department of Neurology, the Affiliated Hospital of Putian University, Putian 351100, Fujian Province, China; Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Bin Li
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Peng-Xing Lin
- Department of Neurology, the Affiliated Hospital of Putian University, Putian 351100, Fujian Province, China
| | - Wang Song
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Li-Min Yan
- Department of Neurology, The Second Affiliated Hospital of Hainan Medical University, 570311 Haikou, Hainan, China
| | - Heng Meng
- Department of Neurology, the First Affiliated Hospital of Jinan University, Guangzhou 510632, China.
| | - Na He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
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2
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Girard A, Moreau C, Michaud JL, Minassian B, Cossette P, Girard SL. Unraveling the role of non-coding rare variants in epilepsy. PLoS One 2023; 18:e0291935. [PMID: 37756314 PMCID: PMC10529579 DOI: 10.1371/journal.pone.0291935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
The discovery of new variants has leveled off in recent years in epilepsy studies, despite the use of very large cohorts. Consequently, most of the heritability is still unexplained. Rare non-coding variants have been largely ignored in studies on epilepsy, although non-coding single nucleotide variants can have a significant impact on gene expression. We had access to whole genome sequencing (WGS) from 247 epilepsy patients and 377 controls. To assess the functional impact of non-coding variants, ExPecto, a deep learning algorithm was used to predict expression change in brain tissues. We compared the burden of rare non-coding deleterious variants between cases and controls. Rare non-coding highly deleterious variants were significantly enriched in Genetic Generalized Epilepsy (GGE), but not in Non-Acquired Focal Epilepsy (NAFE) or all epilepsy cases when compared with controls. In this study we showed that rare non-coding deleterious variants are associated with epilepsy, specifically with GGE. Larger WGS epilepsy cohort will be needed to investigate those effects at a greater resolution. Nevertheless, we demonstrated the importance of studying non-coding regions in epilepsy, a disease where new discoveries are scarce.
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Affiliation(s)
- Alexandre Girard
- Centre Intersectoriel en Santé Durable, University of Quebec in Chicoutimi, Saguenay, Canada
| | - Claudia Moreau
- Centre Intersectoriel en Santé Durable, University of Quebec in Chicoutimi, Saguenay, Canada
| | - Jacques L. Michaud
- CHU Sainte-Justine, Montréal, Canada
- Department of Neurosciences and Department of Pediatrics, University of Montreal, Montréal, Canada
| | - Berge Minassian
- The Hospital for Sick Children, Department of Pediatrics, Toronto, Canada
- Department of Pediatrics, University of Texas Southwestern Medical School, Dallas, Texas, United States of America
| | - Patrick Cossette
- CHUM Research Center, Montréal, Canada
- Department of Neurosciences, University of Montreal, Montréal, Canada
| | - Simon L. Girard
- Centre Intersectoriel en Santé Durable, University of Quebec in Chicoutimi, Saguenay, Canada
- CERVO Research Center, Laval University, Québec, Canada
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3
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Harms FL, Weiss D, Lisfeld J, Alawi M, Kutsche K. A deep intronic variant in DNM1 in a patient with developmental and epileptic encephalopathy creates a splice acceptor site and affects only transcript variants including exon 10a. Neurogenetics 2023; 24:171-180. [PMID: 37039969 DOI: 10.1007/s10048-023-00716-w] [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: 01/30/2023] [Accepted: 03/28/2023] [Indexed: 04/12/2023]
Abstract
DNM1 developmental and epileptic encephalopathy (DEE) is characterized by severe to profound intellectual disability, hypotonia, movement disorder, and refractory epilepsy, typically presenting with infantile spasms. Most of the affected individuals had de novo missense variants in DNM1. DNM1 undergoes alternative splicing that results in expression of six different transcript variants. One alternatively spliced region affects the tandemly arranged exons 10a and 10b, producing isoforms DNM1A and DNM1B, respectively. Pathogenic variants in the DNM1 coding region affect all transcript variants. Recently, a de novo DNM1 NM_001288739.1:c.1197-8G > A variant located in intron 9 has been reported in several unrelated individuals with DEE that causes in-frame insertion of two amino acids and leads to disease through a dominant-negative mechanism. We report on a patient with DEE and a de novo DNM1 variant NM_001288739.2:c.1197-46C > G in intron 9, upstream of exon 10a. By RT-PCR and Sanger sequencing using fibroblast-derived cDNA of the patient, we identified aberrantly spliced DNM1 mRNAs with exon 9 spliced to the last 45 nucleotides of intron 9 followed by exon 10a (NM_001288739.2:r.1196_1197ins[1197-1_1197-45]). The encoded DNM1A mutant is predicted to contain 15 novel amino acids between Ile398 and Arg399 [NP_001275668.1:p.(Ile398_Arg399ins15)] and likely functions in a dominant-negative manner, similar to other DNM1 mutants. Our data confirm the importance of the DNM1 isoform A for normal human brain function that is underscored by previously reported predominant expression of DMN1A transcripts in pediatric brain, functional differences of the mouse Dnm1a and Dnm1b isoforms, and the Dnm1 fitful mouse, an epilepsy mouse model.
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Affiliation(s)
- Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Deike Weiss
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jasmin Lisfeld
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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4
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Rihar N, Krgovic D, Kokalj-Vokač N, Stangler-Herodez S, Zorc M, Dovc P. Identification of potentially pathogenic variants for autism spectrum disorders using gene-burden analysis. PLoS One 2023; 18:e0273957. [PMID: 37167322 PMCID: PMC10174571 DOI: 10.1371/journal.pone.0273957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/19/2023] [Indexed: 05/13/2023] Open
Abstract
Gene- burden analyses have lately become a very successful way for the identification of genes carrying risk variants underlying the analysed disease. This approach is also suitable for complex disorders like autism spectrum disorder (ASD). The gene-burden analysis using Testing Rare Variants with Public Data (TRAPD) software was conducted on whole exome sequencing data of Slovenian patients with ASD to determine potentially novel disease risk variants in known ASD-associated genes as well as in others. To choose the right control group for testing, principal component analysis based on the 1000 Genomes and ASD cohort samples was conducted. The subsequent protein structure and ligand binding analysis usingI-TASSER package were performed to detect changes in protein structure and ligand binding to determine a potential pathogenic consequence of observed mutation. The obtained results demonstrate an association of two variants-p.Glu198Lys (PPP2R5D:c.592G>A) and p.Arg253Gln (PPP2R5D:c.758G>A) with the ASD. Substitution p.Glu198Lys (PPP2R5D:c.592G>A) is a variant, previously described as pathogenic in association with ASD combined with intellectual disability, whereas p.Arg253Gln (PPP2R5D:c.758G>A) has not been described as an ASD-associated pathogenic variant yet. The results indicate that the filtering process was suitable and could be used in the future for detection of novel pathogenic variants when analysing groups of ASD patients.
