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Large-scale exome sequencing study implicates both developmental and functional changes in the neurobiology of autism

F. Kyle Satterstrom, Jack A. Kosmicki, Jiebiao Wang, Michael S. Breen, Silvia De Rubeis, Joon-Yong An, Minshi Peng, Ryan Collins, Jakob Grove, Lambertus Klei, Christine Stevens, Jennifer Reichert, Maureen S. Mulhern, View ORCID ProfileMykyta Artomov, Sherif Gerges, Brooke Sheppard, Xinyi Xu, Aparna Bhaduri, Utku Norman, Harrison Brand, Grace Schwartz, Rachel Nguyen, Elizabeth E. Guerrero, Caroline Dias, Branko Aleksic, View ORCID ProfileRichard Anney, Mafalda Barbosa, Somer Bishop, View ORCID ProfileAlfredo Brusco, Jonas Bybjerg-Grauholm, Angel Carracedo, Marcus C.Y. Chan, Andreas G. Chiocchetti, Brian H. Y. Chung, Hilary Coon, Michael L. Cuccaro, Aurora Currò, Bernardo Dalla Bernardina, Ryan Doan, Enrico Domenici, Shan Dong, Chiara Fallerini, Montserrat Fernández-Prieto, Giovanni Battista Ferrero, Christine M. Freitag, Menachem Fromer, J. Jay Gargus, Daniel Geschwind, Elisa Giorgio, Javier González-Peñas, Stephen Guter, Danielle Halpern, Emily Hansen-Kiss, Xin He, Gail E. Herman, Irva Hertz-Picciotto, David M. Hougaard, Christina M. Hultman, Iuliana Ionita-Laza, Suma Jacob, Jesslyn Jamison, Astanand Jugessur, Miia Kaartinen, Gun Peggy Knudsen, Alexander Kolevzon, Itaru Kushima, So Lun Lee, Terho Lehtimäki, Elaine T. Lim, Carla Lintas, W. Ian Lipkin, Diego Lopergolo, Fátima Lopes, Yunin Ludena, Patricia Maciel, Per Magnus, Behrang Mahjani, Nell Maltman, Dara S. Manoach, Gal Meiri, View ORCID ProfileIdan Menashe, Judith Miller, Nancy Minshew, Eduarda Montenegro M. de Souza, Danielle Moreira, View ORCID ProfileEric M. Morrow, Ole Mors, Preben Bo Mortensen, Matthew Mosconi, Pierandrea Muglia, Benjamin Neale, Merete Nordentoft, Norio Ozaki, Aarno Palotie, Mara Parellada, Maria Rita Passos-Bueno, Margaret Pericak-Vance, Antonio Persico, Isaac Pessah, Kaija Puura, Abraham Reichenberg, Alessandra Renieri, Evelise Riberi, Elise B. Robinson, Kaitlin E. Samocha, Sven Sandin, Susan L. Santangelo, Gerry Schellenberg, Stephen W. Scherer, Sabine Schlitt, Rebecca Schmidt, Lauren Schmitt, Isabela Maya W. Silva, Tarjinder Singh, Paige M. Siper, Moyra Smith, Gabriela Soares, Camilla Stoltenberg, Pål Suren, Ezra Susser, John Sweeney, Peter Szatmari, Lara Tang, Flora Tassone, Karoline Teufel, Elisabetta Trabetti, Maria del Pilar Trelles, Christopher Walsh, Lauren A. Weiss, Thomas Werge, Donna Werling, Emilie M. Wigdor, Emma Wilkinson, Jeremy A. Willsey, Tim Yu, Mullin H.C. Yu, Ryan Yuen, Elaine Zachi, iPSYCH consortium, Catalina Betancur, Edwin H. Cook, Louise Gallagher, Michael Gill, James S. Sutcliffe, Audrey Thurm, Michael E. Zwick, Anders D. Børglum, Matthew W. State, A. Ercument Cicek, Michael E. Talkowski, David J. Cutler, Bernie Devlin, View ORCID ProfileStephan J. Sanders, Kathryn Roeder, Mark J. Daly, Joseph D. Buxbaum
doi: https://doi.org/10.1101/484113
F. Kyle Satterstrom
1Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
2Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Jack A. Kosmicki
1Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
2Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
4Harvard Medical School, Boston, Massachusetts, USA
5Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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Jiebiao Wang
6Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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Michael S. Breen
7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
9The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Silvia De Rubeis
7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
9The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Joon-Yong An
10Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
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Minshi Peng
6Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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Ryan Collins
5Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
11Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, Massachusetts, USA
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Jakob Grove
12The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
13Center for Genomics and Personalized Medicine, Aarhus, Denmark
14Department of Biomedicine - Human Genetics, Aarhus University, Aarhus, Denmark
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Lambertus Klei
15Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Christine Stevens
1Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
4Harvard Medical School, Boston, Massachusetts, USA
5Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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Jennifer Reichert
7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Maureen S. Mulhern
7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Mykyta Artomov
1Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
4Harvard Medical School, Boston, Massachusetts, USA
5Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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  • ORCID record for Mykyta Artomov
Sherif Gerges
1Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
4Harvard Medical School, Boston, Massachusetts, USA
5Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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Brooke Sheppard
10Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
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Xinyi Xu
7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Aparna Bhaduri
16Department of Neurology, University of California San Francisco, San Francisco, California, USA
17The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, California, USA
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Utku Norman
18Computer Engineering Department, Bilkent University, Ankara, Turkey
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Harrison Brand
5Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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Grace Schwartz
10Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
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Rachel Nguyen
19Center for Autism Research and Translation, University of California Irvine, Irvine, California, USA
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Elizabeth E. Guerrero
20MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, California, USA
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Caroline Dias
21Division of Genetics, Boston Children’s Hospital, Boston, Massachusetts, USA
