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1. Using brain cell-type-specific protein interactomes to interpret neurodevelopmental genetic signals in schizophrenia

Author

Yu-Han H. Hsu, Greta Pintacuda, Ruize Liu, Eugeniu Nacu, April Kim, Kalliopi Tsafou, Natalie Petrossian, William Crotty, Jung Min Suh, Jackson Riseman, Jacqueline M. Martin, Julia C. Biagini, Daya Mena, Joshua K.T. Ching, Edyta Malolepsza, Taibo Li, Tarjinder Singh, Tian Ge, Shawn B. Egri, Benjamin Tanenbaum, Caroline R. Stanclift, Annie M. Apffel, Steven A. Carr, Monica Schenone, Jake Jaffe, Nadine Fornelos, Hailiang Huang, Kevin C. Eggan, Kasper Lage, Stephan Ripke, Benjamin M. Neale, Aiden Corvin, James T.R. Walters, Kai-How Farh, Peter A. Holmans, Phil Lee, Brendan Bulik-Sullivan, David A. Collier, Tune H. Pers, Ingrid Agartz, Esben Agerbo, Margot Albus, Madeline Alexander, Farooq Amin, Silviu A. Bacanu, Martin Begemann, Richard A. Belliveau, Jr., Judit Bene, Sarah E. Bergen, Elizabeth Bevilacqua, Tim B. Bigdeli, Donald W. Black, Richard Bruggeman, Nancy G. Buccola, Randy L. Buckner, William Byerley, Wiepke Cahn, Guiqing Cai, Dominique Campion, Rita M. Cantor, Vaughan J. Carr, Noa Carrera, Stanley V. Catts, Kimberley D. Chambert, Raymond C.K. Chan, Ronald Y.L. Chan, Eric Y.H. Chen, Wei Cheng, Eric FC. Cheung, Siow Ann Chong, C. Robert Cloninger, David Cohen, Nadine Cohen, Paul Cormican, Nick Craddock, James J. Crowley, David Curtis, Michael Davidson, Kenneth L. Davis, Franziska Degenhardt, Jurgen Del Favero, Ditte Demontis, Dimitris Dikeos, Timothy Dinan, Srdjan Djurovic, Gary Donohoe, Elodie Drapeau, Jubao Duan, Frank Dudbridge, Naser Durmishi, Peter Eichhammer, Johan Eriksson, Valentina Escott-Price, Laurent Essioux, Ayman H. Fanous, Martilias S. Farrell, Josef Frank, Lude Franke, Robert Freedman, Nelson B. Freimer, Marion Friedl, Joseph I. Friedman, Menachem Fromer, Giulio Genovese, Lyudmila Georgieva, Ina Giegling, Paola Giusti-Rodríguez, Stephanie Godard, Jacqueline I. Goldstein, Vera Golimbet, Srihari Gopal, Jacob Gratten, Lieuwe de Haan, Christian Hammer, 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, Masashi Ikeda, Inge Joa, Antonio Julià, René S. Kahn, Luba Kalaydjieva, Sena Karachanak-Yankova, Juha Karjalainen, David Kavanagh, Matthew C. Keller, James L. Kennedy, Andrey Khrunin, Yunjung Kim, Janis Klovins, James A. Knowles, Bettina Konte, Vaidutis Kucinskas, Zita Ausrele Kucinskiene, Hana Kuzelova-Ptackova, Anna K. Kähler, Claudine Laurent, Jimmy Lee, S. Hong Lee, Sophie E. Legge, Bernard Lerer, Miaoxin Li, Tao Li, Kung-Yee Liang, Jeffrey Lieberman, Svetlana Limborska, Carmel M. Loughland, Jan Lubinski, Jouko Lönnqvist, Milan Macek, Patrik K.E. Magnusson, Brion S. Maher, Wolfgang Maier, Jacques Mallet, Sara Marsal, Manuel Mattheisen, Morten Mattingsdal, Robert W. McCarley, Colm McDonald, Andrew M. McIntosh, Sandra Meier, Carin J. Meijer, Bela Melegh, Ingrid Melle, Raquelle I. Mesholam-Gately, Andres Metspalu, Patricia T. Michie, Lili Milani, Vihra Milanova, Younes Mokrab, Derek W. Morris, Ole Mors, Kieran C. Murphy, Robin M. Murray, Inez Myin-Germeys, Bertram Müller-Myhsok, Mari Nelis, Igor Nenadic, Deborah A. Nertney, Gerald Nestadt, Kristin K. Nicodemus, Liene Nikitina-Zake, Laura Nisenbaum, Annelie Nordin, Eadbhard O'Callaghan, Colm O'Dushlaine, F. Anthony O'Neill, Sang-Yun Oh, Ann Olincy, Line Olsen, Jim Van Os, 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, Chris C.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 H.M. Wong, Brandon K. Wormley, Hualin Simon Xi, Clement C. Zai, Xuebin Zheng, Fritz Zimprich, Naomi R. Wray, Kari Stefansson, Peter M. Visscher, Rolf Adolfsson, Ole A. Andreassen, Douglas H.R. 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, Shengying Qin, Akira Sawa, Rene Kahn, Kyung Sue Hong, Wenzhao Shi, Ming Tsuang, Masanari Itokawa, Gang Feng, Stephen J. Glatt, Xiancang Ma, Jinsong Tang, Yunfeng Ruan, Feng Zhu, Yasue Horiuchi, Byung Dae Lee, Eun-Jeong Joo, Woojae Myung, Kyooseob Ha, Hong-Hee Won, Ji Hyung Baek, Young Chul Chung, Sung-Wan Kim, Agung Kusumawardhani, Wei J. Chen, Hai-Gwo Hwu, Akitoyo Hishimoto, Ikuo Otsuka, Ichiro Sora, Tomoko Toyota, Takeo Yoshikawa, Hiroshi Kunugi, Kotaro Hattori, Sayuri Ishiwata, Shusuke Numata, Tetsuro Ohmori, Makoto Arai, Yuji Ozeki, Kumiko Fujii, Se Joo Kim, Heon-Jeong Lee, Yong Min Ahn, Se Hyun Kim, Kazufumi Akiyama, Kazutaka Shimoda, and Makoto Kinoshita

Subjects
Molecular interaction, Developmental neuroscience, Cellular neuroscience, Proteomics, Science
Abstract

Summary: Genetics have nominated many schizophrenia risk genes and identified convergent signals between schizophrenia and neurodevelopmental disorders. However, functional interpretation of the nominated genes in the relevant brain cell types is often lacking. We executed interaction proteomics for six schizophrenia risk genes that have also been implicated in neurodevelopment in human induced cortical neurons. The resulting protein network is enriched for common variant risk of schizophrenia in Europeans and East Asians, is down-regulated in layer 5/6 cortical neurons of individuals affected by schizophrenia, and can complement fine-mapping and eQTL data to prioritize additional genes in GWAS loci. A sub-network centered on HCN1 is enriched for common variant risk and contains proteins (HCN4 and AKAP11) enriched for rare protein-truncating mutations in individuals with schizophrenia and bipolar disorder. Our findings showcase brain cell-type-specific interactomes as an organizing framework to facilitate interpretation of genetic and transcriptomic data in schizophrenia and its related disorders.

Published
2023
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2. Comprehensive identification of somatic nucleotide variants in human brain tissue

Author

Yifan Wang, Taejeong Bae, Jeremy Thorpe, Maxwell A. Sherman, Attila G. Jones, Sean Cho, Kenneth Daily, Yanmei Dou, Javier Ganz, Alon Galor, Irene Lobon, Reenal Pattni, Chaggai Rosenbluh, Simone Tomasi, Livia Tomasini, Xiaoxu Yang, Bo Zhou, Schahram Akbarian, Laurel L. Ball, Sara Bizzotto, Sarah B. Emery, Ryan Doan, Liana Fasching, Yeongjun Jang, David Juan, Esther Lizano, Lovelace J. Luquette, John B. Moldovan, Rujuta Narurkar, Matthew T. Oetjens, Rachel E. Rodin, Shobana Sekar, Joo Heon Shin, Eduardo Soriano, Richard E. Straub, Weichen Zhou, Andrew Chess, Joseph G. Gleeson, Tomas Marquès-Bonet, Peter J. Park, Mette A. Peters, Jonathan Pevsner, Christopher A. Walsh, Daniel R. Weinberger, Brain Somatic Mosaicism Network, Flora M. Vaccarino, John V. Moran, Alexander E. Urban, Jeffrey M. Kidd, Ryan E. Mills, and Alexej Abyzov

Subjects
Biology (General), QH301-705.5, Genetics, QH426-470
Abstract

Abstract Background Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells. Results Here, the Brain Somatic Mosaicism Network conducts a coordinated, multi-institutional study to examine the ability of existing methods to detect simulated somatic single-nucleotide variants (SNVs) in DNA mixing experiments, generate multiple replicates of whole-genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual, devise strategies to discover somatic SNVs, and apply various approaches to validate somatic SNVs. These efforts lead to the identification of 43 bona fide somatic SNVs that range in variant allele fractions from ~ 0.005 to ~ 0.28. Guided by these results, we devise best practices for calling mosaic SNVs from 250× whole-genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrate that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees. Conclusions This study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.

Published
2021
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3. Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs

Author

Emily E. Burke, Joshua G. Chenoweth, Joo Heon Shin, Leonardo Collado-Torres, Suel-Kee Kim, Nicola Micali, Yanhong Wang, Carlo Colantuoni, Richard E. Straub, Daniel J. Hoeppner, Huei-Ying Chen, Alana Sellers, Kamel Shibbani, Gregory R. Hamersky, Marcelo Diaz Bustamante, BaDoi N. Phan, William S. Ulrich, Cristian Valencia, Amritha Jaishankar, Amanda J. Price, Anandita Rajpurohit, Stephen A. Semick, Roland W. Bürli, James C. Barrow, Daniel J. Hiler, Stephanie C. Page, Keri Martinowich, Thomas M. Hyde, Joel E. Kleinman, Karen F. Berman, Jose A. Apud, Alan J. Cross, Nicholas J. Brandon, Daniel R. Weinberger, Brady J. Maher, Ronald D. G. McKay, and Andrew E. Jaffe

Subjects
Science
Abstract

Here, authors present results of a hiPSC transcriptomics study on corticogenesis from multiple donors across four transitions in differentiation. They present a bulk data deconvolution method and show that co-culturing human NPCs with rodent astrocytes results in mutually synergistic maturation.