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Affiliation(s)
- Nika Rihar
- Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia
| | - Danijela Krgovic
- Laboratory of Medical Genetics, University Medical Centre Maribor, Maribor, Slovenia
- Maribor Medical Faculty, University of Maribor, Maribor, Slovenia
| | - Nadja Kokalj-Vokač
- Laboratory of Medical Genetics, University Medical Centre Maribor, Maribor, Slovenia
- Maribor Medical Faculty, University of Maribor, Maribor, Slovenia
| | - Spela Stangler-Herodez
- Laboratory of Medical Genetics, University Medical Centre Maribor, Maribor, Slovenia
- Maribor Medical Faculty, University of Maribor, Maribor, Slovenia
| | - Minja Zorc
- Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia
| | - Peter Dovc
- Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia
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5
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Shimelis H, Oetjens MT, Walsh LK, Wain KE, Znidarsic M, Myers SM, Finucane BM, Ledbetter DH, Martin CL. Prevalence and Penetrance of Rare Pathogenic Variants in Neurodevelopmental Psychiatric Genes in a Health Care System Population. Am J Psychiatry 2023; 180:65-72. [PMID: 36475376 PMCID: PMC10017070 DOI: 10.1176/appi.ajp.22010062] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Autism, schizophrenia, and other clinically distinct neurodevelopmental psychiatric disorders (NPDs) have shared genetic etiologies, including single-gene and multigenic copy number variants (CNVs). Because rare variants are primarily investigated in clinical cohorts, population-based estimates of their prevalence and penetrance are lacking. The authors determined the prevalence, penetrance, and NPD risk of pathogenic single-gene variants in a large health care system population. METHODS The authors analyzed linked genomic and electronic health record (EHR) data in a subset of 90,595 participants from Geisinger's MyCode Community Health Initiative, known as the DiscovEHR cohort. Loss-of-function pathogenic variants in 94 high-confidence NPD genes were identified through exome sequencing, and NPD penetrance was calculated using preselected EHR diagnosis codes. NPD risk was estimated using a case-control comparison of DiscovEHR participants with and without NPD diagnoses. Results from single-gene variant analyses were also compared with those from 31 previously reported pathogenic NPD CNVs. RESULTS Pathogenic variants were identified in 0.34% of the DiscovEHR cohort and demonstrated a 34.3% penetrance for NPDs. Similar to CNVs, sequence variants collectively conferred a substantial risk for several NPD diagnoses, including autism, schizophrenia, and bipolar disorder. Significant NPD risk remained after participants with intellectual disability were excluded from the analysis, confirming the association with major psychiatric disorders in individuals without severe cognitive deficits. CONCLUSIONS Collectively, rare single-gene variants and CNVs were found in >1% of individuals in a large health care system population and play an important contributory role in mental health disorders. Diagnostic genetic testing for pathogenic variants among symptomatic individuals with NPDs could improve clinical outcomes through early intervention and anticipatory therapeutic support.
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Affiliation(s)
- Hermela Shimelis
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - Matthew T Oetjens
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - Lauren K Walsh
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - Karen E Wain
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - Masa Znidarsic
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - Scott M Myers
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - Brenda M Finucane
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - David H Ledbetter
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
| | - Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger, Lewisburg, Pa. (all authors)
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6
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Cherian C, Appendino JP, Ashtiani S, Federico P, Molnar CP, Kerr M, Khan A, Au PYB, Klein KM. The phenotypic spectrum of KCNT1: a new family with variable epilepsy syndromes including mild focal epilepsy. J Neurol 2021; 269:2162-2171. [PMID: 34537872 DOI: 10.1007/s00415-021-10808-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND AND OBJECTIVE Pathogenic variants in KCNT1 have been associated with severe forms of epilepsy, typically sleep-related hypermotor epilepsy or epilepsy of infancy with migrating focal seizures. To show that pathogenic variants in KCNT1 can be associated with mild extra-frontal epilepsy, we report a KCNT1 family with a wide spectrum of phenotypes ranging from developmental and epileptic encephalopathy to mild focal epilepsy without cognitive regression and not consistent with sleep-related hypermotor epilepsy. METHODS A large Canadian family of Caucasian descent including 9 affected family members was recruited. Family members were phenotyped by direct interview and review of existing medical records. Clinical epilepsy gene panel analysis and exome sequencing were performed. RESULTS Phenotypic information was available for five family members of which two had developmental and epileptic encephalopathy and three had normal development and focal epilepsy with presumed extra-frontal onset. All three had predominantly nocturnal seizures that did not show hyperkinetic features. All three reported clusters of seizures at night with a feeling of being unable to breathe associated with gasping for air, choking and/or repetitive swallowing possibly suggesting insular or opercular involvement. Genetic analysis identified a heterozygous KCNT1 c.2882G > A, p.Arg961His variant that was predicted to be deleterious. DISCUSSION This family demonstrates that the phenotypic spectrum associated with KCNT1 pathogenic variants is broader than previously assumed. Our findings indicate that variants in KCNT1 can be associated with mild focal epilepsy and should not be excluded during variant interpretation in such patients based solely on gene-disease validity.
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Affiliation(s)
- Christina Cherian
- Department of Clinical Neurosciences, Cumming School of Medicine, Foothills Medical Centre, University of Calgary, 1403 29 Street NW, Calgary, AB, T2N 2T9, Canada
| | - Juan P Appendino
- Division of Clinical Neuroscience, Department of Pediatrics, Cumming School of Medicine, Alberta Children's Hospital, University of Calgary, Calgary, AB, Canada
| | - Setareh Ashtiani
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Paolo Federico
- Department of Clinical Neurosciences, Cumming School of Medicine, Foothills Medical Centre, University of Calgary, 1403 29 Street NW, Calgary, AB, T2N 2T9, Canada.,Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada.,Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Seaman Family MR Research Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Christine P Molnar
- Department of Radiology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Marina Kerr
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Aneal Khan
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Ping Yee Billie Au
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Karl Martin Klein
- Department of Clinical Neurosciences, Cumming School of Medicine, Foothills Medical Centre, University of Calgary, 1403 29 Street NW, Calgary, AB, T2N 2T9, Canada. .,Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada. .,Cumming School of Medicine, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada. .,Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada. .,Epilepsy Center Frankfurt Rhine-Main, Department of Neurology, Center of Neurology and Neurosurgery, University Hospital, Goethe-University, Frankfurt, Germany. .,Center for Personalized Translational Epilepsy Research (CePTER), Goethe University, Frankfurt, Germany.
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7
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Ren Z, Povysil G, Hostyk JA, Cui H, Bhardwaj N, Goldstein DB. ATAV: a comprehensive platform for population-scale genomic analyses. BMC Bioinformatics 2021; 22:149. [PMID: 33757430 PMCID: PMC7988908 DOI: 10.1186/s12859-021-04071-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/14/2021] [Indexed: 11/21/2022] Open
Abstract
Background A common approach for sequencing studies is to do joint-calling and store variants of all samples in a single file. If new samples are continually added or controls are re-used for several studies, the cost and time required to perform joint-calling for each analysis can become prohibitive. Results We present ATAV, an analysis platform for large-scale whole-exome and whole-genome sequencing projects. ATAV stores variant and per site coverage data for all samples in a centralized database, which is efficiently queried by ATAV to support diagnostic analyses for trios and singletons, as well as rare-variant collapsing analyses for finding disease associations in complex diseases. Runtime logs ensure full reproducibility and the modularized ATAV framework makes it extensible to continuous development. Besides helping with the identification of disease-causing variants for a range of diseases, ATAV has also enabled the discovery of disease-genes by rare-variant collapsing on datasets containing more than 20,000 samples. Analyses to date have been performed on data of more than 110,000 individuals demonstrating the scalability of the framework. To allow users to easily access variant-level data directly from the database, we provide a web-based interface, the ATAV data browser (http://atavdb.org/). Through this browser, summary-level data for more than 40,000 samples can be queried by the general public representing a mix of cases and controls of diverse ancestries. Users have access to phenotype categories of variant carriers, as well as predicted ancestry, gender, and quality metrics. In contrast to many other platforms, the data browser is able to show data of newly-added samples in real-time and therefore evolves rapidly as more and more samples are sequenced. Conclusions Through ATAV, users have public access to one of the largest variant databases for patients sequenced at a tertiary care center and can look up any genes or variants of interest. Additionally, since the entire code is freely available on GitHub, ATAV can easily be deployed by other groups that wish to build their own platform, database, and user interface.
