Annotation-Informed Causal Mixture Modeling (AI-MiXeR) reveals phenotype-specific differences in polygenicity and effect size distribution across functional annotation categories

Hilary K Finucane, Brendan Bulik-Sullivan, Alexander Gusev, Gosia Trynka, Yakir Reshef, Po-Ru Loh, Verneri Anttila, Han Xu, Chongzhi Zang, Kyle Farh, Stephan Ripke, Felix R Day, ReproGen Consortium, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Raci Consortium, Shaun Purcell, Eli Stahl, Sara Lindstrom, John RB Perry, Yukinori Okada, Soumya Raychaudhuri, Mark J Daly, Nick Patterson, Benjamin M Neale, Alkes L Price, None, Partitioning heritability by functional annotation using genome-wide association summary statistics Nature Genetics. ,vol. 47, pp. 1228- 1235 ,(2015) , 10.1038/NG.3404

Dmitry Shungin, Thomas W Winkler, Damien C Croteau-Chonka, Teresa Ferreira, Adam E Locke, Reedik Mägi, Rona J Strawbridge, Tune H Pers, Krista Fischer, Anne E Justice, Tsegaselassie Workalemahu, Joseph MW Wu, Martin L Buchkovich, Nancy L Heard-Costa, Tamara S Roman, Alexander W Drong, Ci Song, Stefan Gustafsson, Felix R Day, Tonu Esko, Tove Fall, Zoltán Kutalik, Jian’an Luan, Joshua C Randall, André Scherag, Sailaja Vedantam, Andrew R Wood, Jin Chen, Rudolf Fehrmann, Juha Karjalainen, Bratati Kahali, Ching-Ti Liu, Ellen M Schmidt, Devin Absher, Najaf Amin, Denise Anderson, Marian Beekman, Jennifer L Bragg-Gresham, Steven Buyske, Ayse Demirkan, Georg B Ehret, Mary F Feitosa, Anuj Goel, Anne U Jackson, Toby Johnson, Marcus E Kleber, Kati Kristiansson, Massimo Mangino, Irene Mateo Leach, Carolina Medina-Gomez, Cameron D Palmer, Dorota Pasko, Sonali Pechlivanis, Marjolein J Peters, Inga Prokopenko, Alena Stančáková, Yun Ju Sung, Toshiko Tanaka, Alexander Teumer, Jana V Van Vliet-Ostaptchouk, Loïc Yengo, Weihua Zhang, Eva Albrecht, Johan Ärnlöv, Gillian M Arscott, Stefania Bandinelli, Amy Barrett, Claire Bellis, Amanda J Bennett, Christian Berne, Matthias Blüher, Stefan Böhringer, Fabrice Bonnet, Yvonne Böttcher, Marcel Bruinenberg, Delia B Carba, Ida H Caspersen, Robert Clarke, E Warwick Daw, Joris Deelen, Ewa Deelman, Graciela Delgado, Alex SF Doney, Niina Eklund, Michael R Erdos, Karol Estrada, Elodie Eury, Nele Friedrich, Melissa E Garcia, Vilmantas Giedraitis, Bruna Gigante, Alan S Go, Alain Golay, Harald Grallert, Tanja B Grammer, Jürgen Gräßler, Jagvir Grewal, Christopher J Groves, Toomas Haller, Goran Hallmans, Catharina A Hartman, Maija Hassinen, Caroline Hayward, Kauko Heikkilä, Karl-Heinz Herzig, Quinta Helmer, Hans L Hillege, Oddgeir Holmen, Steven C Hunt, Aaron Isaacs, Till Ittermann, Alan L James, Ingegerd Johansson, Thorhildur Juliusdottir, Ioanna-Panagiota Kalafati, Leena Kinnunen, Wolfgang Koenig, Ishminder K Kooner, Wolfgang Kratzer, Claudia Lamina, Karin Leander, Nanette R Lee, Peter Lichtner, Lars Lind, Jaana Lindström, Stéphane Lobbens, Mattias Lorentzon, François Mach, Patrik KE Magnusson, Anubha Mahajan, Wendy L McArdle, Cristina Menni, Sigrun Merger, Evelin Mihailov, Lili Milani, Rebecca Mills, Alireza Moayyeri, Keri L Monda, Simon P Mooijaart, Thomas W Mühleisen, Antonella Mulas, Gabriele Müller, Martina Müller-Nurasyid, Ramaiah Nagaraja, Michael A Nalls, Narisu Narisu, Nicola Glorioso, Ilja M Nolte, Matthias Olden, Nigel W Rayner, None, New genetic loci link adipose and insulin biology to body fat distribution Nature. ,vol. 518, pp. 187- 196 ,(2015) , 10.1038/NATURE14132