Published
2020
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4. Author Correction: Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function

Author

Gail Davies, Max Lam, Sarah E. Harris, Joey W. Trampush, Michelle Luciano, W. David Hill, Saskia P. Hagenaars, Stuart J. Ritchie, Riccardo E. Marioni, Chloe Fawns-Ritchie, David C. M. Liewald, Judith A. Okely, Ari V. Ahola-Olli, Catriona L. K. Barnes, Lars Bertram, Joshua C. Bis, Katherine E. Burdick, Andrea Christoforou, Pamela DeRosse, Srdjan Djurovic, Thomas Espeseth, Stella Giakoumaki, Sudheer Giddaluru, Daniel E. Gustavson, Caroline Hayward, Edith Hofer, M. Arfan Ikram, Robert Karlsson, Emma Knowles, Jari Lahti, Markus Leber, Shuo Li, Karen A. Mather, Ingrid Melle, Derek Morris, Christopher Oldmeadow, Teemu Palviainen, Antony Payton, Raha Pazoki, Katja Petrovic, Chandra A. Reynolds, Muralidharan Sargurupremraj, Markus Scholz, Jennifer A. Smith, Albert V. Smith, Natalie Terzikhan, Anbupalam Thalamuthu, Stella Trompet, Sven J. van der Lee, Erin B. Ware, B. Gwen Windham, Margaret J. Wright, Jingyun Yang, Jin Yu, David Ames, Najaf Amin, Philippe Amouyel, Ole A. Andreassen, Nicola J. Armstrong, Amelia A. Assareh, John R. Attia, Deborah Attix, Dimitrios Avramopoulos, David A. Bennett, Anne C. Böhmer, Patricia A. Boyle, Henry Brodaty, Harry Campbell, Tyrone D. Cannon, Elizabeth T. Cirulli, Eliza Congdon, Emily Drabant Conley, Janie Corley, Simon R. Cox, Anders M. Dale, Abbas Dehghan, Danielle Dick, Dwight Dickinson, Johan G. Eriksson, Evangelos Evangelou, Jessica D. Faul, Ian Ford, Nelson A. Freimer, He Gao, Ina Giegling, Nathan A. Gillespie, Scott D. Gordon, Rebecca F. Gottesman, Michael E. Griswold, Vilmundur Gudnason, Tamara B. Harris, Annette M. Hartmann, Alex Hatzimanolis, Gerardo Heiss, Elizabeth G. Holliday, Peter K. Joshi, Mika Kähönen, Sharon L. R. Kardia, Ida Karlsson, Luca Kleineidam, David S. Knopman, Nicole A. Kochan, Bettina Konte, John B. Kwok, Stephanie Le Hellard, Teresa Lee, Terho Lehtimäki, Shu-Chen Li, Christina M. Lill, Tian Liu, Marisa Koini, Edythe London, Will T. Longstreth, Oscar L. Lopez, Anu Loukola, Tobias Luck, Astri J. Lundervold, Anders Lundquist, Leo-Pekka Lyytikäinen, Nicholas G. Martin, Grant W. Montgomery, Alison D. Murray, Anna C. Need, Raymond Noordam, Lars Nyberg, William Ollier, Goran Papenberg, Alison Pattie, Ozren Polasek, Russell A. Poldrack, Bruce M. Psaty, Simone Reppermund, Steffi G. Riedel-Heller, Richard J. Rose, Jerome I. Rotter, Panos Roussos, Suvi P. Rovio, Yasaman Saba, Fred W. Sabb, Perminder S. Sachdev, Claudia L. Satizabal, Matthias Schmid, Rodney J. Scott, Matthew A. Scult, Jeannette Simino, P. Eline Slagboom, Nikolaos Smyrnis, Aïcha Soumaré, Nikos C. Stefanis, David J. Stott, Richard E. Straub, Kjetil Sundet, Adele M. Taylor, Kent D. Taylor, Ioanna Tzoulaki, Christophe Tzourio, André Uitterlinden, Veronique Vitart, Aristotle N. Voineskos, Jaakko Kaprio, Michael Wagner, Holger Wagner, Leonie Weinhold, K. Hoyan Wen, Elisabeth Widen, Qiong Yang, Wei Zhao, Hieab H. H. Adams, Dan E. Arking, Robert M. Bilder, Panos Bitsios, Eric Boerwinkle, Ornit Chiba-Falek, Aiden Corvin, Philip L. De Jager, Stéphanie Debette, Gary Donohoe, Paul Elliott, Annette L. Fitzpatrick, Michael Gill, David C. Glahn, Sara Hägg, Narelle K. Hansell, Ahmad R. Hariri, M. Kamran Ikram, J. Wouter Jukema, Eero Vuoksimaa, Matthew C. Keller, William S. Kremen, Lenore Launer, Ulman Lindenberger, Aarno Palotie, Nancy L. Pedersen, Neil Pendleton, David J. Porteous, Katri Räikkönen, Olli T. Raitakari, Alfredo Ramirez, Ivar Reinvang, Igor Rudan, Dan Rujescu, Reinhold Schmidt, Helena Schmidt, Peter W. Schofield, Peter R. Schofield, John M. Starr, Vidar M. Steen, Julian N. Trollor, Steven T. Turner, Cornelia M. Van Duijn, Arno Villringer, Daniel R. Weinberger, David R. Weir, James F. Wilson, Anil Malhotra, Andrew M. McIntosh, Catharine R. Gale, Sudha Seshadri, Thomas H. Mosley, Jan Bressler, Todd Lencz, and Ian J. Deary

Subjects
Science
Abstract

Christina M. Lill, who contributed to analysis of data, was inadvertently omitted from the author list in the originally published version of this article. This has now been corrected in both the PDF and HTML versions of the article.

Published
2019
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5. Variations in Dysbindin-1 are associated with cognitive response to antipsychotic drug treatment

Author

Diego Scheggia, Rosa Mastrogiacomo, Maddalena Mereu, Sara Sannino, Richard E. Straub, Marco Armando, Francesca Managò, Simone Guadagna, Fabrizio Piras, Fengyu Zhang, Joel E. Kleinman, Thomas M. Hyde, Sanne S. Kaalund, Maria Pontillo, Genny Orso, Carlo Caltagirone, Emiliana Borrelli, Maria A. De Luca, Stefano Vicari, Daniel R. Weinberger, Gianfranco Spalletta, and Francesco Papaleo

Subjects
Science
Abstract

Patients with schizophrenia show varied response to antipsychotics. Here, the authors demonstrate in patients under antipsychotics treatment that a haplotype associated with lower dysbindin-1 expression correlated with better executive functions, providing further mechanistic support from mouse models.

Published
2018
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6. Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function

Author

Gail Davies, Max Lam, Sarah E. Harris, Joey W. Trampush, Michelle Luciano, W. David Hill, Saskia P. Hagenaars, Stuart J. Ritchie, Riccardo E. Marioni, Chloe Fawns-Ritchie, David C. M. Liewald, Judith A. Okely, Ari V. Ahola-Olli, Catriona L. K. Barnes, Lars Bertram, Joshua C. Bis, Katherine E. Burdick, Andrea Christoforou, Pamela DeRosse, Srdjan Djurovic, Thomas Espeseth, Stella Giakoumaki, Sudheer Giddaluru, Daniel E. Gustavson, Caroline Hayward, Edith Hofer, M. Arfan Ikram, Robert Karlsson, Emma Knowles, Jari Lahti, Markus Leber, Shuo Li, Karen A. Mather, Ingrid Melle, Derek Morris, Christopher Oldmeadow, Teemu Palviainen, Antony Payton, Raha Pazoki, Katja Petrovic, Chandra A. Reynolds, Muralidharan Sargurupremraj, Markus Scholz, Jennifer A. Smith, Albert V. Smith, Natalie Terzikhan, Anbupalam Thalamuthu, Stella Trompet, Sven J. van der Lee, Erin B. Ware, B. Gwen Windham, Margaret J. Wright, Jingyun Yang, Jin Yu, David Ames, Najaf Amin, Philippe Amouyel, Ole A. Andreassen, Nicola J. Armstrong, Amelia A. Assareh, John R. Attia, Deborah Attix, Dimitrios Avramopoulos, David A. Bennett, Anne C. Böhmer, Patricia A. Boyle, Henry Brodaty, Harry Campbell, Tyrone D. Cannon, Elizabeth T. Cirulli, Eliza Congdon, Emily Drabant Conley, Janie Corley, Simon R. Cox, Anders M. Dale, Abbas Dehghan, Danielle Dick, Dwight Dickinson, Johan G. Eriksson, Evangelos Evangelou, Jessica D. Faul, Ian Ford, Nelson A. Freimer, He Gao, Ina Giegling, Nathan A. Gillespie, Scott D. Gordon, Rebecca F. Gottesman, Michael E. Griswold, Vilmundur Gudnason, Tamara B. Harris, Annette M. Hartmann, Alex Hatzimanolis, Gerardo Heiss, Elizabeth G. Holliday, Peter K. Joshi, Mika Kähönen, Sharon L. R. Kardia, Ida Karlsson, Luca Kleineidam, David S. Knopman, Nicole A. Kochan, Bettina Konte, John B. Kwok, Stephanie Le Hellard, Teresa Lee, Terho Lehtimäki, Shu-Chen Li, Christina M. Lill, Tian Liu, Marisa Koini, Edythe London, Will T. Longstreth, Oscar L. Lopez, Anu Loukola, Tobias Luck, Astri J. Lundervold, Anders Lundquist, Leo-Pekka Lyytikäinen, Nicholas G. Martin, Grant W. Montgomery, Alison D. Murray, Anna C. Need, Raymond Noordam, Lars Nyberg, William Ollier, Goran Papenberg, Alison Pattie, Ozren Polasek, Russell A. Poldrack, Bruce M. Psaty, Simone Reppermund, Steffi G. Riedel-Heller, Richard J. Rose, Jerome I. Rotter, Panos Roussos, Suvi P. Rovio, Yasaman Saba, Fred W. Sabb, Perminder S. Sachdev, Claudia L. Satizabal, Matthias Schmid, Rodney J. Scott, Matthew A. Scult, Jeannette Simino, P. Eline Slagboom, Nikolaos Smyrnis, Aïcha Soumaré, Nikos C. Stefanis, David J. Stott, Richard E. Straub, Kjetil Sundet, Adele M. Taylor, Kent D. Taylor, Ioanna Tzoulaki, Christophe Tzourio, André Uitterlinden, Veronique Vitart, Aristotle N. Voineskos, Jaakko Kaprio, Michael Wagner, Holger Wagner, Leonie Weinhold, K. Hoyan Wen, Elisabeth Widen, Qiong Yang, Wei Zhao, Hieab H. H. Adams, Dan E. Arking, Robert M. Bilder, Panos Bitsios, Eric Boerwinkle, Ornit Chiba-Falek, Aiden Corvin, Philip L. De Jager, Stéphanie Debette, Gary Donohoe, Paul Elliott, Annette L. Fitzpatrick, Michael Gill, David C. Glahn, Sara Hägg, Narelle K. Hansell, Ahmad R. Hariri, M. Kamran Ikram, J. Wouter Jukema, Eero Vuoksimaa, Matthew C. Keller, William S. Kremen, Lenore Launer, Ulman Lindenberger, Aarno Palotie, Nancy L. Pedersen, Neil Pendleton, David J. Porteous, Katri Räikkönen, Olli T. Raitakari, Alfredo Ramirez, Ivar Reinvang, Igor Rudan, Dan Rujescu, Reinhold Schmidt, Helena Schmidt, Peter W. Schofield, Peter R. Schofield, John M. Starr, Vidar M. Steen, Julian N. Trollor, Steven T. Turner, Cornelia M. Van Duijn, Arno Villringer, Daniel R. Weinberger, David R. Weir, James F. Wilson, Anil Malhotra, Andrew M. McIntosh, Catharine R. Gale, Sudha Seshadri, Thomas H. Mosley, Jan Bressler, Todd Lencz, and Ian J. Deary

Subjects
Science
Abstract

Cognitive function is associated with health and important life outcomes. Here, the authors perform a genome-wide association study for general cognitive function in 300,486 individuals and identify genetic loci that implicate neural and cell developmental pathways in this trait.