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Affiliation(s)
- Zhong Ren
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA.
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Joseph A Hostyk
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Hongzhu Cui
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Nitin Bhardwaj
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
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8
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Eade K, Gantner ML, Hostyk JA, Nagasaki T, Giles S, Fallon R, Harkins-Perry S, Baldini M, Lim EW, Scheppke L, Dorrell MI, Cai C, Baugh EH, Wolock CJ, Wallace M, Berlow RB, Goldstein DB, Metallo CM, Friedlander M, Allikmets R. Serine biosynthesis defect due to haploinsufficiency of PHGDH causes retinal disease. Nat Metab 2021; 3:366-377. [PMID: 33758422 PMCID: PMC8084205 DOI: 10.1038/s42255-021-00361-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 02/10/2021] [Indexed: 02/08/2023]
Abstract
Macular telangiectasia type 2 (MacTel) is a progressive, late-onset retinal degenerative disease linked to decreased serum levels of serine that elevate circulating levels of a toxic ceramide species, deoxysphingolipids (deoxySLs); however, causal genetic variants that reduce serine levels in patients have not been identified. Here we identify rare, functional variants in the gene encoding the rate-limiting serine biosynthetic enzyme, phosphoglycerate dehydrogenase (PHGDH), as the single locus accounting for a significant fraction of MacTel. Under a dominant collapsing analysis model of a genome-wide enrichment analysis of rare variants predicted to impact protein function in 793 MacTel cases and 17,610 matched controls, the PHGDH gene achieves genome-wide significance (P = 1.2 × 10-13) with variants explaining ~3.2% of affected individuals. We further show that the resulting functional defects in PHGDH cause decreased serine biosynthesis and accumulation of deoxySLs in retinal pigmented epithelial cells. PHGDH is a significant locus for MacTel that explains the typical disease phenotype and suggests a number of potential treatment options.
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Affiliation(s)
- Kevin Eade
- Lowy Medical Research Institute, La Jolla, CA, USA
| | | | - Joseph A Hostyk
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | | | - Sarah Giles
- Lowy Medical Research Institute, La Jolla, CA, USA
| | - Regis Fallon
- Lowy Medical Research Institute, La Jolla, CA, USA
| | - Sarah Harkins-Perry
- Lowy Medical Research Institute, La Jolla, CA, USA
- The Scripps Research Institute, La Jolla, CA, USA
| | - Michelle Baldini
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Esther W Lim
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Lea Scheppke
- Lowy Medical Research Institute, La Jolla, CA, USA
| | | | - Carolyn Cai
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Charles J Wolock
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Martina Wallace
- Department of Bioengineering, University of California, San Diego, CA, USA
| | | | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | | | - Martin Friedlander
- Lowy Medical Research Institute, La Jolla, CA, USA
- The Scripps Research Institute, La Jolla, CA, USA
- Scripps Clinic Medical Group, La Jolla, CA, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
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9
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Datta AN, Bahi-Buisson N, Bienvenu T, Buerki SE, Gardiner F, Cross JH, Heron B, Kaminska A, Korff CM, Lepine A, Lesca G, McTague A, Mefford HC, Mignot C, Milh M, Piton A, Pressler RM, Ruf S, Sadleir LG, de Saint Martin A, Van Gassen K, Verbeek NE, Ville D, Villeneuve N, Zacher P, Scheffer IE, Lemke JR. The phenotypic spectrum of X-linked, infantile onset ALG13-related developmental and epileptic encephalopathy. Epilepsia 2021; 62:325-334. [PMID: 33410528 PMCID: PMC7898319 DOI: 10.1111/epi.16761] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/27/2020] [Accepted: 10/23/2020] [Indexed: 12/20/2022]
Abstract
Objective Asparagine‐linked glycosylation 13 (ALG13) deficiencies have been repeatedly described in the literature with the clinical phenotype of a developmental and epileptic encephalopathy (DEE). Most cases were females carrying the recurrent ALG13 de novo variant, p.(Asn107Ser), with normal transferrin electrophoresis. Methods We delineate the phenotypic spectrum of 38 individuals, 37 girls and one boy, 16 of them novel and 22 published, with the most common pathogenic ALG13 variant p.(Asn107Ser) and additionally report the phenotype of three individuals carrying other likely pathogenic ALG13 variants. Results The phenotypic spectrum often comprised pharmacoresistant epilepsy with epileptic spasms, mostly with onset within the first 6 months of life and with spasm persistence in one‐half of the cases. Tonic seizures were the most prevalent additional seizure type. Electroencephalography showed hypsarrhythmia and at a later stage of the disease in one‐third of all cases paroxysms of fast activity with electrodecrement. ALG13‐related DEE was usually associated with severe to profound developmental delay; ambulation was acquired by one‐third of the cases, whereas purposeful hand use was sparse or completely absent. Hand stereotypies and dyskinetic movements including dystonia or choreoathetosis were relatively frequent. Verbal communication skills were absent or poor, and eye contact and pursuit were often impaired. Significance X‐linked ALG13‐related DEE usually manifests as West syndrome with severe to profound developmental delay. It is predominantly caused by the recurrent de novo missense variant p.(Asn107Ser). Comprehensive functional studies will be able to prove or disprove an association with congenital disorder of glycosylation.