22Division of Developmental Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA
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Branko Aleksic
23Department of Psychiatry, Graduate School of Medicine, Nagoya University, Nagoya, Japan
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Richard Anney
24Division of Psychological Medicine & Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics & Genomics, Cardiff University, Cardiff, United Kingdom
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Mafalda Barbosa
9The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Somer Bishop
10Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
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Alfredo Brusco
25Department of Medical Sciences, University of Torino, Turin, Italy
26Medical Genetics Unit, Città della Salute e della Scienza Hospital, Turin, Italy
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Jonas Bybjerg-Grauholm
12The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
27Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
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Angel Carracedo
28Grupo de Medicina Xenómica, Centro de Investigaciónen en Red de Enfermedades Raras (CIBERER), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
29Fundación Pública Galega de Medicina Xenómica, Servicio Galego de Saúde (SERGAS), Santiago de Compostela, Spain
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Marcus C.Y. Chan
30Department of Pediatrics & Adolescent Medicine, Duchess of Kent Children’s Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
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Andreas G. Chiocchetti
31Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University Frankfurt, Frankfurt, Germany
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Brian H. Y. Chung
30Department of Pediatrics & Adolescent Medicine, Duchess of Kent Children’s Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
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Hilary Coon
32Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA
33Department of Psychiatry, University of Utah, Salt Lake City, Utah, USA
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Michael L. Cuccaro
34John P Hussman Institute for Human Genomics, University of Miami, Miami, USA
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Aurora Currò
35Medical Genetics, University of Siena, Siena, Italy
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Bernardo Dalla Bernardina
36Child Neuropsychiatry Department, Department of Surgical Sciences, Dentistry, Gynecology and Pediatrics. University of Verona, Verona, Italy
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Ryan Doan
21Division of Genetics, Boston Children’s Hospital, Boston, Massachusetts, USA
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Enrico Domenici
37Centre for Integrative Biology, University of Trento, Trento, Italy
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Shan Dong
10Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
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Chiara Fallerini
35Medical Genetics, University of Siena, Siena, Italy
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Montserrat Fernández-Prieto
28Grupo de Medicina Xenómica, Centro de Investigaciónen en Red de Enfermedades Raras (CIBERER), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
38Neurogenetics Group, Instituto de Investigación Sanitaria de Santiago (IDIS-SERGAS), Santiago de Compostela, Spain
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Giovanni Battista Ferrero
39Department of Public Health and Pediatrics, University of Torino, Turin, Italy
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Christine M. Freitag
31Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University Frankfurt, Frankfurt, Germany
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Menachem Fromer
3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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J. Jay Gargus
19Center for Autism Research and Translation, University of California Irvine, Irvine, California, USA
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Daniel Geschwind
40Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
41Center for Autism Research and Treatment and Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
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Elisa Giorgio
25Department of Medical Sciences, University of Torino, Turin, Italy
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Javier González-Peñas
42Department of Child and Adolescent Psychiatry, Hospital General Universitario Gregorio Marañón, IiSGM, CIBERSAM, School of Medicine Complutense University, Madrid, Spain
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Stephen Guter
43Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
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Danielle Halpern
7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Emily Hansen-Kiss
44The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
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Xin He
45Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
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Gail E. Herman
44The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, USA
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Irva Hertz-Picciotto
20MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, California, USA
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David M. Hougaard
12The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
27Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
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Christina M. Hultman
46Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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Iuliana Ionita-Laza
47Department of Biostatistics, Columbia University, New York, New York, USA
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Suma Jacob
43Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
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Jesslyn Jamison
7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Astanand Jugessur
48Norwegian Institute of Public Health, Oslo, Norway
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Miia Kaartinen
49Department of Child Psychiatry, University of Tampere and Tampere University Hospital, Tampere, Finland
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Gun Peggy Knudsen
48Norwegian Institute of Public Health, Oslo, Norway