Published
2018
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7. Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets

Author

Max Lam, Joey W. Trampush, Jin Yu, Emma Knowles, Gail Davies, David C. Liewald, John M. Starr, Srdjan Djurovic, Ingrid Melle, Kjetil Sundet, Andrea Christoforou, Ivar Reinvang, Pamela DeRosse, Astri J. Lundervold, Vidar M. Steen, Thomas Espeseth, Katri Räikkönen, Elisabeth Widen, Aarno Palotie, Johan G. Eriksson, Ina Giegling, Bettina Konte, Panos Roussos, Stella Giakoumaki, Katherine E. Burdick, Antony Payton, William Ollier, Ornit Chiba-Falek, Deborah K. Attix, Anna C. Need, Elizabeth T. Cirulli, Aristotle N. Voineskos, Nikos C. Stefanis, Dimitrios Avramopoulos, Alex Hatzimanolis, Dan E. Arking, Nikolaos Smyrnis, Robert M. Bilder, Nelson A. Freimer, Tyrone D. Cannon, Edythe London, Russell A. Poldrack, Fred W. Sabb, Eliza Congdon, Emily Drabant Conley, Matthew A. Scult, Dwight Dickinson, Richard E. Straub, Gary Donohoe, Derek Morris, Aiden Corvin, Michael Gill, Ahmad R. Hariri, Daniel R. Weinberger, Neil Pendleton, Panos Bitsios, Dan Rujescu, Jari Lahti, Stephanie Le Hellard, Matthew C. Keller, Ole A. Andreassen, Ian J. Deary, David C. Glahn, Anil K. Malhotra, and Todd Lencz

Subjects
GWAS, general cognitive ability, nootropics, gene expression, neurodevelopment, synapse, calcium channel, potassium channel, cerebellum, Biology (General), QH301-705.5
Abstract

Here, we present a large (n = 107,207) genome-wide association study (GWAS) of general cognitive ability (“g”), further enhanced by combining results with a large-scale GWAS of educational attainment. We identified 70 independent genomic loci associated with general cognitive ability. Results showed significant enrichment for genes causing Mendelian disorders with an intellectual disability phenotype. Competitive pathway analysis implicated the biological processes of neurogenesis and synaptic regulation, as well as the gene targets of two pharmacologic agents: cinnarizine, a T-type calcium channel blocker, and LY97241, a potassium channel inhibitor. Transcriptome-wide and epigenome-wide analysis revealed that the implicated loci were enriched for genes expressed across all brain regions (most strongly in the cerebellum). Enrichment was exclusive to genes expressed in neurons but not oligodendrocytes or astrocytes. Finally, we report genetic correlations between cognitive ability and disparate phenotypes including psychiatric disorders, several autoimmune disorders, longevity, and maternal age at first birth.

Published
2017
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8. Publisher Correction: Variations in Dysbindin-1 are associated with cognitive response to antipsychotic drug treatment

Author

Diego Scheggia, Rosa Mastrogiacomo, Maddalena Mereu, Sara Sannino, Richard E. Straub, Marco Armando, Francesca Managò, Simone Guadagna, Fabrizio Piras, Fengyu Zhang, Joel E. Kleinman, Thomas M. Hyde, Sanne S. Kaalund, Maria Pontillo, Genny Orso, Carlo Caltagirone, Emiliana Borrelli, Maria A. De Luca, Stefano Vicari, Daniel R. Weinberger, Gianfranco Spalletta, and Francesco Papaleo

Subjects
Science
Abstract

In the original version of this Article, references in the Methods section incorrectly referred to references in the Supplementary References section. The relevant references (now numbered 20, 27, 42, 47, 69–80) have been removed from the Supplementary References section of the Supplementary Information file and added to the References section of the main manuscript, in both the PDF and HTML versions of the Article.

Published
2018
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9. Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability

Author

Taejeong, Bae, Liana, Fasching, Yifan, Wang, Joo Heon, Shin, Milovan, Suvakov, Yeongjun, Jang, Scott, Norton, Caroline, Dias, Jessica, Mariani, Alexandre, Jourdon, Feinan, Wu, Arijit, Panda, Reenal, Pattni, Yasmine, Chahine, Rebecca, Yeh, Rosalinda C, Roberts, Anita, Huttner, Joel E, Kleinman, Thomas M, Hyde, Richard E, Straub, Christopher A, Walsh, Alexander E, Urban, James F, Leckman, Daniel R, Weinberger, Flora M, Vaccarino, and Sirisha, Pochareddy

Subjects
Aging, Enhancer Elements, Genetic, Multidisciplinary, Gene Expression Regulation, Whole Genome Sequencing, Mutagenesis, Mutation, Brain, Humans, Autistic Disorder, Protein Binding, Transcription Factors
Abstract

We analyzed 131 human brains (44 neurotypical, 19 with Tourette syndrome, 9 with schizophrenia, and 59 with autism) for somatic mutations after whole genome sequencing to a depth of more than 200×. Typically, brains had 20 to 60 detectable single-nucleotide mutations, but ~6% of brains harbored hundreds of somatic mutations. Hypermutability was associated with age and damaging mutations in genes implicated in cancers and, in some brains, reflected in vivo clonal expansions. Somatic duplications, likely arising during development, were found in ~5% of normal and diseased brains, reflecting background mutagenesis. Brains with autism were associated with mutations creating putative transcription factor binding motifs in enhancer-like regions in the developing brain. The top-ranked affected motifs corresponded to MEIS (myeloid ectopic viral integration site) transcription factors, suggesting a potential link between their involvement in gene regulation and autism.

Published
2022

10. 302. Investigating the Impact of Common Genetic Risk Variants for Schizophrenia on Neuronal Function Elucidates Relationships Between Cellular Phenotypes, Clinical Status and Cognitive Performance

Author

Srinidhi Rao Sripathy, Stephanie Cerceo Page, Federica Farinelli, Zengyou Ye, Yanhong Wang, Debamitra Das, Gina Shim, Daniel J. Hiler, Elizabeth A. Pattie, Claudia V. Nguyen, Madhavi Tippani, Huei-Ying Chen, Matthew N. Tran, Nicholas J. Eagles, Joshua M. Stolz, Joseph L. Catallini, Olivia R. Soudry, Dwight Dickinson, Daniel R. Weinberger, Keri Martinowich, Matthew L. MacDonald, Joo Heon Shin, Andrew E. Jaffe, Richard E. Straub, and Brady J. Maher