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Affiliation(s)
- Alexandre N Datta
- Pediatric Neurology and Developmental Medicine Department, University Children's Hospital, University of Basel, Basel, Switzerland
| | - Nadia Bahi-Buisson
- Pediatric Neurology, Necker-Enfants Malades Children's Hospital, Paris and Institute IMAGINE, INSERM U1163, University of Paris, Paris, France
| | - Thierry Bienvenu
- Paris Institute of Psychiatry and Neuroscience, University of Paris, Paris, France
| | - Sarah E Buerki
- Pediatric Neurology Department, University Children's Hospital Zürich, Switzerland
| | - Fiona Gardiner
- Austin Health, University of Melbourne, Melbourne, Victoria, Australia
| | - J Helen Cross
- Clinical Neuroscience, University College London-Great Ormond Street Institute of Child Health, London, UK
| | - Bénédicte Heron
- Pediatric Neurology Department, Armand Trousseau-La Roche Guyon University Hospital, APHP and GRC No. 19, Sorbonne Universities, Paris, France
| | - Anna Kaminska
- Department of Clinical Neurophysiology, Necker-Enfants Malades Hospital, Public Hospital Network of Paris, Paris, France
| | - Christian M Korff
- Pediatric Neurology Unit, Department of Pediatrics, Geneva University Hospital, Geneva, Switzerland
| | - Anne Lepine
- Pediatric Neurology and Metabolic Diseases Department, University Hospital La Timone, Marseilles, France
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | - Amy McTague
- Clinical Neuroscience, University College London-Great Ormond Street Institute of Child Health, London, UK
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Cyrill Mignot
- Department of Genetics and Reference Center for Intellectual Deficiencies of Rare Causes, , Sorbonne University, Paris, France
| | - Matthieu Milh
- Pediatric Neurology Unit, Department of Pediatrics, Geneva University Hospital, Geneva, Switzerland
| | - Amélie Piton
- Department of Molecular Genetics, University Hospital Strasbourg, Strasbourg, France
| | - Ronit M Pressler
- Clinical Neuroscience, University College London-Great Ormond Street Institute of Child Health, London, UK.,Department of Neurophysiology, Great Ormond Street Hospital for Children, National Health Service Foundation Trust, London, UK
| | - Susanne Ruf
- Department of Pediatric Neurology and Developmental Medicine, University Children's Hospital, Tübingen, Germany
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, New Zealand
| | - Anne de Saint Martin
- Pediatric Neurology Unit, Department of Pediatrics, University Hospital Strasbourg, Strasbourg, France
| | - Koen Van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nienke E Verbeek
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Dorothée Ville
- Pediatric Neurology Department and Reference Center of Rare Epilepsies, Mother Child Women's Hospital, Lyon University Hospital, France
| | - Nathalie Villeneuve
- Pediatric Neurology and Metabolic Diseases Department, University Hospital La Timone, Marseilles, France
| | - Pia Zacher
- Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Ingrid E Scheffer
- Austin Health, University of Melbourne, Melbourne, Victoria, Australia.,Department of Paediatrics, Royal Children's Hospital, Florey and Murdoch Children's Research Institutes, University of Melbourne, Melbourne, Victoria, Australia
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
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10
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Stanley KE, Giordano J, Thorsten V, Buchovecky C, Thomas A, Ganapathi M, Liao J, Dharmadhikari AV, Revah-Politi A, Ernst M, Lippa N, Holmes H, Povysil G, Hostyk J, Parker CB, Goldenberg R, Saade GR, Dudley DJ, Pinar H, Hogue C, Reddy UM, Silver RM, Aggarwal V, Allen AS, Wapner RJ, Goldstein DB. Causal Genetic Variants in Stillbirth. N Engl J Med 2020; 383:1107-1116. [PMID: 32786180 PMCID: PMC7604888 DOI: 10.1056/nejmoa1908753] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND In the majority of cases, the cause of stillbirth remains unknown despite detailed clinical and laboratory evaluation. Approximately 10 to 20% of stillbirths are attributed to chromosomal abnormalities. However, the causal nature of single-nucleotide variants and small insertions and deletions in exomes has been understudied. METHODS We generated exome sequencing data for 246 stillborn cases and followed established guidelines to identify causal variants in disease-associated genes. These genes included those that have been associated with stillbirth and strong candidate genes. We also evaluated the contribution of 18,653 genes in case-control analyses stratified according to the degree of depletion of functional variation (described here as "intolerance" to variation). RESULTS We identified molecular diagnoses in 15 of 246 cases of stillbirth (6.1%) involving seven genes that have been implicated in stillbirth and six disease genes that are good candidates for phenotypic expansion. Among the cases we evaluated, we also found an enrichment of loss-of-function variants in genes that are intolerant to such variation in the human population (odds ratio, 2.15; 95% confidence interval [CI], 1.46 to 3.06). Loss-of-function variants in intolerant genes were concentrated in genes that have not been associated with human disease (odds ratio, 2.22; 95% CI, 1.41 to 3.34), findings that differ from those in two postnatal clinical populations that were also evaluated in this study. CONCLUSIONS Our findings establish the diagnostic utility of clinical exome sequencing to evaluate the role of small genomic changes in stillbirth. The strength of the novel risk signal (as generated through the stratified analysis) was similar to that in known disease genes, which indicates that the genetic cause of stillbirth remains largely unknown. (Funded by the Institute for Genomic Medicine.).
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Affiliation(s)
- Kate E Stanley
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Jessica Giordano
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Vanessa Thorsten
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Christie Buchovecky
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Amanda Thomas
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Mythily Ganapathi
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Jun Liao
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Avinash V Dharmadhikari
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Anya Revah-Politi
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Michelle Ernst
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Natalie Lippa
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Halie Holmes
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Gundula Povysil
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Joseph Hostyk
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Corette B Parker
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Robert Goldenberg
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - George R Saade
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Donald J Dudley
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Halit Pinar
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Carol Hogue
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Uma M Reddy
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Robert M Silver
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Vimla Aggarwal
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Andrew S Allen
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - Ronald J Wapner
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
| | - David B Goldstein
- From the Institute for Genomic Medicine at Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center (K.E.S., J.G., A.R.-P., M.E., N.L., H.H., G.P., J.H., V.A., R.J.W., D.B.G.), and the Departments of Obstetrics and Gynecology (J.G., R.G., R.J.W.) and Pathology and Cell Biology (C.B., A.T., M.G., J.L., A.V.D., V.A.), Columbia University Medical Center, New York; RTI International, Research Triangle Park (V.T., C.B.P.), and the Department of Biostatistics and Bioinformatics, Duke University, Durham (A.S.A.) - both in North Carolina; the Departments of Obstetrics and Gynecology and Cell Biology, University of Texas Medical Branch, Galveston (G.R.S.); the Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Virginia School of Medicine, Charlottesville (D.J.D.); the Division of Perinatal and Pediatric Pathology, Women and Infants Hospital, Warren Alpert School of Medicine of Brown University, Providence, RI (H.P.); Rollins School of Public Health, Emory University, Atlanta (C.H.); Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Pregnancy and Perinatology Branch, Bethesda, MD (U.M.R.); and the University of Utah and Intermountain Healthcare, Salt Lake City (R.M.S.)
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Qi M, Fan S, Wang Z, Yang X, Xie Z, Chen K, Zhang L, Lin T, Liu W, Lin X, Yan Y, Yang Y, Zhao H. Identifying Common Genes, Cell Types and Brain Regions Between Diseases of the Nervous System. Front Genet 2019; 10:1202. [PMID: 31850066 PMCID: PMC6895906 DOI: 10.3389/fgene.2019.01202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 10/30/2019] [Indexed: 12/12/2022] Open
Abstract
Background: Diseases of the nervous system are widely considered to be caused by genetic mutations, and they have been shown to share pathogenic genes. Discovering the shared mechanisms of these diseases is useful for designing common treatments. Method: In this study, by reviewing 518 articles published after 2007 on 20 diseases of the nervous system, we compiled data on 1607 mutations occurring in 365 genes, totals that are 1.9 and 3.2 times larger than those collected in the Clinvar database, respectively. A combination with the Clinvar data gives 2434 pathogenic mutations and 424 genes. Using this information, we measured the genetic similarities between the diseases according to the number of genes causing two diseases simultaneously. Further detection was carried out on the similarity between diseases in terms of cell types. Disease-related cell types were defined as those with disease-related gene enrichment among the marker genes of cells, as ascertained by analyzing single-cell sequencing data. Enrichment profiles of the disease-related genes over 25 cell types were constructed. The disease similarity in terms of cell types was obtained by calculating the distances between the enrichment profiles of these genes. The same strategy was applied to measure the disease similarity in terms of brain regions by analyzing the gene expression data from 10 brain regions. Results: The disease similarity was first measured in terms of genes. The result indicated that the proportions of overlapped genes between diseases were significantly correlated to the DMN scores (phenotypic similarity), with a Pearson correlation coefficient of 0.40 and P-value = 6.0×10-3. The disease similarity analysis for cell types identified that the distances between enrichment profiles of the disease-related genes were negatively correlated to the DMN scores, with Spearman correlation coefficient = -0.26 (P-value = 1.5 × 10-2). However, the brain region enrichment profile distances of the disease-related genes were not significantly correlated with the DMN score. Besides the similarity of diseases, this study identified novel relationships between diseases and cell types. Conclusion: We manually constructed the most comprehensive dataset to date for genes with mutations related to 20 nervous system diseases. By using this dataset, the similarities between diseases in terms of genes and cell types were found to be significantly correlated to their phenotypic similarity. However, the disease similarities in terms of brain regions were not significantly correlated with the phenotypic similarities. Thus, the phenotypic similarity between the diseases is more likely to be caused by dysfunctions of the same genes or the same types of neurons rather than the same brain regions. The data are collected into the database NeurodisM, which is available at http://biomed-ai.org/neurodism.
