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A contribution of novel CNVs to schizophrenia from a genome-wide study of 41,321 subjects

By Christian R. Marshall, Daniel P Howrigan, Daniele Merico, Bhooma Thiruvahindrapuram, Wenting Wu, Douglas S. Greer, Danny Antaki, Aniket Shetty, Peter A Holmans, Dalila Pinto, Madhusudan Gujral, William M Brandler, Dheeraj Malhotra, Zhouzhi Wang, Karin V. Fuentes Fajarado, Stephan Ripke, Ingrid Agartz, Esben Agerbo, Margot Albus, Madeline Alexander, Farooq Amin, Joshua Atkins, Silviu A Bacanu, Richard A Belliveau, Sarah E Bergen, Marcelo Bertalan, Elizabeth Bevilacqua, Tim B Bigdeli, Donald W Black, Richard Bruggeman, Nancy G Buccola, Randy L. Buckner, Brendan Bulik-Sullivan, William Byerley, Wiepke Cahn, Guiqing Cai, Murray J Cairns, Dominique Campion, Rita M Cantor, Vaughan J Carr, Noa Carrera, Stanley V Catts, Kimberley D Chambert, Wei Cheng, C Robert Cloninger, David Cohen, Paul Cormican, Nick Craddock, Benedicto Crespo-Facorro, James J. Crowley, David Curtis, Michael Davidson, Kenneth L Davis, Franziska Degenhardt, Jurgen Del Favero, Lynn E DeLisi, Ditte Demontis, Dimitris Dikeos, Timothy Dinan, Srdjan Djurovic, Gary Donohoe, Elodie Drapeau, Jubao Duan, Frank Dudbridge, Peter Eichhammer, Johan Eriksson, Valentina Escott-Price, Laurent Essioux, Ayman H. Fanous, Kai-How Farh, Martilias S Farrell, Josef Frank, Lude Franke, Robert Freedman, Nelson B. Freimer, Joseph I Friedman, Andreas J. Forstner, Menachem Fromer, Giulio Genovese, Lyudmila Georgieva, Elliot S Gershon, Ina Giegling, Paola Giusti-Rodríguez, Stephanie Godard, Jacqueline I Goldstein, Jacob Gratten, Lieuwe de Haan, Marian L Hamshere, Mark Hansen, Thomas Hansen, Vahram Haroutunian, Annette M Hartmann, Frans A Henskens, Stefan Herms, Joel N Hirschhorn, Per Hoffmann, Andrea Hofman, Mads V Hollegaard, David M Hougaard, Hailiang Huang, Masashi Ikeda, Inge Joa, K Kähler Anna, René S. Kahn, Luba Kalaydjieva, Juha Karjalainen, David Kavanagh, Matthew C. Keller, Brian J Kelly, James L Kennedy, Yunjung Kim, James A. Knowles, Bettina Konte, Claudine Laurent, Phil Lee, S. Hong Lee, Sophie E Legge, Bernard Lerer, Deborah L. Levy, Kung-Yee Liang, Jeffrey Lieberman, Jouko Lönnqvist, Carmel M Loughland, Patrik K.E. Magnusson, Brion S Maher, Wolfgang Maier, Jacques Mallet, Manuel Mattheisen, Morten Mattingsdal, Robert W McCarley, Colm McDonald, Andrew M McIntosh, Sandra Meier, Carin J Meijer, Ingrid Melle, Raquelle I Mesholam-Gately, Andres Metspalu, Patricia T Michie, Lili Milani, Vihra Milanova, Younes Mokrab, Derek W Morris, Ole Mors, Bertram Müller-Myhsok, Kieran C Murphy, Robin M Murray, Inez Myin-Germeys, Igor Nenadic, Deborah A Nertney, Gerald Nestadt, Kristin K Nicodemus, Laura Nisenbaum, Annelie Nordin, Eadbhard O’ Callaghan, Colm O’ Dushlaine, Sang-Yun Oh, Ann Olincy, Line Olsen, F. Anthony O’ Neill, Jim Van Os, Christos Pantelis, George N Papadimitriou, Elena Parkhomenko, Michele T Pato, Tiina Paunio, Psychosis Endophenotypes International Consortium, Diana O Perkins, Tune H. Pers, Olli