Subjects
Biological Psychiatry
Published
2023

11. Sex-Dependent Shared and Nonshared Genetic Architecture Across Mood and Psychotic Disorders

Author

Gabriëlla A.M. Blokland, Jakob Grove, Chia-Yen Chen, Chris Cotsapas, Stuart Tobet, Robert Handa, David St Clair, Todd Lencz, Bryan J. Mowry, Sathish Periyasamy, Murray J. Cairns, Paul A. Tooney, Jing Qin Wu, Brian Kelly, George Kirov, Patrick F. Sullivan, Aiden Corvin, Brien P. Riley, Tõnu Esko, Lili Milani, Erik G. Jönsson, Aarno Palotie, Hannelore Ehrenreich, Martin Begemann, Agnes Steixner-Kumar, Pak C. Sham, Nakao Iwata, Daniel R. Weinberger, Pablo V. Gejman, Alan R. Sanders, Joseph D. Buxbaum, Dan Rujescu, Ina Giegling, Bettina Konte, Annette M. Hartmann, Elvira Bramon, Robin M. Murray, Michele T. Pato, Jimmy Lee, Ingrid Melle, Espen Molden, Roel A. Ophoff, Andrew McQuillin, Nicholas J. Bass, Rolf Adolfsson, Anil K. Malhotra, Nicholas G. Martin, Janice M. Fullerton, Philip B. Mitchell, Peter R. Schofield, Andreas J. Forstner, Franziska Degenhardt, Sabrina Schaupp, Ashley L. Comes, Manolis Kogevinas, José Guzman-Parra, Andreas Reif, Fabian Streit, Lea Sirignano, Sven Cichon, Maria Grigoroiu-Serbanescu, Joanna Hauser, Jolanta Lissowska, Fermin Mayoral, Bertram Müller-Myhsok, Beata Świątkowska, Thomas G. Schulze, Markus M. Nöthen, Marcella Rietschel, John Kelsoe, Marion Leboyer, Stéphane Jamain, Bruno Etain, Frank Bellivier, John B. Vincent, Martin Alda, Claire O’Donovan, Pablo Cervantes, Joanna M. Biernacka, Mark Frye, Susan L. McElroy, Laura J. Scott, Eli A. Stahl, Mikael Landén, Marian L. Hamshere, Olav B. Smeland, Srdjan Djurovic, Arne E. Vaaler, Ole A. Andreassen, Bernhard T. Baune, Tracy Air, Martin Preisig, Rudolf Uher, Douglas F. Levinson, Myrna M. Weissman, James B. Potash, Jianxin Shi, James A. Knowles, Roy H. Perlis, Susanne Lucae, Dorret I. Boomsma, Brenda W.J.H. Penninx, Jouke-Jan Hottenga, Eco J.C. de Geus, Gonneke Willemsen, Yuri Milaneschi, Henning Tiemeier, Hans J. Grabe, Alexander Teumer, Sandra Van der Auwera, Uwe Völker, Steven P. Hamilton, Patrik K.E. Magnusson, Alexander Viktorin, Divya Mehta, Niamh Mullins, Mark J. Adams, Gerome Breen, Andrew M. McIntosh, Cathryn M. Lewis, David M. Hougaard, Merete Nordentoft, Ole Mors, Preben B. Mortensen, Thomas Werge, Thomas D. Als, Anders D. Børglum, Tracey L. Petryshen, Jordan W. Smoller, Jill M. Goldstein, Stephan Ripke, Benjamin M. Neale, James T.R. Walters, Kai-How Farh, Peter A. Holmans, Phil Lee, Brendan Bulik-Sullivan, David A. Collier, Hailiang Huang, Tune H. Pers, Ingrid Agartz, Esben Agerbo, Margot Albus, Madeline Alexander, Farooq Amin, Silviu A. Bacanu, Richard A. Belliveau, Judit Bene, Sarah E. Bergen, Elizabeth Bevilacqua, Tim B. Bigdeli, Donald W. Black, Richard Bruggeman, Nancy G. Buccola, Randy L. Buckner, William Byerley, Wiepke Cahn, Guiqing Cai, Dominique Campion, Rita M. Cantor, Vaughan J. Carr, Noa Carrera, Stanley V. Catts, Kimberly D. Chambert, Raymond C.K. Chan, Ronald Y.L. Chen, Eric Y.H. Chen, Wei Cheng, Eric F.C. Cheung, Siow Ann Chong, C. Robert Cloninger, David Cohen, Nadine Cohen, Paul Cormican, Nick Craddock, James J. Crowley, David Curtis, Michael Davidson, Kenneth L. Davis, Jurgen Del Favero, Ditte Demontis, Dimitris Dikeos, Timothy Dinan, Gary Donohoe, Elodie Drapeau, Jubao Duan, Frank Dudbridge, Naser Durmishi, Peter Eichhammer, Johan Eriksson, Valentina Escott-Price, Laurent Essioux, Ayman H. Fanous, Martilias S. Farrell, Josef Frank, Lude Franke, Robert Freedman, Nelson B. Freimer, Marion Friedl, Joseph I. Friedman, Menachem Fromer, Giulio Genovese, Lyudmila Georgieva, Paola Giusti-Rodríguez, Stephanie Godard, Jacqueline I. Goldstein, Vera Golimbet, Srihari Gopal, Jacob Gratten, Lieuwe de Haan, Christian Hammer, Mark Hansen, Thomas Hansen, Vahram Haroutunian, Frans A. Henskens, Stefan Herms, Joel N. Hirschhorn, Per Hoffmann, Andrea Hofman, Mads V. Hollegaard, Masashi Ikeda, Inge Joa, Antonio Julià, René S. Kahn, Luba Kalaydjieva, Sena Karachanak-Yankova, Juha Karjalainen, David Kavanagh, Matthew C. Keller, James L. Kennedy, Andrey Khrunin, Yunjung Kim, Janis Klovins, Vaidutis Kucinskas, Zita Ausrele Kucinskiene, Hana Kuzelova-Ptackova, Anna K. Kähler, Claudine Laurent, Jimmy Lee Chee Keong, S. Hong Lee, Sophie E. Legge, Bernard Lerer, Miaoxin Li, Tao Li, Kung-Yee Liang, Jeffrey Lieberman, Svetlana Limborska, Carmel M. Loughland, Jan Lubinski, Jouko Lönnqvist, Milan Macek, Brion S. Maher, Wolfgang Maier, Jacques Mallet, Sara Marsal, Manuel Mattheisen, Morten Mattingsdal, Robert W. McCarley, Colm McDonald, Sandra Meier, Carin J. Meijer, Bela Melegh, Raquelle I. Mesholam-Gately, Andres Metspalu, Patricia T. Michie, Vihra Milanova, Younes Mokrab, Derek W. Morris, Kieran C. Murphy, Inez Myin-Germeys, Mari Nelis, Igor Nenadic, Deborah A. Nertney, Gerald Nestadt, Kristin K. Nicodemus, Liene Nikitina-Zake, Laura Nisenbaum, Annelie Nordin, Eadbhard O’Callaghan, Colm O’Dushlaine, F. Anthony O’Neill, Sang-Yun Oh, Ann Olincy, Line Olsen, Jim Van Os, Christos Pantelis, George N. Papadimitriou, Sergi Papiol, Elena Parkhomenko, 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, Ulrich Schall, Christian R. Schubert, Sibylle G. Schwab, Edward M. Scolnick, Rodney J. Scott, Larry J. Seidman, Engilbert Sigurdsson, Teimuraz Silagadze, Jeremy M. Silverman, Kang Sim, Petr Slominsky, Hon-Cheong So, Chris C.A. Spencer, 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 H.M. Wong, Brandon K. Wormley, Hualin Simon Xi, Clement C. Zai, Xuebin Zheng, Fritz Zimprich, Naomi R. Wray, Kari Stefansson, Peter M. Visscher, Douglas H.R. Blackwood, Ariel Darvasi, Enrico Domenici, Michael Gill, Hugh Gurling, Christina M. Hultman, Assen V. Jablensky, Kenneth S. Kendler, Jo Knight, Qingqin S. Li, Jianjun Liu, Steven A. McCarroll, Jennifer L. Moran, Michael J. Owen, Carlos N. Pato, Danielle Posthuma, Pamela Sklar, Jens R. Wendland, Mark J. Daly, Michael C. O’Donovan, Peter Donnelly, Ines Barroso, Jenefer M. Blackwell, Matthew A. Brown, Juan P. Casas, Panos Deloukas, Audrey Duncanson, Janusz Jankowski, Hugh S. Markus, Christopher G. Mathew, Colin N.A. Palmer, Robert Plomin, Anna Rautanen, Stephen J. Sawcer, Richard C. Trembath, Ananth C. Viswanathan, Nicholas W. Wood, Gavin Band, Céline Bellenguez, Colin Freeman, Eleni Giannoulatou, Garrett Hellenthal, Richard Pearson, Matti Pirinen, Amy Strange, Zhan Su, Damjan Vukcevic, Cordelia Langford, Hannah Blackburn, Suzannah J. Bumpstead, Serge Dronov, Sarah Edkins, Matthew Gillman, Emma Gray, Rhian Gwilliam, Naomi Hammond, Sarah E. Hunt, Alagurevathi Jayakumar, Jennifer Liddle, Owen T. McCann, Simon C. Potter, Radhi Ravindrarajah, Michelle Ricketts, Avazeh Tashakkori-Ghanbaria, Matthew Waller, Paul Weston, Pamela Whittaker, Sara Widaa, Mark I. McCarthy, Maria J. Arranz, Steven Bakker, Stephan Bender, Benedicto Crespo-Facorro, Jeremy Hall, Conrad Iyegbe, Stephen Lawrie, Kuang Lin, Don H. Linszen, Ignacio Mata, Muriel Walshe, Matthias Weisbrod, Durk Wiersma, Vassily Trubetskoy, Yunpeng Wang, Jonathan R.I. Coleman, Héléna A. Gaspar, Christiaan A. de Leeuw, Jennifer M. Whitehead Pavlides, Maciej Trzaskowski, Enda M. Byrne, Liam Abbott, Huda Akil, Diego Albani, Ney Alliey-Rodriguez, Adebayo Anjorin, Verneri Antilla, Swapnil Awasthi, Judith A. Badner, Marie Bækvad-Hansen, Jack D. Barchas, Nicholas Bass, Michael Bauer, Richard Belliveau, Carsten Bøcker Pedersen, Erlend Bøen, Marco P. Boks, James Boocock, Monika Budde, William Bunney, Margit Burmeister, Jonas Bybjerg-Grauholm, Miquel Casas, Felecia Cerrato, Kimberly Chambert, Alexander W. Charney, Danfeng Chen, Claire Churchhouse, Toni-Kim Clarke, William Coryell, David W. Craig, Cristiana Cruceanu, Piotr M. Czerski, Anders M. Dale, Simone de Jong, Jurgen Del-Favero, J. Raymond DePaulo, Amanda L. Dobbyn, Ashley Dumont, Torbjørn Elvsåshagen, Chun Chieh Fan, Sascha B. Fischer, Matthew Flickinger, Tatiana M. Foroud, Liz Forty, Christine Fraser, Katrin Gade, Diane Gage, Julie Garnham, Claudia Giambartolomei, Marianne Giørtz Pedersen, Jaqueline Goldstein, Scott D. Gordon, Katherine Gordon-Smith, Elaine K. Green, Melissa J. Green, Tiffany A. Greenwood, Weihua Guan, Martin Hautzinger, Urs Heilbronner, Maria Hipolito, Dominic Holland, Laura Huckins, Jessica S. Johnson, Radhika Kandaswamy, Robert Karlsson, Sarah Kittel-Schneider, Anna C. Koller, Ralph Kupka, Catharina Lavebratt, Jacob Lawrence, William B. Lawson, Markus Leber, Phil H. Lee, Shawn E. Levy, Jun Z. Li, Chunyu Liu, Anna Maaser, Donald J. MacIntyre, Pamela B. Mahon, Lina Martinsson, Steve McCarroll, Peter McGuffin, Melvin G. McInnis, James D. McKay, Helena Medeiros, Sarah E. Medland, Fan Meng, Grant W. Montgomery, Thomas W. Mühleisen, Hoang Nguyen, Caroline M. Nievergelt, Annelie Nordin Adolfsson, Evaristus A. Nwulia, Claire O'Donovan, Loes M. Olde Loohuis, Anil P.S. Ori, Lilijana Oruc, Urban Ösby, Amy Perry, Andrea Pfennig, Eline J. Regeer, Céline S. Reinbold, John P. Rice, Fabio Rivas, Margarita Rivera, Euijung Ryu, Cristina Sánchez-Mora, Alan F. Schatzberg, William A. Scheftner, Nicholas J. Schork, Cynthia Shannon Weickert, Tatyana Shehktman, Paul D. Shilling, Claire Slaney, Janet L. Sobell, Christine Søholm Hansen, Anne T. Spijker, Michael Steffens, John S. Strauss, Szabolcs Szelinger, Robert C. Thompson, Thorgeir E. Thorgeirsson, Jens Treutlein, Helmut Vedder, Weiqing Wang, Stanley J. Watson, Thomas W. Weickert, Simon Xi, Wei Xu, Allan H. Young, Peter Zandi, Peng Zhang, Sebastian Zöllner, Abdel Abdellaoui, Tracy M. Air, Till F.M. Andlauer, Silviu-Alin Bacanu, Aartjan T.F. Beekman, Elisabeth B. Binder, Julien Bryois, Henriette N. Buttenschøn, Na Cai, Enrique Castelao, Jane Hvarregaard Christensen, Lucía Colodro-Conde, Baptiste Couvy-Duchesne, Gregory E. Crawford, Gail Davies, Ian J. Deary, Eske M. Derks, Nese Direk, Conor V. Dolan, Erin C. Dunn, Thalia C. Eley, Farnush Farhadi Hassan Kiadeh, Hilary K. Finucane, Jerome C. Foo, Fernando S. Goes, Lynsey S. Hall, Thomas F. Hansen, Ian B. Hickie, Georg Homuth, Carsten Horn, David M. Howard, Marcus Ising, Rick Jansen, Ian Jones, Lisa A. Jones, Eric Jorgenson, Isaac S. Kohane, Julia Kraft, Warren W. Kretzschmar, Zoltán Kutalik, Yihan Li, Penelope A. Lind, Dean F. MacKinnon, Robert M. Maier, Jonathan Marchini, Hamdi Mbarek, Patrick McGrath, Christel M. Middeldorp, Evelin Mihailov, Francis M. Mondimore, Sara Mostafavi, Matthias Nauck, Bernard Ng, Michel G. Nivard, Dale R. Nyholt, Paul F. O'Reilly, Hogni Oskarsson, Jodie N. Painter, Roseann E. Peterson, Wouter J. Peyrot, Giorgio Pistis, Jorge A. Quiroz, Per Qvist, Saira Saeed Mirza, Robert Schoevers, Eva C. Schulte, Ling Shen, Stanley I. Shyn, Grant C.B. Sinnamon, Johannes H. Smit, Daniel J. Smith, Katherine E. Tansey, Henning Teismann, Wesley Thompson, Pippa A. Thomson, Matthew Traylor, André G. Uitterlinden, Daniel Umbricht, Albert M. van Hemert, Shantel Marie Weinsheimer, Jürgen Wellmann, Yang Wu, Hualin S. Xi, Jian Yang, Futao Zhang, Volker Arolt, Klaus Berger, Udo Dannlowski, Katharina Domschke, Caroline Hayward, Andrew C. Heath, Stefan Kloiber, Glyn Lewis, Pamela AF. Madden, Patrik K. Magnusson, Preben Bo Mortensen, Michael C. O'Donovan, Sara A. Paciga, Nancy L. Pedersen, David J. Porteous, Catherine Schaefer, Henry Völzke, Marco Bortolato, Janita Bralten, Cynthia M. Bulik, Christie L. Burton, Caitlin E. Carey, Lea K. Davis, Laramie E. Duncan, Howard J. Edenberg, Lauren Erdman, Stephen V. Faraone, Slavina B. Goleva, Wei Guo, Christopher Hübel, Laura M. Huckins, Ekaterina A. Khramtsova, Joanna Martin, Carol A. Mathews, Elise Robinson, Eli Stahl, Barbara E. Stranger, Michela Traglia, Raymond K. Walters, Lauren A. Weiss, Stacey J. Winham, Yin Yao, Kristjar Skajaa, Markus Nöthen, Michael Owen, Robert H. Yolken, Niels Plath, Jonathan Mill, Daniel Geschwind, Psychiatry 1, RS: MHeNs - R2 - Mental Health, Psychiatrie & Neuropsychologie, Centre of Excellence in Complex Disease Genetics, Research Programme of Molecular Medicine, Research Programs Unit, Aarno Palotie / Principal Investigator, Institute for Molecular Medicine Finland, Genomics of Neurological and Neuropsychiatric Disorders, Functional Genomics, Biological Psychology, APH - Mental Health, APH - Methodology, Sociology and Social Gerontology, APH - Personalized Medicine, APH - Health Behaviors & Chronic Diseases, Blokland, Gabriella AM, Grove, Jakob, Chen, Chia Yen, Cotsapas, Chris, Tobet, Stuart, Handa, Robert, Lee, Sang Hong, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Bipolar Disorder Working Group of the Psychiatric Genomics Consortium, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Sex Differences Cross-Disorder Analysis Group of the Psychiatric Genomics Consortium, iPSYCH, Psychiatry, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, Human genetics, Amsterdam Neuroscience - Compulsivity, Impulsivity & Attention, Amsterdam Reproduction & Development (AR&D), Child and Adolescent Psychiatry / Psychology, Adult Psychiatry, ANS - Complex Trait Genetics, and ANS - Mood, Anxiety, Psychosis, Stress & Sleep