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Affiliation(s)
- Mengling Qi
- Sun Yat-sen Memorial Hospital, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
| | - Shichao Fan
- Sun Yat-sen Memorial Hospital, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
| | - Zhi Wang
- Sun Yat-sen Memorial Hospital, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
| | - Xiaoxing Yang
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
| | - Zicong Xie
- Software Institute, Nanjing University, Nanjing, China
| | - Ken Chen
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
| | - Lei Zhang
- Department of Hepatobiliary Surgery II, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Tao Lin
- Zhongshan Medical College, Sun Yat-sen University, Guangzhou, China
| | - Wei Liu
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xinlei Lin
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yan Yan
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yuedong Yang
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
| | - Huiying Zhao
- Sun Yat-sen Memorial Hospital, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
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12
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Barcia G, Chemaly N, Kuchenbuch M, Eisermann M, Gobin-Limballe S, Ciorna V, Macaya A, Lambert L, Dubois F, Doummar D, Billette de Villemeur T, Villeneuve N, Barthez MA, Nava C, Boddaert N, Kaminska A, Bahi-Buisson N, Milh M, Auvin S, Bonnefont JP, Nabbout R. Epilepsy with migrating focal seizures: KCNT1 mutation hotspots and phenotype variability. NEUROLOGY-GENETICS 2019; 5:e363. [PMID: 31872048 PMCID: PMC6878841 DOI: 10.1212/nxg.0000000000000363] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 09/04/2019] [Indexed: 01/29/2023]
Abstract
Objective To report new sporadic cases and 1 family with epilepsy of infancy with migrating focal seizures (EIMFSs) due to KCNT1 gain-of-function and to assess therapies' efficacy including quinidine. Methods We reviewed the clinical, EEG, and molecular data of 17 new patients with EIMFS and KCNT1 mutations, in collaboration with the network of the French reference center for rare epilepsies. Results The mean seizure onset age was 1 month (range: 1 hour to 4 months), and all children had focal motor seizures with autonomic signs and migrating ictal pattern on EEG. Three children also had infantile spasms and hypsarrhythmia. The identified KCNT1 variants clustered as “hot spots” on the C-terminal domain, and all mutations occurred de novo except the p.R398Q mutation inherited from the father with nocturnal frontal lobe epilepsy, present in 2 paternal uncles, one being asymptomatic and the other with single tonic-clonic seizure. In 1 patient with EIMFS, we identified the p.R1106Q mutation associated with Brugada syndrome and saw no abnormality in cardiac rhythm. Quinidine was well tolerated when administered to 2 and 4-year-old patients but did not reduce seizure frequency. Conclusions The majority of the KCNT1 mutations appear to cluster in hot spots essential for the channel activity. A same mutation can be linked to a spectrum of conditions ranging from EMFSI to asymptomatic carrier, even in the same family. None of the antiepileptic therapies displayed clinical efficacy, including quinidine in 2 patients.
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Affiliation(s)
- Giulia Barcia
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Nicole Chemaly
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Mathieu Kuchenbuch
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Monika Eisermann
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Stéphanie Gobin-Limballe
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Viorica Ciorna
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Alfons Macaya
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laetitia Lambert
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Fanny Dubois
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Diane Doummar
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Thierry Billette de Villemeur
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Nathalie Villeneuve
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Marie-Anne Barthez
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Caroline Nava
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Nathalie Boddaert
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Anna Kaminska
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Nadia Bahi-Buisson
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Mathieu Milh
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Stéphane Auvin
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Jean-Paul Bonnefont
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Rima Nabbout
- Service de Génétique (G.B., J.-P.B., S.G.-L.), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1163 (G.B., N.B-.B., R.N.), Université Paris Descartes, PRES Sorbonne Paris Cité, Paris, France; Service de Neurologie Pédiatrique (N.C., N.B-.B., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Centre de Référence des Epilepsies Rares (N.C., A.K., R.N.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; INSERM U1129 (N.N., A.K., R.N.), Paris, France; Service de Neurophysiologie Clinique et Pédiatrie (M.K.), INSERM U1099, Hôpital Universitaire de Rennes, Université de Rennes, France; Service de Neurophysiologie Clinique (M.E., A.K.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Génétique Clinique (V.C.), Hôpital Femme Mère Enfant, Metz-Thionville, France; Pediatric Neurology Research Group (A.M.), Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain; Service de Génétique Clinique (L.L.), Hôpital d'Enfants, CHU de Nancy, Vandoeuvre-Lès-Nancy, France; Service de Pédiatrie (F.D.), CHU de Grenoble, France; Service de Neurologie Pédiatrique (D.D., T.B.V.), Hôpital Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Neurologie Pédiatrique (N.V., M.M.), APHM, Hôpital d'Enfants de La Timone, Marseille, France; Service de Neurologie Pédiatrique (M-.A.B., M.M.), Centre Hospitalier Universitaire de Tours, Tours, France; Département de Génétique (C.N., M.M.), Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France; Service de Radiologie Pédiatrique (N.B., M.M.), Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Aix-Marseille (M.M.), INSERM, MMG, UMR-S 1251, Faculté de Médecine, Marseille, France; and Unité de Neurologie Pédiatrique (S.A.), Hôpital Rober Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
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Povysil G, Petrovski S, Hostyk J, Aggarwal V, Allen AS, Goldstein DB. Rare-variant collapsing analyses for complex traits: guidelines and applications. Nat Rev Genet 2019; 20:747-759. [PMID: 31605095 DOI: 10.1038/s41576-019-0177-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2019] [Indexed: 12/11/2022]
Abstract
The first phase of genome-wide association studies (GWAS) assessed the role of common variation in human disease. Advances optimizing and economizing high-throughput sequencing have enabled a second phase of association studies that assess the contribution of rare variation to complex disease in all protein-coding genes. Unlike the early microarray-based studies, sequencing-based studies catalogue the full range of genetic variation, including the evolutionarily youngest forms. Although the experience with common variants helped establish relevant standards for genome-wide studies, the analysis of rare variation introduces several challenges that require novel analysis approaches.
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Affiliation(s)
- Gundula Povysil
- Institute for Genomic Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.,Department of Medicine, The University of Melbourne, Austin Health and Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Joseph Hostyk
- Institute for Genomic Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Vimla Aggarwal
- Institute for Genomic Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY, USA
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, Columbia University, New York, NY, USA.
