High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies
Developmental and epileptic encephalopathy (DEE) is a group of conditions characterized by the co-occurrence of epilepsy and intellectual disability (ID), typically with developmental plateauing or regression associated with frequent epileptiform activity. The cause of DEE remains unknown in the maj...
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| Published in | American journal of human genetics Vol. 101; no. 5; pp. 664 - 685 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
02.11.2017
Elsevier (Cell Press) Elsevier |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Developmental and epileptic encephalopathy (DEE) is a group of conditions characterized by the co-occurrence of epilepsy and intellectual disability (ID), typically with developmental plateauing or regression associated with frequent epileptiform activity. The cause of DEE remains unknown in the majority of cases. We performed whole-genome sequencing (WGS) in 197 individuals with unexplained DEE and pharmaco-resistant seizures and in their unaffected parents. We focused our attention on de novo mutations (DNMs) and identified candidate genes containing such variants. We sought to identify additional subjects with DNMs in these genes by performing targeted sequencing in another series of individuals with DEE and by mining various sequencing datasets. We also performed meta-analyses to document enrichment of DNMs in candidate genes by leveraging our WGS dataset with those of several DEE and ID series. By combining these strategies, we were able to provide a causal link between DEE and the following genes: NTRK2, GABRB2, CLTC, DHDDS, NUS1, RAB11A, GABBR2, and SNAP25. Overall, we established a molecular diagnosis in 63/197 (32%) individuals in our WGS series. The main cause of DEE in these individuals was de novo point mutations (53/63 solved cases), followed by inherited mutations (6/63 solved cases) and de novo CNVs (4/63 solved cases). De novo missense variants explained a larger proportion of individuals in our series than in other series that were primarily ascertained because of ID. Moreover, these DNMs were more frequently recurrent than those identified in ID series. These observations indicate that the genetic landscape of DEE might be different from that of ID without epilepsy. |
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| AbstractList | Developmental and epileptic encephalopathy (DEE) is a group of conditions characterized by the co-occurrence of epilepsy and intellectual disability (ID), typically with developmental plateauing or regression associated with frequent epileptiform activity. The cause of DEE remains unknown in the majority of cases. We performed whole-genome sequencing (WGS) in 197 individuals with unexplained DEE and pharmaco-resistant seizures and in their unaffected parents. We focused our attention on de novo mutations (DNMs) and identified candidate genes containing such variants. We sought to identify additional subjects with DNMs in these genes by performing targeted sequencing in another series of individuals with DEE and by mining various sequencing datasets. We also performed meta-analyses to document enrichment of DNMs in candidate genes by leveraging our WGS dataset with those of several DEE and ID series. By combining these strategies, we were able to provide a causal link between DEE and the following genes: NTRK2, GABRB2, CLTC, DHDDS, NUS1, RAB11A, GABBR2, and SNAP25. Overall, we established a molecular diagnosis in 63/197 (32%) individuals in our WGS series. The main cause of DEE in these individuals was de novo point mutations (53/63 solved cases), followed by inherited mutations (6/63 solved cases) and de novo CNVs (4/63 solved cases). De novo missense variants explained a larger proportion of individuals in our series than in other series that were primarily ascertained because of ID. Moreover, these DNMs were more frequently recurrent than those identified in ID series. These observations indicate that the genetic landscape of DEE might be different from that of ID without epilepsy. Developmental and epileptic encephalopathy (DEE) is a group of conditions characterized by the co-occurrence of epilepsy and intellectual disability (ID), typically with developmental plateauing or regression associated with frequent epileptiform activity. The cause of DEE remains unknown in the majority of cases. We performed whole-genome sequencing (WGS) in 197 individuals with