Subjects
0301 basic medicine, Male, Bipolar Disorder, Schizophrenia/genetics, LD SCORE REGRESSION, Genome-wide association study, 0302 clinical medicine, Receptors, SCHIZOPHRENIA, Psychotic Disorders/genetics, KYNURENINE PATHWAY METABOLISM, Genetics, RISK, Sex Characteristics, Vascular Endothelial Growth Factor, Bipolar Disorder/genetics, Major/genetics, Single Nucleotide, AFFECTIVE STIMULI IMPACT, Schizophrenia, Sulfurtransferases, Major depressive disorder, Female, Depressive Disorder, Major/genetics, Bipolar disorder, Locus (genetics), Genomics, Biology, Polymorphism, Single Nucleotide, Article, DYSPHORIC MOOD, 03 medical and health sciences, Sex differences, medicine, Humans, Genetic Predisposition to Disease, ddc:610, Polymorphism, GENOME-WIDE ASSOCIATION, Genotype-by-sex interaction, Biological Psychiatry, Depressive Disorder, Major, Depressive Disorder, GENDER-DIFFERENCES, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], PARAVENTRICULAR NUCLEUS, 3112 Neurosciences, Endothelial Cells, MAJOR DEPRESSION, medicine.disease, Genetic architecture, 030104 developmental biology, Mood, Receptors, Vascular Endothelial Growth Factor, Psychotic Disorders, 3111 Biomedicine, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

Contains fulltext : 248656.pdf (Publisher’s version ) (Closed access) BACKGROUND: Sex differences in incidence and/or presentation of schizophrenia (SCZ), major depressive disorder (MDD), and bipolar disorder (BIP) are pervasive. Previous evidence for shared genetic risk and sex differences in brain abnormalities across disorders suggest possible shared sex-dependent genetic risk. METHODS: We conducted the largest to date genome-wide genotype-by-sex (G×S) interaction of risk for these disorders using 85,735 cases (33,403 SCZ, 19,924 BIP, and 32,408 MDD) and 109,946 controls from the PGC (Psychiatric Genomics Consortium) and iPSYCH. RESULTS: Across disorders, genome-wide significant single nucleotide polymorphism-by-sex interaction was detected for a locus encompassing NKAIN2 (rs117780815, p = 3.2 × 10(-8)), which interacts with sodium/potassium-transporting ATPase (adenosine triphosphatase) enzymes, implicating neuronal excitability. Three additional loci showed evidence (p < 1 × 10(-6)) for cross-disorder G×S interaction (rs7302529, p = 1.6 × 10(-7); rs73033497, p = 8.8 × 10(-7); rs7914279, p = 6.4 × 10(-7)), implicating various functions. Gene-based analyses identified G×S interaction across disorders (p = 8.97 × 10(-7)) with transcriptional inhibitor SLTM. Most significant in SCZ was a MOCOS gene locus (rs11665282, p = 1.5 × 10(-7)), implicating vascular endothelial cells. Secondary analysis of the PGC-SCZ dataset detected an interaction (rs13265509, p = 1.1 × 10(-7)) in a locus containing IDO2, a kynurenine pathway enzyme with immunoregulatory functions implicated in SCZ, BIP, and MDD. Pathway enrichment analysis detected significant G×S interaction of genes regulating vascular endothelial growth factor receptor signaling in MDD (false discovery rate-corrected p < .05). CONCLUSIONS: In the largest genome-wide G×S analysis of mood and psychotic disorders to date, there was substantial genetic overlap between the sexes. However, significant sex-dependent effects were enriched for genes related to neuronal development and immune and vascular functions across and within SCZ, BIP, and MDD at the variant, gene, and pathway levels.

Published
2022

12. Dysregulated protocadherin-pathway activity as an intrinsic defect in induced pluripotent stem cell–derived cortical interneurons from subjects with schizophrenia

Author

Roy H. Perlis, Hualin Simon Xi, Leonard M. Eisenberg, Sangmi Chung, Alexander A. Moghadam, Donna L. McPhie, Bruce M. Cohen, Weihua Huang, Woong Bin Kim, Patric K. Stanton, Changhong Yin, Sarah E. Cote, Teruyoshi Hirayama, Joyce Zhao, Judith L. Rapoport, Emi Fukuda, Takeshi Yagi, Kevin Eggan, Elizabeth Noyes, Sulagna Ghosh, Dost Öngür, James M. Park, Daniel R. Weinberger, Teagan Parsons, Kelvin Zheng, Joshua J. Park, Thomas A. Lanz, Karen F. Berman, Jun-Hyeong Cho, Christine T. O. Nguyen, Haneul Noh, Hae Young Kim, Joseph T. Coyle, Jose A. Apud, Peiyan Ni, Richard E. Straub, and Zhicheng Shao

Subjects
0301 basic medicine, animal structures, Kinase, General Neuroscience, virus diseases, Protocadherin, Biology, medicine.disease, female genital diseases and pregnancy complications, Pathogenesis, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, nervous system, Schizophrenia, Excitatory postsynaptic potential, medicine, Protein kinase A, Induced pluripotent stem cell, Prefrontal cortex, neoplasms, Neuroscience, 030217 neurology & neurosurgery
Abstract

We generated cortical interneurons (cINs) from induced pluripotent stem cells derived from 14 healthy controls and 14 subjects with schizophrenia. Both healthy control cINs and schizophrenia cINs were authentic, fired spontaneously, received functional excitatory inputs from host neurons, and induced GABA-mediated inhibition in host neurons in vivo. However, schizophrenia cINs had dysregulated expression of protocadherin genes, which lie within documented schizophrenia loci. Mice lacking protocadherin-α showed defective arborization and synaptic density of prefrontal cortex cINs and behavioral abnormalities. Schizophrenia cINs similarly showed defects in synaptic density and arborization that were reversed by inhibitors of protein kinase C, a downstream kinase in the protocadherin pathway. These findings reveal an intrinsic abnormality in schizophrenia cINs in the absence of any circuit-driven pathology. They also demonstrate the utility of homogenous and functional populations of a relevant neuronal subtype for probing pathogenesis mechanisms during development.

Published
2019

13. Schizophrenia risk variants influence multiple classes of transcripts of sorting nexin 19 (SNX19)

Author

Alan J. Cross, Stephen A. Semick, Andrew E. Jaffe, Daniel R. Weinberger, Thomas M. Hyde, Ran Tao, Liang Ma, Joel E. Kleinman, Qiang Chen, Richard E. Straub, Amanda J. Price, Nicholas J. Brandon, Yankai Jia, Chao Li, and Joo Heon Shin

Subjects
0301 basic medicine, Genetics, Locus (genetics), Genome-wide association study, Biology, 03 medical and health sciences, Cellular and Molecular Neuroscience, Psychiatry and Mental health, Exon, 030104 developmental biology, 0302 clinical medicine, Expression quantitative trait loci, DNA methylation, Epigenetics, Allele, Molecular Biology, Gene, 030217 neurology & neurosurgery
Abstract

Genome-wide association studies (GWAS) have identified many genomic loci associated with risk for schizophrenia, but unambiguous identification of the relationship between disease-associated variants and specific genes, and in particular their effect on risk conferring transcripts, has proven difficult. To better understand the specific molecular mechanism(s) at the schizophrenia locus in 11q25, we undertook cis expression quantitative trait loci (cis-eQTL) mapping for this 2 megabase genomic region using postmortem human brain samples. To comprehensively assess the effects of genetic risk upon local expression, we evaluated multiple transcript features: genes, exons, and exon-exon junctions in multiple brain regions-dorsolateral prefrontal cortex (DLPFC), hippocampus, and caudate. Genetic risk variants strongly associated with expression of SNX19 transcript features that tag multiple rare classes of SNX19 transcripts, whereas they only weakly affected expression of an exon-exon junction that tags the majority of abundant transcripts. The most prominent class of SNX19 risk-associated transcripts is predicted to be overexpressed, defined by an exon-exon splice junction between exons 8 and 10 (junc8.10) and that is predicted to encode proteins that lack the characteristic nexin C terminal domain. Risk alleles were also associated with either increased or decreased expression of multiple additional classes of transcripts. With RACE, molecular cloning, and long read sequencing, we found a number of novel SNX19 transcripts that further define the set of potential etiological transcripts. We explored epigenetic regulation of SNX19 expression and found that DNA methylation at CpG sites near the primary transcription start site and within exon 2 partially mediate the effects of risk variants on risk-associated expression. ATAC sequencing revealed that some of the most strongly risk-associated SNPs are located within a region of open chromatin, suggesting a nearby regulatory element is involved. These findings indicate a potentially complex molecular etiology, in which risk alleles for schizophrenia generate epigenetic alterations and dysregulation of multiple classes of SNX19 transcripts.