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14
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Bar C, Barcia G, Jennesson M, Le Guyader G, Schneider A, Mignot C, Lesca G, Breuillard D, Montomoli M, Keren B, Doummar D, Billette de Villemeur T, Afenjar A, Marey I, Gerard M, Isnard H, Poisson A, Dupont S, Berquin P, Meyer P, Genevieve D, De Saint Martin A, El Chehadeh S, Chelly J, Guët A, Scalais E, Dorison N, Myers CT, Mefford HC, Howell KB, Marini C, Freeman JL, Nica A, Terrone G, Sekhara T, Lebre A, Odent S, Sadleir LG, Munnich A, Guerrini R, Scheffer IE, Kabashi E, Nabbout R. Expanding the genetic and phenotypic relevance of
KCNB1
variants in developmental and epileptic encephalopathies: 27 new patients and overview of the literature. Hum Mutat 2019; 41:69-80. [DOI: 10.1002/humu.23915] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/28/2019] [Accepted: 09/09/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Claire Bar
- Department of Pediatric Neurology, Reference Centre for Rare EpilepsiesHôpital Necker‐Enfants MaladesParis France
- Imagine institute, laboratory of Translational Research for Neurological Disorders, INSERM UMR 1163Imagine InstituteParis France
- Université Paris Descartes‐Sorbonne Paris CitéParis France
| | - Giulia Barcia
- Imagine institute, laboratory of Translational Research for Neurological Disorders, INSERM UMR 1163Imagine InstituteParis France
- Université Paris Descartes‐Sorbonne Paris CitéParis France
- Department of genetics, Necker Enfants Malades hospitalAssistance Publique‐Hôpitaux de ParisParis France
| | | | - Gwenaël Le Guyader
- Department of geneticsUniversity hospital PoitiersPoitiers Cedex France
- EA3808‐NEUVACOD Unité Neurovasculaire et Troubles Cognitifs, Pôle Biologie SantéUniversité de PoitiersPoitiers France
| | - Amy Schneider
- Department of Medicine, Epilepsy Research Centre, Austin HealthThe University of MelbourneHeidelberg Victoria Australia
| | - Cyril Mignot
- Institut du Cerveau et de la Moelle épinière, INSERM, U 1127, CNRS UMR 7225Sorbonne Universités UPMC Univ Paris 06 UMR S 1127 Paris France
- Département de Génétique et de Cytogénétique, Centre de Reference Déficience Intellectuelle de Causes Rares, APHP, Hôpital Pitié‐SalpêtrièreGRC UPMC (Déficience Intellectuelle et Autisme)Paris France
| | - Gaetan Lesca
- Department of geneticsHospices Civils de LyonLyon France
- Neurosciences centre of Lyon, INSERM U1028, UMR CNRS 5292Université Claude Bernard Lyon 1Bron Cedex France
| | - Delphine Breuillard
- Department of Pediatric Neurology, Reference Centre for Rare EpilepsiesHôpital Necker‐Enfants MaladesParis France
| | - Martino Montomoli
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Department of Neuroscience, A Meyer Children's HospitalUniversity of FlorenceFlorence Italy
| | - Boris Keren
- Département de Génétique et de Cytogénétique, Centre de Reference Déficience Intellectuelle de Causes Rares, APHP, Hôpital Pitié‐SalpêtrièreGRC UPMC (Déficience Intellectuelle et Autisme)Paris France
| | - Diane Doummar
- Department of Pediatric Neurology, Hôpital Armand TrousseauAP‐HPParis France
| | | | - Alexandra Afenjar
- Département de Génétique et Embryologie Médicale, Pathologies Congénitales du Cervelet‐LeucoDystrophies, Centre de Référence déficiences intellectuelles de causes rares, AP‐HP, Hôpital Armand Trousseau, GRC n°19Sorbonne UniversitéParis France
| | - Isabelle Marey
- Département de Génétique et de Cytogénétique, Centre de Reference Déficience Intellectuelle de Causes Rares, APHP, Hôpital Pitié‐SalpêtrièreGRC UPMC (Déficience Intellectuelle et Autisme)Paris France
| | | | | | - Alice Poisson
- Reference Center for Diagnosis and Management of Genetic Psychiatric Disorders, Centre Hospitalier le Vinatier and EDR‐Psy TeamCentre National de la Recherche Scientifique & Lyon 1 Claude Bernard UniversityVilleurbanne France
| | - Sophie Dupont
- Institut du Cerveau et de la Moelle épinière, INSERM, U 1127, CNRS UMR 7225Sorbonne Universités UPMC Univ Paris 06 UMR S 1127 Paris France
- Epileptology and Rehabilitation department, GH Pitie‐Salpêtrière‐Charles FoixAP‐HPParis France
| | - Patrick Berquin
- Department of pediatric neurology Amiens‐Picardie university hospitalUniversité de Picardie Jules VerneAmiens France
| | - Pierre Meyer
- Department of pediatric neurologyMontpellier university hospitalMontpellier France
- PhyMedExp, U1046 INSERMUMR9214 CNRSMontpellier France
| | - David Genevieve
- Service de génétique clinique et du Département de Génétique Médicale, Maladies Rares et Médecine Personnalisée, Centre de référence maladies rares anomalies du développementCHU MontpellierMontpellier France
| | - Anne De Saint Martin
- Department of Pediatric NeurologyStrasbourg University HospitalStrasbourg France
| | - Salima El Chehadeh
- Department of genetics, Hôpital de HautepierreHôpitaux Universitaires de StrasbourgStrasbourg France
| | - Jamel Chelly
- Department of genetics, Hôpital de HautepierreHôpitaux Universitaires de StrasbourgStrasbourg France
| | - Agnès Guët
- Department of PediatricLouis‐Mourier HospitalColombes France
| | - Emmanuel Scalais
- Department of Pediatric Neurology, Centre Hospitalier de LuxembourgLuxembourg CityLuxembourg City Luxembourg
| | - Nathalie Dorison
- Department of pediatric NeurosurgeryRothschild Foundation HospitalParis France
| | - Candace T. Myers
- Department of PediatricsUniversity of WashingtonSeattle Washington
| | - Heather C. Mefford
- Department of Pediatrics, Division of Genetic MedicineUniversity of WashingtonSeattle Washington
| | - Katherine B. Howell
- Departments of Neurology and Paediatrics, Royal Children's HospitalUniversity of MelbourneMelbourne Victoria Australia
- Murdoch Children's Research InstituteMelbourne Victoria Australia
| | - Carla Marini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Department of Neuroscience, A Meyer Children's HospitalUniversity of FlorenceFlorence Italy
| | - Jeremy L. Freeman
- Departments of Neurology and Paediatrics, Royal Children's HospitalUniversity of MelbourneMelbourne Victoria Australia
- Murdoch Children's Research InstituteMelbourne Victoria Australia
| | - Anca Nica
- Department of Neurology, Center for Clinical Research (CIC 1414)Rennes University HospitalRennes France
| | - Gaetano Terrone
- Department of Translational Medical Sciences, Section of Pediatrics‐Child Neurology UnitFederico II UniversityNaples Italy
| | - Tayeb Sekhara
- Department of Pediatric NeurologyC.H.I.R.E.CBrussels Belgium
| | - Anne‐Sophie Lebre
- Department of genetics, Maison Blanche hospitalUniversity hospital, ReimsReims France
| | - Sylvie Odent
- Reference Centre for Rare Developmental AbnormalitiesCLAD‐Ouest, CHU RennesRennes France
- Institute of genetics and developmentCNRS UMR 6290, Rennes universityRennes France
| | - Lynette G. Sadleir
- Department of Paediatrics and Child HealthUniversity of OtagoWellington New Zealand
| | - Arnold Munnich
- Université Paris Descartes‐Sorbonne Paris CitéParis France
- Department of genetics, Necker Enfants Malades hospitalAssistance Publique‐Hôpitaux de ParisParis France
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Department of Neuroscience, A Meyer Children's HospitalUniversity of FlorenceFlorence Italy