unexplained DEE and pharmaco-resistant seizures and in their unaffected parents. We focused our attention on de novo mutations (DNMs) and identified candidate genes containing such variants. We sought to identify additional subjects with DNMs in these genes by performing targeted sequencing in another series of individuals with DEE and by mining various sequencing datasets. We also performed meta-analyses to document enrichment of DNMs in candidate genes by leveraging our WGS dataset with those of several DEE and ID series. By combining these strategies, we were able to provide a causal link between DEE and the following genes: NTRK2, GABRB2, CLTC, DHDDS, NUS1, RAB11A, GABBR2, and SNAP25. Overall, we established a molecular diagnosis in 63/197 (32%) individuals in our WGS series. The main cause of DEE in these individuals was de novo point mutations (53/63 solved cases), followed by inherited mutations (6/63 solved cases) and de novo CNVs (4/63 solved cases). De novo missense variants explained a larger proportion of individuals in our series than in other series that were primarily ascertained because of ID. Moreover, these DNMs were more frequently recurrent than those identified in ID series. These observations indicate that the genetic landscape of DEE might be different from that of ID without epilepsy.Developmental and epileptic encephalopathy (DEE) is a group of conditions characterized by the co-occurrence of epilepsy and intellectual disability (ID), typically with developmental plateauing or regression associated with frequent epileptiform activity. The cause of DEE remains unknown in the majority of cases. We performed whole-genome sequencing (WGS) in 197 individuals with unexplained DEE and pharmaco-resistant seizures and in their unaffected parents. We focused our attention on de novo mutations (DNMs) and identified candidate genes containing such variants. We sought to identify additional subjects with DNMs in these genes by performing targeted sequencing in another series of individuals with DEE and by mining various sequencing datasets. We also performed meta-analyses to document enrichment of DNMs in candidate genes by leveraging our WGS dataset with those of several DEE and ID series. By combining these strategies, we were able to provide a causal link between DEE and the following genes: NTRK2, GABRB2, CLTC, DHDDS, NUS1, RAB11A, GABBR2, and SNAP25. Overall, we established a molecular diagnosis in 63/197 (32%) individuals in our WGS series. The main cause of DEE in these individuals was de novo point mutations (53/63 solved cases), followed by inherited mutations (6/63 solved cases) and de novo CNVs (4/63 solved cases). De novo missense variants explained a larger proportion of individuals in our series than in other series that were primarily ascertained because of ID. Moreover, these DNMs were more frequently recurrent than those identified in ID series. These observations indicate that the genetic landscape of DEE might be different from that of ID without epilepsy. Developmental and epileptic encephalopathy (DEE) is a group of conditions characterized by the co-occurrence of epilepsy and intellectual disability (ID), typically with developmental plateauing or regression associated with frequent epileptiform activity. The cause of DEE remains unknown in the majority of cases. We performed whole-genome sequencing (WGS) in 197 individuals with unexplained DEE and pharmaco-resistant seizures and in their unaffected parents. We focused our attention on de novo mutations (DNMs) and identified candidate genes containing such variants. We sought to identify additional subjects with DNMs in these genes by performing targeted sequencing in another series of individuals with DEE and by mining various sequencing datasets. We also performed meta-analyses to document enrichment of DNMs in candidate genes by leveraging our WGS dataset with those of several DEE and ID series. By combining these strategies, we were able to provide a causal link between DEE and the following genes: NTRK2 , GABRB2 , CLTC , DHDDS , NUS1 , RAB11A , GABBR2 , and SNAP25 . Overall, we established a molecular diagnosis in 63/197 (32%) individuals in our WGS series. The main cause of DEE in these individuals was de novo point mutations (53/63 solved cases), followed by inherited mutations (6/63 solved cases) and de novo CNVs (4/63 solved cases). De novo missense variants explained a larger proportion of individuals in our series than in other series that were primarily ascertained because of ID. Moreover, these DNMs were more frequently recurrent than those identified in ID series. These observations indicate that the genetic landscape of DEE might be different from that of ID without epilepsy. |