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Alexander Kolevzon
7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
50Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Itaru Kushima
23Department of Psychiatry, Graduate School of Medicine, Nagoya University, Nagoya, Japan
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So Lun Lee
30Department of Pediatrics & Adolescent Medicine, Duchess of Kent Children’s Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
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Terho Lehtimäki
51Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
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Elaine T. Lim
4Harvard Medical School, Boston, Massachusetts, USA
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Carla Lintas
52Campus Bio-medico, Rome, Italy
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W. Ian Lipkin
47Department of Biostatistics, Columbia University, New York, New York, USA
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Diego Lopergolo
35Medical Genetics, University of Siena, Siena, Italy
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Fátima Lopes
53Life and Health Sciences Research Institute, School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
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Yunin Ludena
20MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, California, USA
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Patricia Maciel
53Life and Health Sciences Research Institute, School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
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Per Magnus
48Norwegian Institute of Public Health, Oslo, Norway
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Behrang Mahjani
7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Nell Maltman
43Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
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Dara S. Manoach
54Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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Gal Meiri
55Pre-School Psychiatry Unit, Soroka University Medical Center, Beer Sheva, Israel
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Idan Menashe
56Department of Public Health, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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  • ORCID record for Idan Menashe
Judith Miller
32Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA
33Department of Psychiatry, University of Utah, Salt Lake City, Utah, USA
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Nancy Minshew
15Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Eduarda Montenegro M. de Souza
57Centro de Pesquisas sobre o Genoma Humano e Células tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Danielle Moreira
57Centro de Pesquisas sobre o Genoma Humano e Células tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Eric M. Morrow
58Department of Molecular Biology, Cell Biology and Biochemistry and Department of Psychiatry and Human Behavior, Brown University, Providence, Rhode Island, USA
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Ole Mors
12The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
59Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
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Preben Bo Mortensen
12The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
13Center for Genomics and Personalized Medicine, Aarhus, Denmark
60National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
61Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
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Matthew Mosconi
43Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
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Pierandrea Muglia
62UCB Pharma, Belgium
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Benjamin Neale
1Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
2Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Merete Nordentoft
12The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
63Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
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Norio Ozaki
23Department of Psychiatry, Graduate School of Medicine, Nagoya University, Nagoya, Japan
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Aarno Palotie
2Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
64Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
65Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA
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Mara Parellada
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70The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
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7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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71Maine Medical Center and Maine Medical Center Research Institute, Portland, Maine, USA
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74Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
75McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
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31Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University Frankfurt, Frankfurt, Germany
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20MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, California, USA
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43Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
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57Centro de Pesquisas sobre o Genoma Humano e Células tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Tarjinder Singh
1Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
2Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
4Harvard Medical School, Boston, Massachusetts, USA
5Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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Paige M. Siper
7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
9The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Moyra Smith
19Center for Autism Research and Translation, University of California Irvine, Irvine, California, USA
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Gabriela Soares
76Center for Medical Genetics Dr. Jacinto Magalhães, National Health Institute Dr. Ricardo Jorge, Porto, Portugal
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Camilla Stoltenberg
48Norwegian Institute of Public Health, Oslo, Norway
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Pål Suren
48Norwegian Institute of Public Health, Oslo, Norway