| | - Ingrid E. Scheffer
- Department of Medicine, Epilepsy Research Centre, Austin HealthThe University of MelbourneHeidelberg Victoria Australia
- Departments of Neurology and Paediatrics, Royal Children's HospitalUniversity of MelbourneMelbourne Victoria Australia
- The Florey Institute of Neurosciences and Mental HealthHeidelberg Victoria Australia
| | - Edor Kabashi
- Imagine institute, laboratory of Translational Research for Neurological Disorders, INSERM UMR 1163Imagine InstituteParis France
- Université Paris Descartes‐Sorbonne Paris CitéParis France
| | - Rima Nabbout
- Department of Pediatric Neurology, Reference Centre for Rare EpilepsiesHôpital Necker‐Enfants MaladesParis France
- Imagine institute, laboratory of Translational Research for Neurological Disorders, INSERM UMR 1163Imagine InstituteParis France
- Université Paris Descartes‐Sorbonne Paris CitéParis France
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15
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Alkelai A, Greenbaum L, Heinzen EL, Baugh EH, Teitelbaum A, Zhu X, Strous RD, Tatarskyy P, Zai CC, Tiwari AK, Tampakeras M, Freeman N, Müller DJ, Voineskos AN, Lieberman JA, Delaney SL, Meltzer HY, Remington G, Kennedy JL, Pulver AE, Peabody EP, Levy DL, Lerer B. New insights into tardive dyskinesia genetics: Implementation of whole-exome sequencing approach. Prog Neuropsychopharmacol Biol Psychiatry 2019; 94:109659. [PMID: 31153890 DOI: 10.1016/j.pnpbp.2019.109659] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 02/07/2023]
Abstract
Tardive dyskinesia (TD) is an adverse movement disorder induced by chronic treatment with antipsychotics drugs. The contribution of common genetic variants to TD susceptibility has been investigated in recent years, but with limited success. The aim of the current study was to investigate the potential contribution of rare variants to TD vulnerability. In order to identify TD risk genes, we performed whole-exome sequencing (WES) and gene-based collapsing analysis focusing on rare (allele frequency < 1%) and putatively deleterious variants (qualifying variants). 82 Jewish schizophrenia patients chronically treated with antipsychotics were included and classified as having severe TD or lack of any abnormal movements based on a rigorous definition of the TD phenotype. First, we performed a case-control, exome-wide collapsing analysis comparing 39 schizophrenia patients with severe TD to 3118 unrelated population controls. Then, we checked the potential top candidate genes among 43 patients without any TD manifestations. All the genes that were found to harbor one or more qualifying variants in patients without any TD features were excluded from the final list of candidate genes. Only one gene, regulating synaptic membrane exocytosis 2 (RIMS2), showed significant enrichment of qualifying variants in TD patients compared with unrelated population controls after correcting for multiple testing (Fisher's exact test p = 5.32E-08, logistic regression p = 2.50E-08). Enrichment was caused by a single variant (rs567070433) due to a frameshift in an alternative transcript of RIMS2. None of the TD negative patients had qualifying variants in this gene. In a validation cohort of 140 schizophrenia patients assessed for TD, the variant was also not detected in any individual. Some potentially suggestive TD genes were detected in the TD cohort and warrant follow-up in future studies. No significant enrichment in previously reported TD candidate genes was identified. To the best of our knowledge, this is the first WES study of TD, demonstrating the potential role of rare loss-of-function variant enrichment in this pharmacogenetic phenotype.
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Affiliation(s)
- Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA.
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Alexander Teitelbaum
- Jerusalem Mental Health Center, Kfar Shaul Psychiatric Hospital, Hebrew University-Hadassah School of Medicine, Jerusalem, Israel
| | - Xiaolin Zhu
- Institute for Genomic Medicine, Columbia University Medical Center, New York, USA
| | - Rael D Strous
- Maayenei Hayeshua Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Pavel Tatarskyy
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Clement C Zai
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Arun K Tiwari
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Maria Tampakeras
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada
| | - Natalie Freeman
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada
| | - Daniel J Müller
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Aristotle N Voineskos
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Jeffrey A Lieberman
- Columbia University, New York State Psychiatric Institute, New York City, NY, USA
| | - Shannon L Delaney
- Columbia University, New York State Psychiatric Institute, New York City, NY, USA
| | - Herbert Y Meltzer
- Psychiatry and Behavioral Sciences, Pharmacology and Physiology, Chemistry of Life Processes Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Gary Remington
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - James L Kennedy
- Tanenbaum Centre for Pharmacogenetics, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Canada; Department of Psychiatry, University of Toronto, Toronto, Canada; Institute of Medical Science, University of Toronto, Toronto, Canada
| | - Ann E Pulver
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emma P Peabody
- Psychology Research Laboratory, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Deborah L Levy
- Psychology Research Laboratory, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Bernard Lerer
- Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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16
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AlSaif S, Umair M, Alfadhel M. Biallelic SCN2A Gene Mutation Causing Early Infantile Epileptic Encephalopathy: Case Report and Review. J Cent Nerv Syst Dis 2019; 11:1179573519849938. [PMID: 31205438 PMCID: PMC6537489 DOI: 10.1177/1179573519849938] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 04/20/2019] [Indexed: 01/13/2023] Open
Abstract
The voltage-gated sodium channel neuronal type 2 alpha subunit (Navα1.2) encoded by the SCN2A gene causes early infantile epileptic encephalopathy (EIEE) inherited in an autosomal dominant manner. Clinically, it has variable presentations, ranging from benign familial infantile seizures (BFIS) to severe EIEE. Diagnosis is achieved through molecular DNA testing of the SCN2A gene. Herein, we report on a 30-month-old Saudi girl who presented on the fourth day of life with EIEE, normal brain magnetic resonance imaging (MRI), normal electroencephalography (EEG), and well-controlled seizures. Genetic investigation revealed a novel homozygous missense mutation (c.5242A > G; p.Asn1748Asp) in the SCN2A gene (NM_001040142.1). This is the first reported autosomal recessive inheritance of a disease allele in the SCN2A and therefore expands the molecular and inheritance spectrum of the SCN2A gene defects.