| Author | Tam, Cory Riou, Emilie Fry, Andrew E. Cadieux-Dion, Maxime Myers, Candace T. Kerr, Bronwyn Hamdan, Fadi F. Brunga, Ledia Donaldson, Alan Boelman, Cyrus Monlong, Jean Diallo, Ousmane Nougues, Marie-Christine Wojcik, Monica H. Blair, Edward Keren, Boris Albert, Dara V.F. Hollingsworth, Georgie Stein, Quinn Mohammad, Shekeeb S. Sadleir, Lynette G. Dallapiccola, Bruno Dubeau, François Schneider, Amy Retterer, Kyle Bacino, Carlos A. Benke, Paul J. Mercimek-Mahmutoglu, Saadet Jones, Dean Thomas, Rhys H. Chung, Wendy K. Minassian, Berge A. Lalani, Seema R. Auvin, Stéphane Rouleau, Guy A. Bruel, Ange-Line Kamsteeg, Erik-Jan Wierenga, Klaas J. Davis-Keppen, Laura Boucher, Renee-Myriam Shao, Yunru Dobrzeniecka, Sylvia Major, Philippe Laporte, Alexandre Dionne Liu, Yu-Chi Mau-Them, Frederic T. Girard, Simon L. Lebel, Robert Roger Campeau, Philippe M. Ware, Tyson Hurst, Jane A. Scheffer, Ingrid E. O’Byrne, James J. Venkateswaran, Sunita Bebin, Martina Cossette, Patrick Tartaglia, Marco Scaglia, Fernando Dorison, Sara J. Lemay, Philippe Verloes, Alain Spiege |
| AuthorAffiliation | Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK |
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Diseases Research Division, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, 00165 Rome, Italy – name: 16 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK – name: 46 Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia – name: 73 Department of Pediatrics and Child Health, University of Otago, Wellington 9016, New Zealand – name: 50 Dipartimento di Pediatria e di Neuropsichiatria Infantile, Università La Sapienza, 00185 Rome, Italy – name: 68 Division of Neurology, Centre Hospitalier Universitaire de Québec, Quebec, QC G1V 4G2, Canada – name: 8 Center for Pediatric Genomic Medicine, Children’s Mercy Kansas City, Kansas City, MO 64108, USA – name: 77 Department of Pediatrics, University of Melbourne Royal Children’s Hospital, Parkville, VIC 3052, Australia – name: 15 Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, 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MRC Centre for Neuropsychiatric Genetics & Genomics, Hadyn Ellis Building, Cathays, Cardiff University, Cardiff CF24 4HQ, UK – name: 65 Arkansas Children’s Research Institute, Little Rock, AR 72205, USA – name: 59 Assistance Publique – Hôpitaux de Paris, Hôpital d’Enfants Armand Trousseau, Service de Neuropédiatrie, Paris 75012, France – name: 39 Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu 51014, Estonia – name: 6 McGill University and Genome Quebec Innovation Center, Montreal, QC H3A 1A4, Canada – name: 42 Nationwide Children’s Hospital and Ohio State University, Department of Pediatrics, Division of Neurology, Columbus, OH 43205, USA – name: 24 West of Scotland Regional Genetics Service, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK – name: 31 Departments of Medicine and Pediatrics, Columbia University Medical Center, New York, NY 10032, USA – name: 66 Texas Children’s 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Oxford Centre for Genomic Medicine, ACE building Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7HE, UK – name: 37 Équipe INSERM 1231, Génétique des Anomalies du Développement, Université de Bourgogne, 21000 Dijon, France – name: 71 Department of Neurology and Neurosurgery, McGill University, Montreal, QC H3A 1A4, Canada – name: 69 Department of Pediatrics, Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada |
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Royal Hobart Hospital, Department of Paediatrics, Hobart, TAS 7000, Australia – sequence: 55 givenname: Yu-Chi surname: Liu fullname: Liu, Yu-Chi organization: Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia – sequence: 56 givenname: Shekeeb S. surname: Mohammad fullname: Mohammad, Shekeeb S. organization: Children’s Hospital at Westmead Clinical School, University of Sydney, Westmead, NSW 2145, Australia – sequence: 57 givenname: Peyman surname: Bizargity fullname: Bizargity, Peyman organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA – sequence: 58 givenname: Carlos A. surname: Bacino fullname: Bacino, Carlos A. organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA – sequence: 59 givenname: Vincenzo surname: Leuzzi fullname: Leuzzi, Vincenzo