Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia

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Richard J.L. Anney, Stephan Ripke, Verneri Anttila, Jakob Grove, Peter Holmans, Hailiang Huang, Lambertus Klei, Phil H. Lee, Sarah E. Medland, Benjamin Neale, Elise Robinson, Lauren A. Weiss, Lonnie Zwaigenbaum, Timothy W. Yu, Kerstin Wittemeyer, A. Jeremy Willsey, Ellen M. Wijsman, Thomas Werge, Thomas H. Wassink, Regina Waltes & 143 others Christopher A. Walsh, Simon Wallace, Jacob A.S. Vorstman, Veronica J. Vieland, Astrid M. Vicente, Herman Vanengeland, Kathryn Tsang, Ann P. Thompson, Peter Szatmari, Oscar Svantesson, Stacy Steinberg, Kari Stefansson, Hreinn Stefansson, Matthew W. State, Latha Soorya, Teimuraz Silagadze, Stephen W. Scherer, Gerard D. Schellenberg, Sven Sandin, Stephan J. Sanders, Evald Saemundsen, Guy A. Rouleau, Bernadette Rogé, Kathryn Roeder, Wendy Roberts, Jennifer Reichert, Abraham Reichenberg, Karola Rehnström, Regina Regan, Fritz Poustka, Christopher S. Poultney, Joseph Piven, Dalila Pinto, Margaret A. Pericak-Vance, Milica Pejovic-Milovancevic, Marianne Giørtz Pedersen, Carsten Bøcker Pedersen, Andrew D. Paterson, Jeremy R. Parr, Alistair T. Pagnamenta, Guiomar Oliveira, John I. Nurnberger, Merete Nordentoft, Michael T. Murtha, Susana Mouga, Preben Bo Mortensen, Ole Mors, Eric M. Morrow, Daniel Moreno-De-Luca, Anthony P. Monaco, Nancy Minshew, Alison Merikangas, William M. McMahon, Susan G. McGrew, Manuel Mattheisen, Igor Martsenkovsky, Donna M. Martin, Shrikant M. Mane, Pall Magnusson, Tiago Magalhaes, Elena Maestrini, Jennifer K. Lowe, Catherine Lord, Pat Levitt, Christa Lese Martin, David H. Ledbetter, Marion Leboyer, Ann S. Lecouteur, Christine Ladd-Acosta, Alexander Kolevzon, Sabine M. Klauck, Suma Jacob, Bozenna Iliadou, Christina M. Hultman, David M. Hougaard, Irva Hertz-Picciotto, Robert Hendren, Christine Søholm Hansen, Jonathan L. Haines, Stephen J. Guter, Dorothy E. Grice, Jonathan M. Green, Andrew Green, Arthur P. Goldberg, Christopher Gillberg, John Gilbert, Louise Gallagher, Christine M. Freitag, Eric Fombonne, Susan E. Folstein, Bridget Fernandez, M. Daniele Fallin, A. Gulhan Ercan-Sencicek, Sean Ennis, Frederico Duque, Eftichia Duketis, Richard Delorme, Silvia Derubeis, Maretha V. Dejonge, Geraldine Dawson, Michael L. Cuccaro, Catarina T. Correia, Judith Conroy, Ines C. Conceição, Andreas G. Chiocchetti, Patrícia B.S. Celestino-Soper, Jillian Casey, Rita M. Cantor, Cátia Café, Jonas Bybjerg-Grauholm, Sean Brennan, Thomas Bourgeron, Patrick F. Bolton, Sven Bölte, Nadia Bolshakova, Catalina Betancur, Raphael Bernier, Arthur L. Beaudet, Agatino Battaglia, Vanessa H. Bal, Gillian Baird, Anthony J. Bailey, Marie Bækvad-Hansen, Joel S. Bader, Elena Bacchelli, Evdokia Anagnostou, David Amaral, Joana Almeida, Anders D. Børglum, Joseph D. Buxbaum, Aravinda Chakravarti, Edwin H. Cook, Hilary Coon, Daniel H. Geschwind, Michael Gill, Hakon Hakonarson, Joachim Hallmayer, Aarno Palotie, Susan Santangelo, James S. Sutcliffe, Dan E. Arking, Bernie Devlin, Mark J. Daly

Background: Over the past decade genome-wide association studies (GWAS) have been applied to aid in the understanding of the biology of traits. The success of this approach is governed by the underlying effect sizes carried by the true risk variants and the corresponding statistical power to observe such effects given the study design and sample size under investigation. Previous ASD GWAS have identified genome-wide significant (GWS) risk loci; however, these studies were of only of low statistical power to identify GWS loci at the lower effect sizes (odds ratio (OR) <1.15). Methods: We conducted a large-scale coordinated international collaboration to combine independent genotyping data to improve the statistical power and aid in robust discovery of GWS loci. This study uses genome-wide genotyping data from a discovery sample (7387 ASD cases and 8567 controls) followed by meta-analysis of summary statistics from two replication sets (7783 ASD cases and 11359 controls; and 1369 ASD cases and 137308 controls). Results: We observe a GWS locus at 10q24.32 that overlaps several genes including PITX3, which encodes a transcription factor identified as playing a role in neuronal differentiation and CUEDC2 previously reported to be associated with social skills in an independent population cohort. We also observe overlap with regions previously implicated in schizophrenia which was further supported by a strong genetic correlation between these disorders (Rg = 0.23; P = 9 × 10-6). We further combined these Psychiatric Genomics Consortium (PGC) ASD GWAS data with the recent PGC schizophrenia GWAS to identify additional regions which may be important in a common neurodevelopmental phenotype and identified 12 novel GWS loci. These include loci previously implicated in ASD such as FOXP1 at 3p13, ATP2B2 at 3p25.3, and a 'neurodevelopmental hub' on chromosome 8p11.23. Conclusions: This study is an important step in the ongoing endeavour to identify the loci which underpin the common variant signal in ASD. In addition to novel GWS loci, we have identified a significant genetic correlation with schizophrenia and association of ASD with several neurodevelopmental-related genes such as EXT1, ASTN2, MACROD2, and HDAC4.

Original languageEnglish
Article number21
JournalMolecular Autism
Number of pages17
Publication statusPublished - 22 May 2017

    Research areas

  • Autism spectrum disorder, Gene-set analysis, Genetic correlation, Genome-wide association study, Heritability, Meta-analysis, Neurodevelopment, Schizophrenia

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