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Ezra Susser
77New York State Psychiatric Institute, New York, New York, USA
78Department of Epidemiology, Mailman School of Public Health, Columbia University, Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA
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John Sweeney
43Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
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Peter Szatmari
79Department of Psychiatry and Behavioural Neurosciences, Offord Centre for Child Studies, McMaster University, Hamilton, Ontario, Canada
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Lara Tang
7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Flora Tassone
20MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, California, USA
80Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Davis, CA, USA
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Karoline Teufel
31Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Goethe University Frankfurt, Frankfurt, Germany
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Elisabetta Trabetti
81Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Verona, Italy
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Maria del Pilar Trelles
7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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21Division of Genetics, Boston Children’s Hospital, Boston, Massachusetts, USA
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Thomas Werge
12The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
82Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
83Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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1Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
2Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Emma Wilkinson
7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Jeremy A. Willsey
10Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
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Tim Yu
21Division of Genetics, Boston Children’s Hospital, Boston, Massachusetts, USA
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Mullin H.C. Yu
30Department of Pediatrics & Adolescent Medicine, Duchess of Kent Children’s Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
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Ryan Yuen
74Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
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Elaine Zachi
57Centro de Pesquisas sobre o Genoma Humano e Células tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Catalina Betancur
84Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
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Edwin H. Cook
43Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
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85Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
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85Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland
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James S. Sutcliffe
86Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
87Department of Molecular Physiology and Biophsysics and Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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88National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, USA
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89Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
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12The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
13Center for Genomics and Personalized Medicine, Aarhus, Denmark
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90Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
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A. Ercument Cicek
6Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
18Computer Engineering Department, Bilkent University, Ankara, Turkey
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5Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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89Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
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15Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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10Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, California, USA
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  • ORCID record for Stephan J. Sanders
Kathryn Roeder
6Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
91Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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Mark J. Daly
1Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts, USA
2Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
3Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
4Harvard Medical School, Boston, Massachusetts, USA
5Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
64Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
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  • For correspondence: mjdaly@atgu.mgh.harvard.edu
Joseph D. Buxbaum
7Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA
8Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
9The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
92Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
93Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
94Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Summary

We present the largest exome sequencing study of autism spectrum disorder (ASD) to date (n=35,584 total samples, 11,986 with ASD). Using an enhanced Bayesian framework to integrate de novo and case-control rare variation, we identify 102 risk genes at a false discovery rate ≤ 0.1. Of these genes, 49 show higher frequencies of disruptive de novo variants in individuals ascertained for severe neurodevelopmental delay, while 53 show higher frequencies in individuals ascertained for ASD; comparing ASD cases with mutations in these groups reveals phenotypic differences. Expressed early in brain development, most of the risk genes have roles in regulation of gene expression or neuronal communication (i.e., mutations effect neurodevelopmental and neurophysiological changes), and 13 fall within loci recurrently hit by copy number variants. In human cortex single-cell gene expression data, expression of risk genes is enriched in both excitatory and inhibitory neuronal lineages, consistent with multiple paths to an excitatory/inhibitory imbalance underlying ASD.

