Warrier, Varun, Zhang, Xinhe, Reed, Patrick, Havdahl, Alexandra, Moore, Tyler M., Cliquet, Freddy, Leblond, Claire S., Rolland, Thomas, Rosengren, Anders, Caceres, Antonia San Jose, Hayward, Hannah, Crawley, Daisy, Faulkner, Jessica, Sabet, Jessica, Ellis, Claire, Oakley, Bethany, Loth, Eva, Charman, Tony, Murphy, Declan, Holt, Rosemary, Waldman, Jack, Upadhyay, Jessica, Gunby, Nicola, Lai, Meng-Chuan, Renouf, Gwilym, Ruigrok, Amber, Taylor, Emily, Ziauddeen, Hisham, Deakin, Julia, di Bruttopilo, Sara Ambrosino, van Dijk, Sarai, Rijks, Yvonne, Koops, Tabitha, Douma, Miriam, Spaan, Alyssia, Selten, Iris, Steffers, Maarten, van Themaat, Anna Ver Loren, Bast, Nico, Baumeister, Sarah, O’Dwyer, Larry, Bours, Carsten, Rausch, Annika, von Rhein, Daniel, Cornelissen, Ineke, de Bruin, Yvette, Graauwmans, Maartje, Kostrzewa, Elzbieta, Cauvet, Elodie, Tammimies, Kristiina, Sitnikow, Rouslan, Dumas, Guillaume, Kim, Yang-Min, Bourgeron, Thomas, Hougaard, David M., Bybjerg-Grauholm, Jonas, Werge, Thomas, Mortensen, Preben Bo, Mors, Ole, Nordentoft, Merete, Adhya, Dwaipayan, Alamanza, Armandina, Allison, Carrie, Garvey, Isabelle, Parsons, Tracey, Smith, Paula, Tsompanidis, Alex, Burton, Graham J., Heazell, Alexander E. P., Gabis, Lidia V., Biron-Shental, Tal, Lancaster, Madeline A., Srivastava, Deepak P., Mill, Jonathan, Rowitch, David H., Hurles, Matthew E., Geschwind, Daniel H., Børglum, Anders D., Robinson, Elise B., Grove, Jakob, Martin, Hilary C., Baron-Cohen, Simon, University of Cambridge [UK] (CAM), Lovisenberg Diakonale Sykehus - Lovisenberg Diaconal Hospital [Oslo], Norwegian Institute of Public Health [Oslo] (NIPH), University of Oslo (UiO), University of Pennsylvania [Philadelphia], Children’s Hospital of Philadelphia (CHOP ), Génétique humaine et fonctions cognitives - Human Genetics and Cognitive Functions (GHFC (UMR_3571 / U-Pasteur_1)), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), The Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), Copenhagen University Hospital, The Wellcome Trust Sanger Institute [Cambridge], University of California [Los Angeles] (UCLA), University of California, Aarhus University [Aarhus], Broad Institute [Cambridge], Harvard University [Cambridge]-Massachusetts Institute of Technology (MIT), Massachusetts General Hospital [Boston], Harvard T.H. Chan School of Public Health, V.W. is funded by St. Catharine’s College, Cambridge. This study was funded by grants to SBC from the Medical Research Council, the Wellcome Trust, the Autism Research Trust, the Templeton World Charity Foundation, and to T.B. from the Institut Pasteur, the CNRS, The Bettencourt-Schueller and the Cognacq-Jay Foundations, the APHP and the Université de Paris. SBC was funded by the Autism Research Trust, the Wellcome Trust, the Templeton World Charitable Foundation, and the NIHR Biomedical Research Centre in Cambridge, during the period of this work. The Medical Research Council (MRC) funded the Cambridge Autism Research Database (CARD) that made this study possible. SBC also received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 777394. The JU receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA and AUTISM SPEAKS, Autistica, SFARI. His research was also supported by the National Institute of Health Research (NIHR) Applied Research Collaboration East of England (ARC EoE) programme. T.M.M. is supported by U.S. National Institutes of Mental Health (NIMH) grant MH117014. The views expressed are those of the authors, and not necessarily those of the NIHR, NHS or Department of Health and Social Care. We acknowledge with gratitude the generous support of Drs Dennis and Mireille Gillings in strengthening the collaboration between S.B.-C. and T.B., and between Cambridge University and the Institut Pasteur. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health. The AIMS-2-TRIALS LEAP receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA and AUTISM SPEAKS, Autistica, SFARI. A full list of the authors and affiliations in the AIMS-2-TRIALS LEAP group is provided in the Supplementary Information. The iPSYCH team was supported by grants from the Lundbeck Foundation (R102-A9118, R155-2014-1724 and R248-2017-2003), NIMH (1U01MH109514-01 to ADB) and the universities and university hospitals of Aarhus and Copenhagen. The Danish National Biobank resource was supported by the Novo Nordisk Foundation. High-performance computer capacity for handling and statistical analysis of iPSYCH data on the GenomeDK HPC facility was provided by the Center for Genomics and Personalized Medicine and the Centre for Integrative Sequencing, iSEQ, Aarhus University, Denmark (grant to ADB). We thank Jonathan Sebat for sharing the de novo variant calls in the SPARK and SSC datasets., Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Warrier, Varun [0000-0003-4532-8571], Havdahl, Alexandra [0000-0002-9268-0423], Moore, Tyler M [0000-0002-1384-0151], Rosengren, Anders [0000-0002-6682-1288], Hurles, Matthew E [0000-0002-2333-7015], Geschwind, Daniel H [0000-0003-2896-3450], Børglum, Anders D [0000-0001-8627-7219], Grove, Jakob [0000-0003-2284-5744], Martin, Hilary C [0000-0002-4454-9084], Bourgeron, Thomas [0000-0001-8164-9220], Baron-Cohen, Simon [0000-0001-9217-2544], Apollo - University of Cambridge Repository, University of Pennsylvania, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University of California (UC), Harvard University-Massachusetts Institute of Technology (MIT), and S.B.-C. received funding from the Wellcome Trust (214322\Z\18\Z). For the purpose of open access, we have applied a CC BY public copyright licence to any author accepted manuscript version arising from this submission. S.B.-C. also received funding from the Autism Centre of Excellence, the SFARI, the Templeton World Charitable Fund, the MRC and the National Institute for Health Research Cambridge Biomedical Research Centre. The research was supported by the National Institute for Health Research Applied Research Collaboration East of England. Any views expressed are those of the author(s) and not necessarily those of the funder. Some of the results leading to this publication have received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement no. 777394 for the project AIMS-2-TRIALS. This joint undertaking receives support from the European Union’s Horizon 2020 research and innovation program and the EFPIA and Autism Speaks, Autistica and the SFARI. V.W. is funded by St. Catharine’s College, Cambridge. T.B. has received funding from the Institut Pasteur, the CNRS, the Bettencourt–Schueller and the Cognacq–Jay Foundations, the APHP and the Université de Paris Cité. We acknowledge with gratitude the generous support of D. and M. Gillings in strengthening the collaboration between S.B.-C. and T.B. and between Cambridge University and the Institut Pasteur. The iPSYCH team was supported by grants from the Lundbeck Foundation (R102-A9118, R155-2014-1724 and R248-2017-2003), the NIMH (1U01MH109514-01 to A.D.B.) and the universities and university hospitals of Aarhus and Copenhagen. The Danish National Biobank resource was supported by the Novo Nordisk Foundation. High-performance computer capacity for handling and statistical analysis of iPSYCH data on the GenomeDK HPC facility was provided by the Center for Genomics and Personalized Medicine and the Centre for Integrative Sequencing, iSEQ, Aarhus University, Denmark (grant to A.D.B.). We thank J. Sebat for sharing the de novo variant calls in the SPARK and SSC datasets. We are grateful to all families at the participating SSC sites as well as the principal investigators (A. Beaudet, R. Bernier, J. Constantino, E. Cook, E. Fombonne, D. Geschwind, R. Goin-Kochel, E. Hanson, D. Grice, A. Klin, D. Ledbetter, C. Lord, C. Martin, D. Martin, R. Maxim, J. Miles, O. Ousley, K. Pelphrey, B. Peterson, J. Piggot, C. Saulnier, M. State, W. Stone, J. Sutcliffe, C. Walsh, Z. Warren and E. Wijsman). We are grateful to all families in the SPARK study, the SPARK clinical sites and SPARK staff.