De novo variants in neurodevelopmental disorders with epilepsy (original) (raw)
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Acknowledgements
We thank all patients and their families who participated in this study, as well as the teams who were involved in recruiting patients and gathering samples and data at the respective study sites. We thank L. Vissers and C. Gilissen for epilepsy and age phenotypes from the cohort of Lelieveld et al.23 and J. McRae for useful discussions on the DDD cohort7. We are grateful to members of the ATGU and the Institute for Human Genetics in Leipzig for insightful discussions. We thank J. Krause for support in figure design and helpful conversations. This work was supported by the Eurocores program EuroEPINOMICS, the Fund for Scientific Research Flanders (FWO), International Coordination Action (ICA) grant G0E8614N, and the University of Antwerp (research fund). H.O.H. was supported by stipends from the Federal Ministry of Education and Research (BMBF), Germany, FKZ: 01EO1501 and the German Research Foundation (DFG): HE7987/1-1. H.S. was supported as a PhD fellow of the Fund for Scientific Research Flanders (1125416 N). I.H. and Y.G.W. were supported by DFG grants WE4896/3-1 and HE5415/6-1. R.G. received funding through the EU Seventh Framework Programme (FP7) under the project DESIRE grant N602531. The DDD study presents independent research commissioned by the Health Innovation Challenge Fund (grant HICF-1009-003), a parallel funding partnership between the Wellcome Trust and the Department of Health, and the Wellcome Trust Sanger Institute (grant WT098051). The views expressed in this publication are those of the authors and not necessarily those of the Wellcome Trust or the Department of Health. The research team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network.
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Author notes
- A list of members and affiliations appears at the end of the paper
Authors and Affiliations
- University of Leipzig Hospitals and Clinics, Leipzig, Germany
Henrike O. Heyne, Rami Abou Jamra & Johannes R. Lemke - Program in Medical and Population Genetics, and Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
Henrike O. Heyne, Tarjinder Singh, Jack A. Kosmicki, Aarno Palotie, Mark J. Daly & Dennis Lal - Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig Hospitals and Clinics, Leipzig, Germany
Henrike O. Heyne - Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
Henrike O. Heyne, Tarjinder Singh, Jack A. Kosmicki, Mark J. Daly & Dennis Lal - Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
Hannah Stamberger, Peter De Jonghe, Tania Djémié, Arvid Suls & Sarah Weckhuysen - Laboratory of Neurogenetics, Institute Born–Bunge, University of Antwerp, Antwerp, Belgium
Hannah Stamberger, Peter De Jonghe, Tania Djémié, Arvid Suls & Sarah Weckhuysen - Division of Neurology, University Hospital Antwerp, Antwerp, Belgium
Hannah Stamberger, Peter De Jonghe, Tania Djémié, Arvid Suls & Sarah Weckhuysen - Department of Molecular Biology and Genetics, Bogaziçi University, Istanbul, Turkey
Hande Caglayan - ‘Carol Davila’ University of Medicine Bucharest, Department of Clinical Neurosciences (No. 6), Pediatric Neurology Clinic, Alexandru Obregia Hospital, Bucharest, Romania
Dana Craiu - Pediatric Neurology and Neurogenetics Unit and Laboratories, A. Meyer Children’s Hospital–University of Florence, Florence, Italy
Renzo Guerrini & Carla Marini - Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
Katherine L. Helbig & Ingo Helbig - Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
Bobby P. C. Koeleman & Carolien de Kovel - Department of Pediatric Neurology, Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
Tarja Linnankivi - Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
Patrick May - Department of Neuropediatrics, University Medical Center Schleswig–Holstein, Christian–Albrechts University, Kiel, Germany
Hiltrud Muhle, Manuela Pendziwiat, Johanna Jähn, Stefanie H. Müller, Ulrich Stephani & Ingo Helbig - Danish Epilepsy Centre, Dianalund, Denmark
Rikke S. Møller - Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
Rikke S. Møller - Department of Pediatric Neurology, University Hospital Giessen, Giessen, Germany
Bernd A. Neubauer - Pediatric Neurology and Muscular Diseases Unit, Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, and Maternal and Child Health, University of Genoa ‘G. Gaslini’ Institute, Genoa, Italy
Pasquale Striano - Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
Sha Tang & Sitao Wu - Epilepsy Genetics Program, Department of Neurology, Division of Epilepsy and Clinical Neurophysiology, Boston Children’s Hospital, Boston, MA, USA
Annapurna Poduri - Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
Niklas Schwarz & Yvonne G. Weber - Department of Clinical and Experimental Epilepsy, NIHR, University College London Hospitals Biomedical Research Centre, UCL Institute of Neurology, London, UK
Sanjay M. Sisodiya - The Epilepsy Society, Chalfont-St-Peter Bucks, UK
Sanjay M. Sisodiya - Cologne Center for Genomics (CCG), Cologne, Germany
Dennis Lal - Department of Physiology and Pharmacology, Tel Aviv University Medical School, Ramat Aviv, Israel