organization: Dipartimento di Pediatria e di Neuropsichiatria Infantile, Università La Sapienza, 00185 Rome, Italy – sequence: 60 givenname: Simone surname: Martinelli fullname: Martinelli, Simone organization: Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, 00161 Rome, Italy – sequence: 61 givenname: Bruno surname: Dallapiccola fullname: Dallapiccola, Bruno organization: Genetics and Rare Diseases Research Division, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, 00165 Rome, Italy – sequence: 62 givenname: Marco surname: Tartaglia fullname: Tartaglia, Marco organization: Genetics and Rare Diseases Research Division, Bambino Gesù Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, 00165 Rome, Italy – sequence: 63 givenname: Lubov surname: Blumkin fullname: Blumkin, Lubov organization: Metabolic Neurogenetic Clinic and Pediatric Movement Disorders Clinic, Wolfson Medical Center, Holon 5822012, Israel – sequence: 64 givenname: Klaas J. surname: Wierenga fullname: Wierenga, Klaas J. organization: University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA – sequence: 65 givenname: Gabriela surname: Purcarin fullname: Purcarin, Gabriela organization: University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA – sequence: 66 givenname: James J. surname: O’Byrne fullname: O’Byrne, James J. organization: University of British Columbia, BC Children’s Hospital, Vancouver, BC V6H 3N1, Canada – sequence: 67 givenname: Sylvia surname: Stockler fullname: Stockler, Sylvia organization: University of British Columbia, BC Children’s Hospital, Vancouver, BC V6H 3N1, Canada – sequence: 68 givenname: Anna surname: Lehman fullname: Lehman, Anna organization: Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada – sequence: 69 givenname: Boris surname: Keren fullname: Keren, Boris organization: Département de Génétique, Centre de Référence des Déficiences Intellectuelles de Causes Rares, Groupe de Recherche Clinique “Déficiences Intellectuelles et Autisme,” Université Pierre et Marie Curie, Hôpital de la Pitié-Salpêtrière, Paris 75013, France – sequence: 70 givenname: Marie-Christine surname: Nougues fullname: Nougues, Marie-Christine organization: Assistance Publique – Hôpitaux de Paris, Hôpital d’Enfants Armand Trousseau, Service de Neuropédiatrie, Paris 75012, France – sequence: 71 givenname: Cyril surname: Mignot fullname: Mignot, Cyril organization: Département de Génétique, Centre de Référence des Déficiences Intellectuelles de Causes Rares, Groupe de Recherche Clinique “Déficiences Intellectuelles et Autisme,” Université Pierre et Marie Curie, Hôpital de la Pitié-Salpêtrière, Paris 75013, France – sequence: 72 givenname: Stéphane surname: Auvin fullname: Auvin, Stéphane organization: Université Paris Diderot, Sorbonne Paris Cité, INSERM UMR 1141, Paris 75019, France – sequence: 73 givenname: Caroline surname: Nava fullname: Nava, Caroline organization: Département de Génétique, Centre de Référence des Déficiences Intellectuelles de Causes Rares, Groupe de Recherche Clinique “Déficiences Intellectuelles et Autisme,” Université Pierre et Marie Curie, Hôpital de la Pitié-Salpêtrière, Paris 75013, France – sequence: 74 givenname: Susan M. surname: Hiatt fullname: Hiatt, Susan M. organization: HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA – sequence: 75 givenname: Martina surname: Bebin fullname: Bebin, Martina organization: Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294, USA – sequence: 76 givenname: Yunru surname: Shao fullname: Shao, Yunru organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA – sequence: 77 givenname: Fernando surname: Scaglia fullname: Scaglia, Fernando organization: Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA – sequence: 79 givenname: Richard E. surname: Frye fullname: Frye, Richard E. organization: Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA – sequence: 80 givenname: Imad T. surname: Jarjour fullname: Jarjour, Imad T. organization: Texas Children’s Hospital and Baylor College of Medicine, Houston, TX 77030, USA – sequence: 81 givenname: Stéphanie surname: Jacques fullname: Jacques, Stéphanie organization: Centre Hospitalier Rouyn-Noranda, Rouyn-Noranda, QC J9X 2B2, Canada – sequence: 82 givenname: Renee-Myriam surname: Boucher fullname: Boucher, Renee-Myriam organization: Division of Neurology, Centre Hospitalier Universitaire de Québec, Quebec, QC G1V 4G2, Canada – sequence: 83 givenname: Emilie surname: Riou fullname: Riou, Emilie organization: Department of Pediatrics, Centre