Published
2019

14. Polygenic risk score increases schizophrenia liability through cognition-relevant pathways

Author

Stacey S. Cherny, Pak C. Sham, Richard E. Straub, Karen F. Berman, Daniel R. Weinberger, Xiaowei Zhang, Timothea Toulopoulou, Dwight Dickinson, and Toulopoulou, Timothea

Subjects
0301 basic medicine, Endophenotypes, Schizophrenia (object-oriented programming), Cognition, Original Articles, Causality, Confidence interval, Polygenic risk scores, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Endophenotype, Genetic variation, Schizophrenia, medicine, Humans, Intermediate phenotypes, Neurology (clinical), medicine.symptom, Psychology, 030217 neurology & neurosurgery, Cognitive deficit, Clinical psychology, Causal model
Abstract

Cognitive deficit is thought to represent, at least in part, genetic mechanisms of risk for schizophrenia, with recent evidence from statistical modelling of twin data suggesting direct causality from the former to the latter. However, earlier evidence was based on inferences from twin not molecular genetic data and it is unclear how much genetic influence ‘passes through’ cognition on the way to diagnosis. Thus, we included direct measurements of genetic risk (e.g. schizophrenia polygenic risk scores) in causation models to assess the extent to which cognitive deficit mediates some of the effect of polygenic risk scores on the disorder. Causal models of family data tested relationships among key variables and allowed parsing of genetic variance components. Polygenic risk scores were calculated from summary statistics from the current largest genome-wide association study of schizophrenia and were represented as a latent trait. Cognition was also modelled as a latent trait. Participants were 1313 members of 1078 families: 416 patients with schizophrenia, 290 unaffected siblings, and 607 controls. Modelling supported earlier findings that cognitive deficit has a putatively causal role in schizophrenia. In total, polygenic risk score explained 8.07% [confidence interval (CI) 5.45–10.74%] of schizophrenia risk in our sample. Of this, more than a third (2.71%, CI 2.41–3.85%) of the polygenic risk score influence was mediated through cognition paths, exceeding the direct influence of polygenic risk score on schizophrenia risk (1.43%, CI 0.46–3.08%). The remainder of the polygenic risk score influence (3.93%, CI 2.37–4.48%) reflected reciprocal causation between schizophrenia liability and cognition (e.g. mutual influences in a cyclical manner). Analysis of genetic variance components of schizophrenia liability indicated that 26.87% (CI 21.45–32.57%) was associated with cognition-related pathways not captured by polygenic risk score. The remaining variance in schizophrenia was through pathways other than cognition-related and polygenic risk score. Although our results are based on inference through statistical modelling and do not provide an absolute proof of causality, we find that cognition pathways mediate a significant part of the influence of cumulative genetic risk on schizophrenia. We estimate from our model that 33.51% (CI 27.34–43.82%) of overall genetic risk is mediated through influences on cognition, but this requires further studies and analyses as the genetics of schizophrenia becomes better characterized.

Published
2018

15. TH71. ELECTROPHYSIOLOGICAL MEASURES FROM HUMAN IPSC-DERIVED NEURONS ARE ASSOCIATED WITH SCHIZOPHRENIA CLINICAL STATUS AND PREDICT INDIVIDUAL COGNITIVE PERFORMANCE

Author

Brady J. Maher, Andrew E. Jaffe, Nicholas J. Eagles, Stephanie Cerceo Page, Madhavi Tippani, R.L. Moses, Sripathy, Farinelli F, Daniel J Hiler, Yangang Wang, Keri Martinowich, Tran Mn, Dwight Dickinson, Ye Z, Jose A. Apud, Chen H, Elizabeth A. Pattie, Richard E. Straub, Joshua M. Stolz, Soudry Or, Joseph L. Catallini, Nguyen Cv, D.R. Weinberger, and Karen F. Berman

Subjects
Pharmacology, business.industry, Schizophrenia (object-oriented programming), Psychiatry and Mental health, Electrophysiology, Text mining, Neurology, Pharmacology (medical), Neurology (clinical), Effects of sleep deprivation on cognitive performance, Psychology, business, Neuroscience, Biological Psychiatry
Published
2021

16. A Comparison of Ten Polygenic Score Methods for Psychiatric Disorders Applied Across Multiple Cohorts

Author

Guiyan Ni, Jian Zeng, Joana A. Revez, Ying Wang, Zhili Zheng, Tian Ge, Restuadi Restuadi, Jacqueline Kiewa, Dale R. Nyholt, Jonathan R.I. Coleman, Jordan W. Smoller, Jian Yang, Peter M. Visscher, Naomi R. Wray, Stephan Ripke, Benjamin M. Neale, Aiden Corvin, James T.R. Walters, Kai-How Farh, Peter A. Holmans, Phil Lee, Brendan Bulik-Sullivan, David A. Collier, Hailiang Huang, Tune H. Pers, Ingrid Agartz, Esben Agerbo, Margot Albus, Madeline Alexander, Farooq Amin, Silviu A. Bacanu, Martin Begemann, Richard A. Belliveau, Judit Bene, Sarah E. Bergen, Elizabeth Bevilacqua, Tim B. Bigdeli, Donald W. Black, Richard Bruggeman, Nancy G. Buccola, Randy L. Buckner, William Byerley, Wiepke Cahn, Guiqing Cai, Dominique Campion, Rita M. Cantor, Vaughan J. Carr, Noa Carrera, Stanley V. Catts, Kimberley D. Chambert, Raymond C.K. Chan, Ronald Y.L. Chen, Eric Y.H. Chen, Wei Cheng, Eric F.C. Cheung, Siow Ann Chong, C. Robert Cloninger, David Cohen, Nadine Cohen, Paul Cormican, Nick Craddock, James J. Crowley, Michael Davidson, Kenneth L. Davis, Franziska Degenhardt, Jurgen Del Favero, Ditte Demontis, Dimitris Dikeos, Timothy Dinan, Srdjan Djurovic, Gary Donohoe, Elodie Drapeau, Jubao Duan, Frank Dudbridge, Naser Durmishi, Peter Eichhammer, Johan Eriksson, Valentina Escott-Price, Laurent Essioux, Ayman H. Fanous, Martilias S. Farrell, Josef Frank, Lude Franke, Robert Freedman, Nelson B. Freimer, Marion Friedl, Joseph I. Friedman, Menachem Fromer, Giulio Genovese, Lyudmila Georgieva, Ina Giegling, Paola Giusti-Rodríguez, Stephanie Godard, Jacqueline I. Goldstein, Vera Golimbet, Srihari Gopal, Jacob Gratten, Lieuwe de Haan, Christian Hammer, 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, Masashi Ikeda, Inge Joa, Antonio Julià, René S. Kahn, Luba Kalaydjieva, Sena Karachanak-Yankova, Juha Karjalainen, David Kavanagh, Matthew C. Keller, James L. Kennedy, Andrey Khrunin, Yunjung Kim, Janis Klovins, James A. Knowles, Bettina Konte, Vaidutis Kucinskas, Zita Ausrele Kucinskiene, Hana Kuzelova-Ptackova, Anna K. Kähler, Claudine Laurent, Jimmy Lee, S. Hong Lee, Sophie E. Legge, Bernard Lerer, Miaoxin Li, Tao Li, Kung-Yee Liang, Jeffrey Lieberman, Svetlana Limborska, Carmel M. Loughland, Jan Lubinski, Jouko Lönnqvist, Milan Macek, Patrik K.E. Magnusson, Brion S. Maher, Wolfgang Maier, Jacques Mallet, Sara Marsal, Manuel Mattheisen, Morten Mattingsdal, Robert W. McCarley, Colm McDonald, Andrew M. McIntosh, Sandra Meier, Carin J. Meijer, Bela Melegh, Ingrid Melle, Raquelle I. Mesholam-Gately, Andres Metspalu, Patricia T. Michie, Lili Milani, Vihra Milanova, Younes Mokrab, Derek W. Morris, Ole Mors, Kieran C. Murphy, Robin M. Murray, Inez Myin-Germeys, Bertram Müller-Myhsok, Mari Nelis, Igor Nenadic, Deborah A. Nertney, Gerald Nestadt, Kristin K. Nicodemus, Liene Nikitina-Zake, Laura Nisenbaum, Annelie Nordin, Eadbhard O’Callaghan, Colm O’Dushlaine, F. Anthony O’Neill, Sang-Yun Oh, Ann Olincy, Line Olsen, Jim Van Os, Psychosis Endophenotypes International Consortium, 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, Hon-Cheong So, Chris C.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 H.M. Wong, Brandon K. Wormley, Hualin Simon Xi, Clement C. Zai, Xuebin Zheng, Fritz Zimprich, Kari Stefansson, Wellcome Trust Case-Control Consortium, Rolf Adolfsson, Ole A. Andreassen, Douglas H.R. 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, Maciej Trzaskowski, Enda M. Byrne, Abdel Abdellaoui, Mark J. Adams, Tracy M. Air, Till F.M. Andlauer, Silviu-Alin Bacanu, Marie Bækvad-Hansen, Aartjan T.F. Beekman, Elisabeth B. Binder, Julien Bryois, Henriette N. Buttenschøn, Jonas Bybjerg-Grauholm, Na Cai, Enrique Castelao, Jane Hvarregaard Christensen, Toni-Kim Clarke, Lucía Colodro-Conde, Baptiste Couvy-Duchesne, Gregory E. Crawford, Gail Davies, Ian J. Deary, Eske M. Derks, Nese Direk, Conor V. Dolan, Erin C. Dunn, Thalia C. Eley, Farnush Farhadi Hassan Kiadeh, Hilary K. Finucane, Jerome C. Foo, Andreas J. Forstner, Héléna A. Gaspar, Fernando S. Goes, Scott D. Gordon, Jakob Grove, Lynsey S. Hall, Christine Søholm Hansen, Thomas F. Hansen, Ian B. Hickie, Georg Homuth, Carsten Horn, Jouke-Jan Hottenga, David M. Howard, Marcus Ising, Rick Jansen, Ian Jones, Lisa A. Jones, Eric Jorgenson, Isaac S. Kohane, Julia Kraft, Warren W. Kretzschmar, Zoltán Kutalik, Yihan Li, Penelope A. Lind, Donald J. MacIntyre, Dean F. MacKinnon, Robert M. Maier, Jonathan Marchini, Hamdi Mbarek, Patrick McGrath, Peter McGuffin, Sarah E. Medland, Divya Mehta, Christel M. Middeldorp, Evelin Mihailov, Yuri Milaneschi, Francis M. Mondimore, Grant W. Montgomery, Sara Mostafavi, Niamh Mullins, Matthias Nauck, Bernard Ng, Michel G. Nivard, Paul F. O’Reilly, Hogni Oskarsson, Jodie N. Painter, Carsten Bøcker Pedersen, Marianne Giørtz Pedersen, Roseann E. Peterson, Wouter J. Peyrot, Giorgio Pistis, Jorge A. Quiroz, Per Qvist, John P. Rice, Margarita Rivera, Saira Saeed Mirza, Robert Schoevers, Eva C. Schulte, Ling Shen, Stanley I. Shyn, Grant C.B. Sinnamon, Johannes H. Smit, Daniel J. Smith, Fabian Streit, Katherine E. Tansey, Henning Teismann, Alexander Teumer, Wesley Thompson, Pippa A. Thomson, Thorgeir E. Thorgeirsson, Matthew Traylor, Jens Treutlein, Vassily Trubetskoy, André G. Uitterlinden, Daniel Umbricht, Sandra Van der Auwera, Albert M. van Hemert, Alexander Viktorin, Yunpeng Wang, Shantel Marie Weinsheimer, Jürgen Wellmann, Gonneke Willemsen, Yang Wu, Hualin S. Xi, Futao Zhang, Volker Arolt, Bernhard T. Baune, Klaus Berger, Dorret I. Boomsma, Udo Dannlowski, E.J.C. de Geus, J. Raymond DePaulo, Katharina Domschke, Hans J. Grabe, Steven P. Hamilton, Caroline Hayward, Andrew C. Heath, Stefan Kloiber, Glyn Lewis, Susanne Lucae, Pamela A.F. Madden, Patrik K. Magnusson, Nicholas G. Martin, Preben Bo Mortensen, Merete Nordentoft, Sara A. Paciga, Nancy L. Pedersen, Adult Psychiatry, APH - Mental Health, ANS - Complex Trait Genetics, ANS - Mood, Anxiety, Psychosis, Stress & Sleep, Ni, Guiyan, Zeng, Jian, Revez, Joana A., Wang, Ying, Zhili, Zheng, Ge, Tian, Restuadi, Restuadi, Kiewa, Jacqueline, Nyholt, Dale R, Coleman, Jonathan RI, Smoller, Jordan W, Lee, S Hong, APH - Methodology, Biological Psychology, APH - Personalized Medicine, APH - Health Behaviors & Chronic Diseases, Econometrics, Psychiatry, Department of Technology and Operations Management, Child and Adolescent Psychiatry / Psychology, Epidemiology, Erasmus MC other, Urology, Internal Medicine, Medical Informatics, Immunology, Human genetics, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Neuroscience - Compulsivity, Impulsivity & Attention, Amsterdam Reproduction & Development (AR&D), and Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep