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Large-scale exome sequencing study implicates both developmental and functional changes in the neurobiology of autism
F. Kyle Satterstrom, Jack A. Kosmicki, Jiebiao Wang, Michael S. Breen, Silvia De Rubeis, Joon-Yong An, Minshi Peng, Ryan Collins, Jakob Grove, Lambertus Klei, Christine Stevens, Jennifer Reichert, Maureen S. Mulhern, Mykyta Artomov, Sherif Gerges, Brooke Sheppard, Xinyi Xu, Aparna Bhaduri, Utku Norman, Harrison Brand, Grace Schwartz, Rachel Nguyen, Elizabeth E. Guerrero, Caroline Dias, Branko Aleksic, Richard Anney, Mafalda Barbosa, Somer Bishop, Alfredo Brusco, Jonas Bybjerg-Grauholm, Angel Carracedo, Marcus C.Y. Chan, Andreas G. Chiocchetti, Brian H. Y. Chung, Hilary Coon, Michael L. Cuccaro, Aurora Currò, Bernardo Dalla Bernardina, Ryan Doan, Enrico Domenici, Shan Dong, Chiara Fallerini, Montserrat Fernández-Prieto, Giovanni Battista Ferrero, Christine M. Freitag, Menachem Fromer, J. Jay Gargus, Daniel Geschwind, Elisa Giorgio, Javier González-Peñas, Stephen Guter, Danielle Halpern, Emily Hansen-Kiss, Xin He, Gail E. Herman, Irva Hertz-Picciotto, David M. Hougaard, Christina M. Hultman, Iuliana Ionita-Laza, Suma Jacob, Jesslyn Jamison, Astanand Jugessur, Miia Kaartinen, Gun Peggy Knudsen, Alexander Kolevzon, Itaru Kushima, So Lun Lee, Terho Lehtimäki, Elaine T. Lim, Carla Lintas, W. Ian Lipkin, Diego Lopergolo, Fátima Lopes, Yunin Ludena, Patricia Maciel, Per Magnus, Behrang Mahjani, Nell Maltman, Dara S. Manoach, Gal Meiri, Idan Menashe, Judith Miller, Nancy Minshew, Eduarda Montenegro M. de Souza, Danielle Moreira, Eric M. Morrow, Ole Mors, Preben Bo Mortensen, Matthew Mosconi, Pierandrea Muglia, Benjamin Neale, Merete Nordentoft, Norio Ozaki, Aarno Palotie, Mara Parellada, Maria Rita Passos-Bueno, Margaret Pericak-Vance, Antonio Persico, Isaac Pessah, Kaija Puura, Abraham Reichenberg, Alessandra Renieri, Evelise Riberi, Elise B. Robinson, Kaitlin E. Samocha, Sven Sandin, Susan L. Santangelo, Gerry Schellenberg, Stephen W. Scherer, Sabine Schlitt, Rebecca Schmidt, Lauren Schmitt, Isabela Maya W. Silva, Tarjinder Singh, Paige M. Siper, Moyra Smith, Gabriela Soares, Camilla Stoltenberg, Pål Suren, Ezra Susser, John Sweeney, Peter Szatmari, Lara Tang, Flora Tassone, Karoline Teufel, Elisabetta Trabetti, Maria del Pilar Trelles, Christopher Walsh, Lauren A. Weiss, Thomas Werge, Donna Werling, Emilie M. Wigdor, Emma Wilkinson, Jeremy A. Willsey, Tim Yu, Mullin H.C. Yu, Ryan Yuen, Elaine Zachi, iPSYCH consortium, Catalina Betancur, Edwin H. Cook, Louise Gallagher, Michael Gill, James S. Sutcliffe, Audrey Thurm, Michael E. Zwick, Anders D. Børglum, Matthew W. State, A. Ercument Cicek, Michael E. Talkowski, David J. Cutler, Bernie Devlin, Stephan J. Sanders, Kathryn Roeder, Mark J. Daly, Joseph D. Buxbaum
bioRxiv 484113; doi: https://doi.org/10.1101/484113