Pietiläinen, Jonathan Pimm, Andrew J Pocklington, John Powell, Alkes Price, Ann E Pulver, Shaun M. Purcell, Digby Quested, Henrik B Rasmussen, Abraham Reichenberg, Mark A Reimers, Alexander L Richards, Joshua L. Roffman, Panos Roussos, Douglas M Ruderfer, Veikko Salomaa, Alan R. Sanders, Adam Savitz, Ulrich Schall, Thomas G. Schulze, Sibylle G Schwab, Edward M Scolnick, Rodney J. Scott, Larry J Seidman, Jianxin Shi, Jeremy M Silverman, Jordan W. Smoller, Erik Söderman, Chris CA Spencer, Eli A Stahl, Eric Strengman, Jana Strohmaier, T Scott Stroup, Jaana Suvisaari, Dragan M Svrakic, Jin P Szatkiewicz, Srinivas Thirumalai, Paul A Tooney, Juha Veijola, Peter M. Visscher, John Waddington, Dermot Walsh, Bradley T Webb, Mark Weiser, Dieter B Wildenauer, Nigel M Williams, Stephanie Williams, Stephanie H. Witt, Aaron R Wolen, Brandon K Wormley, Naomi R. Wray, Jing Qin Wu, Clement C. Zai, Wellcome Trust Case-Control Consortium, Rolf Adolfsson, Ole A Andreassen, Douglas HR Blackwood, Anders D. Børglum, Elvira Bramon, Joseph D. Buxbaum, Sven Cichon, David A. Collier, Aiden Corvin, Mark J. Daly, Ariel Darvasi, Enrico Domenici, Tõnu Esko, Pablo V Gejman, Michael Gill, Hugh Gurling, Christina M Hultman, Nakao Iwata, Assen V Jablensky, Erik G Jönsson, Kenneth S. Kendler, George Kirov, Jo Knight, Douglas F. Levinson, Qingqin S Li, Steven A McCarroll, Andrew McQuillin, Jennifer L Moran, Preben B Mortensen, Bryan J Mowry, Markus M Nöthen, Roel A. Ophoff, Michael J Owen, Aarno Palotie, Carlos N Pato, Tracey L Petryshen, Danielle Posthuma, Marcella Rietschel, Brien P. Riley, Dan Rujescu, Pamela Sklar, David St Clair, James TR Walters, Thomas Werge, Patrick F Sullivan, Michael C O’Donovan, Stephen W Scherer, Benjamin M Neale, Jonathan Sebat

Posted 23 Feb 2016
bioRxiv DOI: 10.1101/040493 (published DOI: 10.1038/ng.3725)

Genomic copy number variants (CNVs) have been strongly implicated in the etiology of schizophrenia (SCZ). However, apart from a small number of risk variants, elucidation of the CNV contribution to risk has been difficult due to the rarity of risk alleles, all occurring in less than 1% of cases. We sought to address this obstacle through a collaborative effort in which we applied a centralized analysis pipeline to a SCZ cohort of 21,094 cases and 20,227 controls. We observed a global enrichment of CNV burden in cases (OR=1.11, P=5.7e-15), which persisted after excluding loci implicated in previous studies (OR=1.07, P=1.7e-6). CNV burden is also enriched for genes associated with synaptic function (OR = 1.68, P = 2.8e-11) and neurobehavioral phenotypes in mouse (OR = 1.18, P= 7.3e-5). We identified genome-wide significant support for eight loci, including 1q21.1, 2p16.3 (NRXN1), 3q29, 7q11.2, 15q13.3, distal 16p11.2, proximal 16p11.2 and 22q11.2. We find support at a suggestive level for nine additional candidate susceptibility and protective loci, which consist predominantly of CNVs mediated by non-allelic homologous recombination (NAHR).

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