Subjects
0301 basic medicine, Multifactorial Inheritance, medicine.medical_specialty, LDpred2, BF, Genomics, Disease, Major depressive disorder, risk prediction, 03 medical and health sciences, 0302 clinical medicine, MegaPRS, SDG 3 - Good Health and Well-being, medicine, Humans, Genetic Predisposition to Disease, ddc:610, Genetic risk, Psychiatry, Biological Psychiatry, Genetic association, Depressive Disorder, Major, business.industry, Mental Disorders, medicine.disease, Genetic architecture, Polygenic scores, Risk prediction, polygenic scores, PRS-CS, psychiatric disorders, 030104 developmental biology, SBayesR, Schizophrenia, Cohort, Lassosum, RC0321, business, Psychiatric disorders, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

BACKGROUND: Polygenic scores (PGSs), which assess the genetic risk of individuals for a disease, are calculated as a weighted count of risk alleles identified in genome-wide association studies. PGS methods differ in which DNA variants are included and the weights assigned to them; some require an independent tuning sample to help inform these choices. PGSs are evaluated in independent target cohorts with known disease status. Variability between target cohorts is observed in applications to real data sets, which could reflect a number of factors, e.g., phenotype definition or technical factors.METHODS: The Psychiatric Genomics Consortium Working Groups for schizophrenia and major depressive disorder bring together many independently collected case-control cohorts. We used these resources (31,328 schizophrenia cases, 41,191 controls; 248,750 major depressive disorder cases, 563,184 controls) in repeated application of leave-one-cohort-out meta-analyses, each used to calculate and evaluate PGS in the left-out (target) cohort. Ten PGS methods (the baseline PC+T method and 9 methods that model genetic architecture more formally: SBLUP, LDpred2-Inf, LDpred-funct, LDpred2, Lassosum, PRS-CS, PRS-CS-auto, SBayesR, MegaPRS) were compared.RESULTS: Compared with PC+T, the other 9 methods gave higher prediction statistics, MegaPRS, LDPred2, and SBayesR significantly so, explaining up to 9.2% variance in liability for schizophrenia across 30 target cohorts, an increase of 44%. For major depressive disorder across 26 target cohorts, these statistics were 3.5% and 59%, respectively.CONCLUSIONS: Although the methods that more formally model genetic architecture have similar performance, MegaPRS, LDpred2, and SBayesR rank highest in most comparisons and are recommended in applications to psychiatric disorders.

Published
2021

17. Comprehensive identification of somatic nucleotide variants in human brain tissue

Author

Schahram Akbarian, Jonathan Pevsner, Joseph G. Gleeson, Reenal Pattni, Matthew T. Oetjens, Ryan E. Mills, Kenneth Daily, Alexander E. Urban, Yifan Wang, Irene Lobon, David Juan, John V. Moran, Taejeong Bae, Shobana Sekar, Christopher A. Walsh, Sara Bizzotto, Mette A. Peters, Yeongjun Jang, Attila G. Jones, Maxwell A. Sherman, Sean Cho, Liana Fasching, Rujuta Narurkar, Chaggai Rosenbluh, Yanmei Dou, Andrew Chess, Alon Galor, Jeremy Thorpe, Esther Lizano, Tomas Marques-Bonet, John B. Moldovan, Livia Tomasini, Laurel L. Ball, Javier Ganz, Weichen Zhou, Daniel R. Weinberger, Richard E. Straub, Ryan N. Doan, Xiaoxu Yang, Flora M. Vaccarino, Jeffrey M. Kidd, S. Emery, Alexej Abyzov, Bo Zhou, Simone Tomasi, Joo Heon Shin, Peter J. Park, and Eduardo Soriano

Subjects
Whole genome sequencing, chemistry.chemical_compound, Lineage (genetic), chemistry, DNA repair, Somatic cell, DNA replication, Identification (biology), Human genome, Computational biology, Biology, DNA
Abstract

Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells. Here, the Brain Somatic Mosaicism Network conducted a coordinated, multi-institutional study to: (i) examine the ability of existing methods to detect simulated somatic single nucleotide variants (SNVs) in DNA mixing experiments; (ii) generate multiple replicates of whole genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual; (iii) devise strategies to discover somatic SNVs; and (iv) apply various approaches to validate somatic SNVs. These efforts led to the identification of 43 bona fide somatic SNVs that ranged in variant allele fractions from ~0.005 to ~0.28. Guided by these results, we devised best practices for calling mosaic SNVs from 250X whole genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrated that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees. Thus, this study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.

Published
2020

18. Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence

Author

Dan Rujescu, Vidar M. Steen, Eva Krapohl, Aarno Palotie, Elisabeth Widen, Ingrid Melle, Patrick Sullivan, Katrina L. Grasby, Stephan Ripke, Anke R. Hammerschlag, Christiaan de Leeuw, Panos Bitsios, Nikos C. Stefanis, Tonya White, Gail Davies, Ahmad R. Hariri, Philip R. Jansen, Peter B. Barr, John M. Starr, Max Lam, Ian J. Deary, Sara Hägg, Dimitrios Avramopoulos, Bettina Konte, Anil K. Malhotra, Delilah Zabaneh, Kjetil Sundet, Tinca J. C. Polderman, Ornit Chiba-Falek, Jakob Kaminski, Danielle M. Dick, Andrea Christoforou, Jin Yu, Gunter Schumann, Matthew A. Scult, Anna C. Need, Jens Hjerling-Leffler, Gonçalo R. Abecasis, Kenneth S. Kendler, Todd Lencz, Dwight Dickinson, Bradley T. Webb, Elizabeth T. Cirulli, Stephanie Le Hellard, Gerome Breen, Astri J. Lundervold, Hannah Young, Erin Burke Quinlan, William Ollier, Nikolaos Smyrnis, Emily Drabant Conley, Danielle Posthuma, Sten Linnarsson, Aristotle N. Voineskos, Edythe D. London, Pamela DeRosse, Russell A. Poldrack, Jonathan R. I. Coleman, Jeanne E. Savage, Sarah E. Medland, Ana B. Muñoz-Manchado, Richard E. Straub, Robert Plomin, Ida K. Karlsson, Nathan G. Skene, Dan E. Arking, Birgit Debrabant, Joey W. Trampush, Matthew C. Keller, Mats Nagel, Gary Donohoe, Chandra A. Reynolds, Panos Roussos, Lene Christiansen, Ivar Reinvang, Ole A. Andreassen, Antony Payton, Robert Karlsson, Margaret J. Wright, Deborah C. Koltai, Jari Lahti, Andreas Heinz, Tyrone D. Cannon, Eliza Congdon, Olav B. Smeland, Stella G. Giakoumaki, Marianne Nygaard, Julien Bryois, M. Arfan Ikram, Nancy L. Pedersen, Katri Räikkönen, Daniel R. Weinberger, Neil Pendleton, Swapnil Awasthi, Sven Stringer, Nelson A. Freimer, Aiden Corvin, Kyoko Watanabe, David C. Glahn, Henning Tiemeier, Grant W. Montgomery, Narelle K. Hansell, Robert M. Bilder, Katherine E. Burdick, Srdjan Djurovic, David C. Liewald, Sophie van der Sluis, Thomas Espeseth, Scott I. Vrieze, Fred W. Sabb, Nicholas G. Martin, Michael Gill, Emma Knowles, Derek W. Morris, Alex Hatzimanolis, Ina Giegling, Johan G. Eriksson, Child and Adolescent Psychiatry / Psychology, Epidemiology, Complex Trait Genetics, Amsterdam Neuroscience - Complex Trait Genetics, Biological Psychology, Functional Genomics, Research Programs Unit, Diabetes and Obesity Research Program, Department of General Practice and Primary Health Care, Johan Eriksson / Principal Investigator, Clinicum, University of Helsinki, Medicum, Helsinki Collegium for Advanced Studies, Department of Psychology and Logopedics, Centre of Excellence in Complex Disease Genetics, Aarno Palotie / Principal Investigator, Institute for Molecular Medicine Finland, Elisabeth Ingrid Maria Widen / Principal Investigator, Developmental Psychology Research Group, Genomics of Neurological and Neuropsychiatric Disorders, Genomic Discoveries and Clinical Translation, Human genetics, Amsterdam Neuroscience - Cellular & Molecular Mechanisms, VU University medical center, Amsterdam Neuroscience - Compulsivity, Impulsivity & Attention, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, and Amsterdam Reproduction & Development (AR&D)

Subjects
0301 basic medicine, Nonsynonymous substitution, Male, GENERAL COGNITIVE FUNCTION, Intelligence, LOCI, Genome-wide association study, ANNOTATION, 0302 clinical medicine, GWAS, 11 Medical and Health Sciences, Genetics & Heredity, RISK, HERITABILITY, Brain, Mendelian Randomization Analysis, Middle Aged, 3. Good health, Schizophrenia, Genome-Wide Association Study/methods, Female, Life Sciences & Biomedicine, TRAITS, Adolescent, Quantitative Trait Loci, Computational biology, Biology, Quantitative trait locus, Brain/physiology, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Genetics, medicine, Humans, Genetic Predisposition to Disease, Gene, Genetic association, EDUCATIONAL-ATTAINMENT, Science & Technology, TEST BATTERIES, CONSORTIUM, Intelligence/genetics, 06 Biological Sciences, medicine.disease, 030104 developmental biology, Expression quantitative trait loci, 3111 Biomedicine, 030217 neurology & neurosurgery, Developmental Biology, Genome-Wide Association Study
Abstract

Intelligence is highly heritable 1 and a major determinant of human health and well-being 2 . Recent genome-wide meta-analyses have identified 24 genomic loci linked to variation in intelligence 3-7 , but much about its genetic underpinnings remains to be discovered. Here, we present a large-scale genetic association study of intelligence (n = 269,867), identifying 205 associated genomic loci (190 new) and 1,016 genes (939 new) via positional mapping, expression quantitative trait locus (eQTL) mapping, chromatin interaction mapping, and gene-based association analysis. We find enrichment of genetic effects in conserved and coding regions and associations with 146 nonsynonymous exonic variants. Associated genes are strongly expressed in the brain, specifically in striatal medium spiny neurons and hippocampal pyramidal neurons. Gene set analyses implicate pathways related to nervous system development and synaptic structure. We confirm previous strong genetic correlations with multiple health-related outcomes, and Mendelian randomization analysis results suggest protective effects of intelligence for Alzheimer's disease and ADHD and bidirectional causation with pleiotropic effects for schizophrenia. These results are a major step forward in understanding the neurobiology of cognitive function as well as genetically related neurological and psychiatric disorders.