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Affiliation(s)
- Shahad AlSaif
- College of Medicine, King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia.,Division of Genetics, Department of Pediatrics, King Saud bin Abdulaziz University for Health Science, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
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17
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Cameron-Christie S, Wolock CJ, Groopman E, Petrovski S, Kamalakaran S, Povysil G, Vitsios D, Zhang M, Fleckner J, March RE, Gelfman S, Marasa M, Li Y, Sanna-Cherchi S, Kiryluk K, Allen AS, Fellström BC, Haefliger C, Platt A, Goldstein DB, Gharavi AG. Exome-Based Rare-Variant Analyses in CKD. J Am Soc Nephrol 2019; 30:1109-1122. [PMID: 31085678 DOI: 10.1681/asn.2018090909] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 03/06/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Studies have identified many common genetic associations that influence renal function and all-cause CKD, but these explain only a small fraction of variance in these traits. The contribution of rare variants has not been systematically examined. METHODS We performed exome sequencing of 3150 individuals, who collectively encompassed diverse CKD subtypes, and 9563 controls. To detect causal genes and evaluate the contribution of rare variants we used collapsing analysis, in which we compared the proportion of cases and controls carrying rare variants per gene. RESULTS The analyses captured five established monogenic causes of CKD: variants in PKD1, PKD2, and COL4A5 achieved study-wide significance, and we observed suggestive case enrichment for COL4A4 and COL4A3. Beyond known disease-associated genes, collapsing analyses incorporating regional variant intolerance identified suggestive dominant signals in CPT2 and several other candidate genes. Biallelic mutations in CPT2 cause carnitine palmitoyltransferase II deficiency, sometimes associated with rhabdomyolysis and acute renal injury. Genetic modifier analysis among cases with APOL1 risk genotypes identified a suggestive signal in AHDC1, implicated in Xia-Gibbs syndrome, which involves intellectual disability and other features. On the basis of the observed distribution of rare variants, we estimate that a two- to three-fold larger cohort would provide 80% power to implicate new genes for all-cause CKD. CONCLUSIONS This study demonstrates that rare-variant collapsing analyses can validate known genes and identify candidate genes and modifiers for kidney disease. In so doing, these findings provide a motivation for larger-scale investigation of rare-variant risk contributions across major clinical CKD categories.
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Affiliation(s)
- Sophia Cameron-Christie
- AstraZeneca Centre for Genomics Research, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK
| | | | - Emily Groopman
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Slavé Petrovski
- AstraZeneca Centre for Genomics Research, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK
| | | | - Gundula Povysil
- AstraZeneca Centre for Genomics Research, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK.,Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Dimitrios Vitsios
- AstraZeneca Centre for Genomics Research, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK
| | - Mengqi Zhang
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York.,Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina; and
| | - Jan Fleckner
- AstraZeneca Centre for Genomics Research, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK
| | - Ruth E March
- Precision Medicine, R&D Oncology, AstraZeneca, Cambridge, UK
| | | | - Maddalena Marasa
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Yifu Li
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York
| | - Andrew S Allen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York.,Department of Biostatistics and Bioinformatics, Duke University, Durham, North Carolina; and
| | - Bengt C Fellström
- Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden; and
| | - Carolina Haefliger
- AstraZeneca Centre for Genomics Research, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK
| | - Adam Platt
- AstraZeneca Centre for Genomics Research, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK;
| | - David B Goldstein
- AstraZeneca Centre for Genomics Research, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK; .,Department of Genetics and Development and.,Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University, New York, New York; .,Institute for Genomic Medicine, Columbia University Medical Center, New York, New York
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18
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A case-control collapsing analysis identifies retinal dystrophy genes associated with ophthalmic disease in patients with no pathogenic ABCA4 variants. Genet Med 2019; 21:2336-2344. [PMID: 30926958 DOI: 10.1038/s41436-019-0495-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 03/12/2019] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Variants in the ABCA4 gene are causal for a variety of retinal dystrophy phenotypes, including Stargardt disease (STGD1). However, 15% of patients who present with symptoms compatible with STGD1/ABCA4 disease do not have identifiable causal ABCA4 variants. We hypothesized that a case-control collapsing analysis in ABCA4-negative patients with compatible symptoms would provide an objective measure to identify additional disease genes. METHODS We performed a genome-wide enrichment analysis of "qualifying variants"-ultrarare variants predicted to impact protein function-in protein-coding genes in 79 unrelated cases and 9028 unrelated controls. RESULTS Despite modest sample size, two known retinal dystrophy genes, PRPH2 and CRX, achieved study-wide significance (p < 1.33 × 10-6) under a dominant disease model, and eight additional known retinal dystrophy genes achieved nominal significance (p < 0.05). Across these ten genes, the excess of qualifying variants explained up to 36.8% of affected individuals. Furthermore, under a recessive model, the cone-rod dystrophy gene CERKL approached study-wide significance. CONCLUSION Our results indicate that case-control collapsing analyses can efficiently identify pathogenic variants in genes in non-ABCA4 retinal dystrophies. The genome-wide collapsing analysis framework is an objective discovery method particularly suitable in settings with overlapping disease phenotypes.
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19
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Hayeck TJ, Stong N, Wolock CJ, Copeland B, Kamalakaran S, Goldstein DB, Allen AS. Improved Pathogenic Variant Localization via a Hierarchical Model of Sub-regional Intolerance. Am J Hum Genet 2019; 104:299-309. [PMID: 30686509 DOI: 10.1016/j.ajhg.2018.12.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/21/2018] [Indexed: 02/04/2023] Open
Abstract
Different parts of a gene can be of differential importance to development and health. This regional heterogeneity is also apparent in the distribution of disease-associated mutations, which often cluster in particular regions of disease-associated genes. The ability to precisely estimate functionally important sub-regions of genes will be key in correctly deciphering relationships between genetic variation and disease. Previous methods have had some success using standing human variation to characterize this variability in importance by measuring sub-regional intolerance, i.e., the depletion in functional variation from expectation within a given region of a gene. However, the ability to precisely estimate local intolerance was restricted by the fact that only information within a given sub-region is used, leading to instability in local estimates, especially for small regions. We show that borrowing information across regions using a Bayesian hierarchical model stabilizes estimates, leading to lower variability and improved predictive utility. Specifically, our approach more effectively identifies regions enriched for ClinVar pathogenic variants. We also identify significant correlations between sub-region intolerance and the distribution of pathogenic variation in disease-associated genes, with AUCs for classifying de novo missense variants in Online Mendelian Inheritance in Man (OMIM) genes of up to 0.86 using exonic sub-regions and 0.91 using sub-regions defined by protein domains. This result immediately suggests that considering the intolerance of regions in which variants are found may improve diagnostic interpretation. We also illustrate the utility of integrating regional intolerance into gene-level disease association tests with a study of known disease-associated genes for epileptic encephalopathy.
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20
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Niazi R, Fanning EA, Depienne C, Sarmady M, Abou Tayoun AN. A mutation update for the PCDH19 gene causing early-onset epilepsy in females with an unusual expression pattern. Hum Mutat 2019; 40:243-257. [PMID: 30582250 DOI: 10.1002/humu.23701] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/26/2018] [Accepted: 12/18/2018] [Indexed: 11/08/2022]
Abstract
The PCDH19 gene consists of six exons encoding a 1,148 amino acid transmembrane protein, Protocadherin 19, which is involved in brain development. Heterozygous pathogenic variants in this gene are inherited in an unusual X-linked dominant pattern in which heterozygous females are affected, while hemizygous males are typically unaffected, although they pass on the pathogenic variant to each affected daughter. PCDH19-related disorder is known to cause early-onset epilepsy in females characterized by seizure clusters exacerbated by fever and in most cases, onset is within the first year of life. This condition was initially described in 1971 and in 2008 PCDH19 was identified as the underlying genetic etiology. This condition is the result of pathogenic loss-of-function variants that may be de novo or inherited from an affected mother or unaffected father and cellular interference has been hypothesized to be the culprit. Heterozygous females are symptomatic because of the presence of both wild-type and mutant cells that interfere with one another due to the production of different surface proteins, whereas nonmosaic hemizygous males produce a homogenous population of cells. Here, we review novel pathogenic variants in the PCDH19 gene since 2012 to date, and summarize any genotype-phenotype correlations.
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Affiliation(s)
- Rojeen Niazi
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elizabeth A Fanning
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany.,Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris, 06 UMR S 1127, Institut du Cerveau et de la Moelle épinière, Paris, France.,IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Mahdi Sarmady
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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