Zaid Afawi - Department of Language and Genetics, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
Carolien de Kovel - Epilepsy Center, Department of Neurosurgery, University Hospital ‘St. Ivan Rilski’, Sofia, Bulgaria
Petia Dimova - Neurology Department, Medical Academy, Lithuanian University of Health Services, Kaunas, Lithuania
Milda Endziniene - Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
Dorota Hoffman-Zacharska - Neuropediatrics Unit, University of Geneva, Geneva, Switzerland
Christian Korff - Folkhälsan Institute of Genetics, Helsinki, Finland
Anna-Elina Lehesjoki - Neuroscience Center, University of Helsinki, Helsinki, Finland
Anna-Elina Lehesjoki - Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
Anna-Elina Lehesjoki - Department of Basic and Clinical Neurosciences, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
Deb Pal & Shan Tang - Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
Kaja Selmer - Neurology Laboratory and Epilepsy Unit, Department of Neurology, IIS–Fundacion Jimenez Diaz, UAM, Madrid, Spain
Jose Serratosa - Centro Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
Jose Serratosa - Department of Pediatric Neurology, Second Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
Katalin Štěrbová - Department of General Paediatrics, Division of Child Neurology and Inherited Metabolic Diseases, Centre for Paediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
Steffen Syrbe - Tallinn Children’s Hospital, Tallinn, Estonia
Inga Talvik - Department of Neuropediatrics, Christian-Albrechts-University, Kiel, Germany
Sarah von Spiczak - Northern German Epilepsy Center for Children & Adolescents, Schwentinental/OT, Raisdorf, Germany
Sarah von Spiczak - Laboratory of Genetics and Neuroscience, Institute of G. Gaslini, Genoa, Italy
Federico Zara
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- Henrike O. Heyne
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Consortia
EuroEPINOMICS RES Consortium
- Zaid Afawi
- , Carolien de Kovel
- , Petia Dimova
- , Tania Djémié
- , Milda Endziniene
- , Dorota Hoffman-Zacharska
- , Johanna Jähn
- , Christian Korff
- , Anna-Elina Lehesjoki
- , Carla Marini
- , Stefanie H. Müller
- , Deb Pal
- , Niklas Schwarz
- , Kaja Selmer
- , Jose Serratosa
- , Ulrich Stephani
- , Katalin Štěrbová
- , Arvid Suls
- , Steffen Syrbe
- , Inga Talvik
- , Shan Tang
- , Sarah von Spiczak
- & Federico Zara
Contributions
H.O.H. performed the analyses and drafted the manuscript. H.O.H. and J.R.L. conceived the study. H.O.H., J.R.L., M.J.D., T.S., D.L. and H.S. contributed to analysis concepts and methods. H.O.H., J.R.L., D.L., I.H., T.S., M.J.D., S.M.S., and S. Weckhuysen interpreted the results. T.S., H.S., R.A.J., H.C., D.C., P.D.J., R.G., K.L.H., B.P.C.K., J.A.K., D.L., T.L., P.M., H.M., R.S.M., B.A.N., A. Palotie, M.P., P.S., S.T., S. Wu, the EuroEPINOMICS RES Consortium, S.T., A. Poduri, Y.G.W., S. Weckhuysen, and I.H. provided patient data or analysis tools. All authors revised and approved the final manuscript.
Corresponding authors
Correspondence toHenrike O. Heyne or Johannes R. Lemke.
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Supplementary information
Supplementary Figures
Supplementary Figures 1–10 and Supplementary Note
Reporting Summary
Supplementary Table 1
Description of cohorts analyzed in this study
Supplementary Table 2
List of all DNVmis, DNVtrunc, and DNVsynonymous of all NDD cohorts (n = 6,753) and controls (n = 1,911) analyzed in this study
Supplementary Table 3
List of 50 dominant and X-linked known EE genes
Supplementary Table 4
Genes with at least two DNVmis+trunc in NDDEE+uE (n = 1,942)
Supplementary Table 5
Genes with at least two DNVmis+trunc in all NDD (NDD EE+uE +woE, n = 6,753)
Supplementary Table 6
Significantly enriched HPO terms in 33 genes with DNV burden in NDD with epilepsy
Supplementary Table 7
Evaluating genes with at least two DNVmis+trunc in NDD with epilepsy for therapeutic consequences
Supplementary Table 8
Gene sets significantly enriched (odds raio > 1) or depleted (odds ratio < 1) for DNV in epilepsy compared to no epilepsy
Supplementary Table 9
DNV in epilepsy vs. no epilepsy
Supplementary Table 10
DNV in NDDuE vs. NDDEE
Supplementary Table 11
Diagnostic sequencing panels from 24 different academic and commercial providers
Supplementary Table 12
191 dominant/X-linked genes in sequencing panels from 24 different academic/commercial providers with three criteria for disease association in NDD with epilepsy (DNV burden, constraint, brain expression)
Supplementary Table 13
Evaluating 50 genes lacking features of DNV-enriched genes (DNV enrichment, constraint, brain expression) for published evidence for disease association using guidelines from the ClinGen Gene Curation Workgroup
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Heyne, H.O., Singh, T., Stamberger, H. et al. De novo variants in neurodevelopmental disorders with epilepsy.Nat Genet 50, 1048–1053 (2018). https://doi.org/10.1038/s41588-018-0143-7
- Received: 20 March 2017
- Accepted: 09 April 2018
- Published: 25 June 2018
- Issue Date: July 2018
- DOI: https://doi.org/10.1038/s41588-018-0143-7