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Large-scale exome sequencing study implicates both developmental and functional changes in the neurobiology of autism
F. Kyle Satterstrom, Jack A. Kosmicki, Jiebiao Wang, Michael S. Breen, Silvia De Rubeis, Joon-Yong An, Minshi Peng, Ryan Collins, Jakob Grove, Lambertus Klei, Christine Stevens, Jennifer Reichert, Maureen S. Mulhern, Mykyta Artomov, Sherif Gerges, Brooke Sheppard, Xinyi Xu, Aparna Bhaduri, Utku Norman, Harrison Brand, Grace Schwartz, Rachel Nguyen, Elizabeth E. Guerrero, Caroline Dias, Branko Aleksic, Richard Anney, Mafalda Barbosa, Somer Bishop, Alfredo Brusco, Jonas Bybjerg-Grauholm, Angel Carracedo, Marcus C.Y. Chan, Andreas G. Chiocchetti, Brian H. Y. Chung, Hilary Coon, Michael L. Cuccaro, Aurora Currò, Bernardo Dalla Bernardina, Ryan Doan, Enrico Domenici, Shan Dong, Chiara Fallerini, Montserrat Fernández-Prieto, Giovanni Battista Ferrero, Christine M. Freitag, Menachem Fromer, J. Jay Gargus, Daniel Geschwind, Elisa Giorgio, Javier González-Peñas, Stephen Guter, Danielle Halpern, Emily Hansen-Kiss, Xin He, Gail E. Herman, Irva Hertz-Picciotto, David M. Hougaard, Christina M. Hultman, Iuliana Ionita-Laza, Suma Jacob, Jesslyn Jamison, Astanand Jugessur, Miia Kaartinen, Gun Peggy Knudsen, Alexander Kolevzon, Itaru Kushima, So Lun Lee, Terho Lehtimäki, Elaine T. Lim, Carla Lintas, W. Ian Lipkin, Diego Lopergolo, Fátima Lopes, Yunin Ludena, Patricia Maciel, Per Magnus, Behrang Mahjani, Nell Maltman, Dara S. Manoach, Gal Meiri, Idan Menashe, Judith Miller, Nancy Minshew, Eduarda Montenegro M. de Souza, Danielle Moreira, Eric M. Morrow, Ole Mors, Preben Bo Mortensen, Matthew Mosconi, Pierandrea Muglia, Benjamin Neale, Merete Nordentoft, Norio Ozaki, Aarno Palotie, Mara Parellada, Maria Rita Passos-Bueno, Margaret Pericak-Vance, Antonio Persico, Isaac Pessah, Kaija Puura, Abraham Reichenberg, Alessandra Renieri, Evelise Riberi, Elise B. Robinson, Kaitlin E. Samocha, Sven Sandin, Susan L. Santangelo, Gerry Schellenberg, Stephen W. Scherer, Sabine Schlitt, Rebecca Schmidt, Lauren Schmitt, Isabela Maya W. Silva, Tarjinder Singh, Paige M. Siper, Moyra Smith, Gabriela Soares, Camilla Stoltenberg, Pål Suren, Ezra Susser, John Sweeney, Peter Szatmari, Lara Tang, Flora Tassone, Karoline Teufel, Elisabetta Trabetti, Maria del Pilar Trelles, Christopher Walsh, Lauren A. Weiss, Thomas Werge, Donna Werling, Emilie M. Wigdor, Emma Wilkinson, Jeremy A. Willsey, Tim Yu, Mullin H.C. Yu, Ryan Yuen, Elaine Zachi, iPSYCH consortium, Catalina Betancur, Edwin H. Cook, Louise Gallagher, Michael Gill, James S. Sutcliffe, Audrey Thurm, Michael E. Zwick, Anders D. Børglum, Matthew W. State, A. Ercument Cicek, Michael E. Talkowski, David J. Cutler, Bernie Devlin, Stephan J. Sanders, Kathryn Roeder, Mark J. Daly, Joseph D. Buxbaum
bioRxiv 484113; doi: https://doi.org/10.1101/484113

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