Hospitalier Universitaire de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada – sequence: 84 givenname: Myriam surname: Srour fullname: Srour, Myriam organization: Department of Pediatrics, McGill University, Montreal, QC H3A 1A4, Canada – sequence: 85 givenname: Lionel surname: Carmant fullname: Carmant, Lionel organization: Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T1C5, Canada – sequence: 86 givenname: Anne surname: Lortie fullname: Lortie, Anne organization: Department of Neurosciences, Université de Montréal, Montreal, QC H3T1J4, Canada – sequence: 87 givenname: Philippe surname: Major fullname: Major, Philippe organization: Department of Neurosciences, Université de Montréal, Montreal, QC H3T1J4, Canada – sequence: 88 givenname: Paola surname: Diadori fullname: Diadori, Paola organization: Department of Neurosciences, Université de Montréal, Montreal, QC H3T1J4, Canada – sequence: 89 givenname: François surname: Dubeau fullname: Dubeau, François organization: Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, QC H3A2B4, Canada – sequence: 90 givenname: Guy surname: D’Anjou fullname: D’Anjou, Guy organization: Department of Neurosciences, Université de Montréal, Montreal, QC H3T1J4, Canada – sequence: 91 givenname: Guillaume surname: Bourque fullname: Bourque, Guillaume organization: McGill University and Genome Quebec Innovation Center, Montreal, QC H3A 1A4, Canada – sequence: 92 givenname: Samuel F. surname: Berkovic fullname: Berkovic, Samuel F. organization: Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia – sequence: 93 givenname: Lynette G. surname: Sadleir fullname: Sadleir, Lynette G. organization: Department of Pediatrics and Child Health, University of Otago, Wellington 9016, New Zealand – sequence: 94 givenname: Philippe M. surname: Campeau fullname: Campeau, Philippe M. organization: Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T1C5, Canada – sequence: 95 givenname: Zoha surname: Kibar fullname: Kibar, Zoha organization: Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T1C5, Canada – sequence: 96 givenname: Ronald G. surname: Lafrenière fullname: Lafrenière, Ronald G. organization: Centre Hospitalier de l’Université de Montréal Research Center, Montreal, QC H2X 0A9, Canada – sequence: 97 givenname: Simon L. surname: Girard fullname: Girard, Simon L. organization: Centre Hospitalier de l’Université de Montréal Research Center, Montreal, QC H2X 0A9, Canada – sequence: 98 givenname: Saadet surname: Mercimek-Mahmutoglu fullname: Mercimek-Mahmutoglu, Saadet organization: Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada – sequence: 99 givenname: Cyrus surname: Boelman fullname: Boelman, Cyrus organization: Division of Neurology, BC Children’s Hospital, Vancouver, BC V6H 3N1, Canada – sequence: 100 givenname: Guy A. surname: Rouleau fullname: Rouleau, Guy A. organization: Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, QC H3A2B4, Canada – sequence: 101 givenname: Ingrid E. surname: Scheffer fullname: Scheffer, Ingrid E. organization: Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia – sequence: 102 givenname: Heather C. surname: Mefford fullname: Mefford, Heather C. organization: Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA – sequence: 103 givenname: Danielle M. surname: Andrade fullname: Andrade, Danielle M. organization: Division of Neurology, Epilepsy Genetics Program, Krembil Neuroscience Centre, Toronto Western Hospital, University of Toronto, Toronto, ON M5G 2C4, Canada – sequence: 104 givenname: Elsa surname: Rossignol fullname: Rossignol, Elsa organization: Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T1C5, Canada – sequence: 105 givenname: Berge A. surname: Minassian fullname: Minassian, Berge A. email: berge.minassian@sickkids.ca organization: Program in Genetics and Genome Biology, Division of Neurology, Department of Pediatrics, Hospital for Sick Children and University of Toronto, Toronto, ON M5G 0A4, Canada – sequence: 106 givenname: Jacques L. surname: Michaud fullname: Michaud, Jacques L. email: jacques.michaud@recherche-ste-justine.qc.ca organization: Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC H3T1C5, Canada |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29100083$$D View this record in MEDLINE/PubMed https://ube.hal.science/hal-01680255$$DView record in HAL |
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| Title | High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies |
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