James J Lee, Shaun M Purcell, Shashaank Vattikuti, Laurent CAM Tellier, Carson C Chow, Christopher C Chang, None, Second-generation PLINK: rising to the challenge of larger and richer datasets GigaScience. ,vol. 4, pp. 7- 7 ,(2015) , 10.1186/S13742-015-0047-8

Christos Pantelis, George N Papadimitriou, Sergi Papiol, Elena Parkhomenko, Michele T Pato, Tiina Paunio, Milica Pejovic-Milovancevic, Diana O Perkins, 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, Ulrich Schall, Christian R Schubert, Thomas G Schulze, Sibylle G Schwab, Edward M Scolnick, Rodney J Scott, Larry J Seidman, Jianxin Shi, Engilbert Sigurdsson, Teimuraz Silagadze, Jeremy M Silverman, Kang Sim, Petr Slominsky, Jordan W Smoller, Hon-Cheong So, ChrisC A Spencer, Eli A Stahl, Hreinn Stefansson, Stacy Steinberg, Elisabeth Stogmann, Richard E Straub, Eric Strengman, Jana Strohmaier, T Scott Stroup, Mythily Subramaniam, Jaana Suvisaari, Dragan M Svrakic, Jin P Szatkiewicz, Erik Söderman, Srinivas Thirumalai, Draga Toncheva, Sarah Tosato, Juha Veijola, John Waddington, Dermot Walsh, Dai Wang, Qiang Wang, Bradley T Webb, Mark Weiser, Dieter B Wildenauer, Nigel M Williams, Stephanie Williams, Stephanie H Witt, Aaron R Wolen, Emily HM Wong, Brandon K Wormley, Hualin Simon Xi, Clement C Zai, Xuebin Zheng, Fritz Zimprich, Naomi R Wray, Kari Stefansson, Peter M Visscher, Wellcome Trust Case-Control Consortium, Rolf Adolfsson, Ole A Andreassen, Douglas HR Blackwood, Elvira Bramon, Joseph D Buxbaum, Anders D Børglum, Sven Cichon, Ariel Darvasi, Enrico Domenici, Hannelore Ehrenreich, 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, Todd Lencz, Douglas F Levinson, Qingqin S Li, Jianjun Liu, Anil K Malhotra, 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, Pak C Sham, Pamela Sklar, David St Clair, Daniel R Weinberger, Jens R Wendland, Thomas Werge, Mark J Daly, Patrick F Sullivan, Michael C O’Donovan, None, Biological insights from 108 schizophrenia-associated genetic loci Nature. ,vol. 511, pp. 421- 427 ,(2014) , 10.1038/NATURE13595

Zhan Su, Jonathan Marchini, Peter Donnelly, HAPGEN2: simulation of multiple disease SNPs Bioinformatics. ,vol. 27, pp. 2304- 2305 ,(2011) , 10.1093/BIOINFORMATICS/BTR341

, A global reference for human genetic variation. Nature. ,vol. 526, pp. 68- 74 ,(2015) , 10.1038/NATURE15393

Donna Karolchik, Angela S Hinrichs, Terrence S Furey, Krishna M Roskin, Charles W Sugnet, David Haussler, W James Kent, The UCSC Table Browser data retrieval tool Nucleic Acids Research. ,vol. 32, pp. 493D- 496 ,(2004) , 10.1093/NAR/GKH103

Andrew J Schork, Wesley K Thompson, Phillip Pham, Ali Torkamani, J Cooper Roddey, Patrick F Sullivan, John R Kelsoe, Michael C O'Donovan, Helena Furberg, Tobacco and Genetics Consortium, Bipolar Disorder Psychiatric Genomics Consortium, Schizophrenia Psychiatric Genomics Consortium, Nicholas J Schork, Ole A Andreassen, Anders M Dale, None, All SNPs are not created equal: genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs. PLOS Genetics. ,vol. 9, pp. 1- 13 ,(2013) , 10.1371/JOURNAL.PGEN.1003449

, Discovery and refinement of loci associated with lipid levels Nature Genetics. ,vol. 45, pp. 1274- 1283 ,(2013) , 10.1038/NG.2797

Brendan K Bulik-Sullivan, , Po-Ru Loh, Hilary K Finucane, Stephan Ripke, Jian Yang, Nick Patterson, Mark J Daly, Alkes L Price, Benjamin M Neale, LD score regression distinguishes confounding from polygenicity in genome-wide association studies : Nature Genetics. ,vol. 47, pp. 291- 295 ,(2015) , 10.1038/NG.3211