Published
2018

19. Schizophrenia polygenic risk score predicts mnemonic hippocampal activity

Author

Ena Xiao, Annchen R. Knodt, Giuseppe Blasi, Daniel R. Weinberger, Karen F. Berman, Gianluca Ursini, Karleigh Mezeivtch, Richard E. Straub, Joseph H. Callicott, Venkata S. Mattay, Ahmad R. Hariri, Qiang Chen, Adrienne L. Romer, Alessandro Bertolino, and Giulio Pergola

Subjects
Adult, Male, 0301 basic medicine, Oncology, Multifactorial Inheritance, medicine.medical_specialty, Genotype, Intelligence, Neurogenetics, Hippocampal formation, Hippocampus, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, Image Processing, Computer-Assisted, medicine, Humans, Genetic Predisposition to Disease, Imputation (statistics), Allele, Association (psychology), business.industry, Original Articles, Odds ratio, medicine.disease, Magnetic Resonance Imaging, Genetic architecture, Oxygen, 030104 developmental biology, Schizophrenia, Female, Neurology (clinical), business, 030217 neurology & neurosurgery
Abstract

The use of polygenic risk scores has become a practical translational approach to investigating the complex genetic architecture of schizophrenia, but the link between polygenic risk scores and pathophysiological components of this disorder has been the subject of limited research. We investigated in healthy volunteers whether schizophrenia polygenic risk score predicts hippocampal activity during simple memory encoding, which has been proposed as a risk-associated intermediate phenotype of schizophrenia. We analysed the relationship between polygenic risk scores and hippocampal activity in a discovery sample of 191 unrelated healthy volunteers from the USA and in two independent replication samples of 76 and 137 healthy unrelated participants from Europe and the USA, respectively. Polygenic risk scores for each individual were calculated as the sum of the imputation probability of reference alleles weighted by the natural log of odds ratio from the recent schizophrenia genome-wide association study. We examined hippocampal activity during simple memory encoding of novel visual stimuli assessed using blood oxygen level-dependent functional MRI. Polygenic risk scores were significantly associated with hippocampal activity in the discovery sample [P = 0.016, family-wise error (FWE) corrected within Anatomical Automatic Labeling (AAL) bilateral hippocampal-parahippocampal mask] and in both replication samples (P = 0.033, FWE corrected within AAL right posterior hippocampal-parahippocampal mask in Bari sample, and P = 0.002 uncorrected in the Duke Neurogenetics Study sample). The relationship between polygenic risk scores and hippocampal activity was consistently negative, i.e. lower hippocampal activity in individuals with higher polygenic risk scores, consistent with previous studies reporting decreased hippocampal-parahippocampal activity during declarative memory tasks in patients with schizophrenia and in their healthy siblings. Polygenic risk scores accounted for more than 8% of variance in hippocampal activity during memory encoding in discovery sample. We conclude that polygenic risk scores derived from the most recent schizophrenia genome-wide association study predict significant variability in hippocampal activity during memory encoding in healthy participants. Our findings validate mnemonic hippocampal activity as a genetic risk associated intermediate phenotype of schizophrenia, indicating that the aggregate neurobiological effect of schizophrenia risk alleles converges on this pattern of neural activity.awy004media15749593779001.

Published
2018

20. qSVA framework for RNA quality correction in differential expression analysis

Author

Joo Heon Shin, Ran Tao, Alexis L. Norris, Abhinav Nellore, Richard E. Straub, Daniel R. Weinberger, Marc Kealhofer, Jeffrey T. Leek, Yankai Jia, Dewey Kim, Thomas M. Hyde, Joel E. Kleinman, and Andrew E. Jaffe

Subjects
DNA Replication, 0301 basic medicine, Genotype, Biology, Transcriptome, 03 medical and health sciences, Text mining, Replication (statistics), Gene expression, medicine, Animals, Humans, Gray Matter, Oligonucleotide Array Sequence Analysis, Genetics, Multidisciplinary, Sequence Analysis, RNA, business.industry, Gene Expression Profiling, Computational Biology, High-Throughput Nucleotide Sequencing, RNA, Statistical model, Human brain, Biological Sciences, Expression (mathematics), 030104 developmental biology, medicine.anatomical_structure, Gene Expression Regulation, Schizophrenia, business, Algorithms
Abstract

RNA sequencing (RNA-seq) is a powerful approach for measuring gene expression levels in cells and tissues, but it relies on high-quality RNA. We demonstrate here that statistical adjustment using existing quality measures largely fails to remove the effects of RNA degradation when RNA quality associates with the outcome of interest. Using RNA-seq data from molecular degradation experiments of human primary tissues, we introduce a method—quality surrogate variable analysis (qSVA)—as a framework for estimating and removing the confounding effect of RNA quality in differential expression analysis. We show that this approach results in greatly improved replication rates (>3×) across two large independent postmortem human brain studies of schizophrenia and also removes potential RNA quality biases in earlier published work that compared expression levels of different brain regions and other diagnostic groups. Our approach can therefore improve the interpretation of differential expression analysis of transcriptomic data from human tissue.

Published
2017

21. Pleiotropic Meta-Analysis of Cognition, Education, and Schizophrenia Differentiates Roles of Early Neurodevelopmental and Adult Synaptic Pathways

Author

Panos Bitsios, Nikos C. Stefanis, Eliza Congdon, Dwight Dickinson, Elizabeth T. Cirulli, Jari Lahti, Neil Pendleton, Thomas Espeseth, Stephanie Le Hellard, Fred W. Sabb, Deborah K. Attix, Anil K. Malhotra, Aarno Palotie, Ina Giegling, W. David Hill, Joey W. Trampush, Edythe D. London, Elisabeth Widen, Todd Lencz, Emily Drabant Conley, Anna C. Need, Ian J. Deary, Srdjan Djurovic, Astri J. Lundervold, Emma Knowles, Gary Donohoe, David C. Liewald, Matthew C. Keller, Johan G. Eriksson, Katri Räikkönen, Laura M. Huckins, Panos Roussos, Gail Davies, Max Lam, Eli A. Stahl, Andrea Christoforou, Annette M. Hartmann, Ivar Reinvang, Ahmad R. Hariri, Matthew A. Scult, Dan E. Arking, Aiden Corvin, Jin Yu, Dimitrios Avramopoulos, Robert M. Bilder, Katherine E. Burdick, Richard E. Straub, Ornit Chiba-Falek, Dan Rujescu, Michael Gill, Daniel R. Weinberger, Vidar M. Steen, Ingrid Melle, Pamela DeRosse, Bettina Konte, Tyrone D. Cannon, David C. Glahn, Alex Hatzimanolis, Nelson A. Freimer, Ole A. Andreassen, Stella Giakoumaki, Antony Payton, Kjetil Sundet, William Ollier, Aristotle N. Voineskos, Nikolaos Smyrnis, Russell A. Poldrack, and Derek W. Morris

Subjects
0301 basic medicine, pathways, Genome-wide association study, Medical and Health Sciences, Synaptic Transmission, 0302 clinical medicine, Cognition, cognitive ability, 2.1 Biological and endogenous factors, GWAS, Aetiology, Genetics (clinical), Genetics & Heredity, 0303 health sciences, Single Nucleotide, Biological Sciences, Serious Mental Illness, genetic correlation, Mental Health, educational attainment, Meta-analysis, Educational Status, Psychology, Biotechnology, Clinical psychology, Adult, Schizophrenia (object-oriented programming), Genetic correlation, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, pleiotropy, mental disorders, Genetics, medicine, Humans, Genetic Predisposition to Disease, Bipolar disorder, Polymorphism, 030304 developmental biology, Genetic association, Prevention, Human Genome, Counterintuitive, Neurosciences, medicine.disease, Educational attainment, Brain Disorders, schizophrenia, 030104 developmental biology, Neurodevelopmental Disorders, Schizophrenia, Autism, Cognition Disorders, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

Liability to schizophrenia is inversely correlated with general cognitive ability at both the phenotypic and genetic level. Paradoxically, a modest but consistent positive genetic correlation has been reported between schizophrenia and educational attainment, despite the strong positive genetic correlation between cognitive ability and educational attainment. Here we leverage published GWAS in cognitive ability, education, and schizophrenia to parse biological mechanisms underlying these results. Association analysis based on subsets (ASSET), a pleiotropic meta-analytic technique, allowed jointly associated loci to be identified and characterized. Specifically, we identified subsets of variants associated in the expected (“Concordant”) direction across all three phenotypes (i.e., greater risk for schizophrenia, lower cognitive ability, and lower educational attainment); these were contrasted with variants demonstrating the counterintuitive (“Discordant”) relationship between education and schizophrenia (i.e., greater risk for schizophrenia and higher educational attainment). ASSET analysis revealed 235 independent loci associated with cognitive ability, education and/or schizophrenia at p−8. Pleiotropic analysis successfully identified more than 100 loci that were not significant in the input GWASs, and many of these have been validated by larger, more recent single-phenotype GWAS. Leveraging the joint genetic correlations of cognitive ability, education, and schizophrenia, we were able to dissociate two distinct biological mechanisms: early neurodevelopmental pathways that characterize concordant allelic variation, and adulthood synaptic pruning pathways that were linked to the paradoxical positive genetic association between education and schizophrenia. Further, genetic correlation analyses revealed that these mechanisms contribute not only to the etiopathogenesis of schizophrenia, but also to the broader biological dimensions that are implicated in both general health outcomes and psychiatric illness.

Published
2019

22. Regional Heterogeneity in Gene Expression, Regulation, and Coherence in the Frontal Cortex and Hippocampus across Development and Schizophrenia

Author

William S Ulrich, Richard E. Straub, Joo Heon Shin, Joel E. Kleinman, Leonardo Collado-Torres, Emily E. Burke, Daniel R. Weinberger, Amanda J. Price, Andrew E. Jaffe, Anandita Rajpurohit, Ran Tao, Thomas M. Hyde, Stephen A. Semick, Amy Peterson, Amy Deep-Soboslay, and Cristian Valencia

Subjects
0301 basic medicine, Adult, Male, Adolescent, Schizophrenia (object-oriented programming), Genome-wide association study, Genomics, RNA-Seq, Biology, behavioral disciplines and activities, Hippocampus, Article, 03 medical and health sciences, Young Adult, 0302 clinical medicine, mental disorders, Hippocampus (mythology), Humans, Genetic Predisposition to Disease, Genetic association, Aged, Regulation of gene expression, Aged, 80 and over, General Neuroscience, Gene Expression Regulation, Developmental, Middle Aged, Frontal Lobe, 030104 developmental biology, Gene Ontology, Expression quantitative trait loci, Schizophrenia, Female, Neuroscience, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

Summary The hippocampus formation, although prominently implicated in schizophrenia pathogenesis, has been overlooked in large-scale genomics efforts in the schizophrenic brain. We performed RNA-seq in hippocampi and dorsolateral prefrontal cortices (DLPFCs) from 551 individuals (286 with schizophrenia). We identified substantial regional differences in gene expression and found widespread developmental differences that were independent of cellular composition. We identified 48 and 245 differentially expressed genes (DEGs) associated with schizophrenia within the hippocampus and DLPFC, with little overlap between the brain regions. 124 of 163 (76.6%) of schizophrenia GWAS risk loci contained eQTLs in any region. Transcriptome-wide association studies in each region identified many novel schizophrenia risk features that were brain region-specific. Last, we identified potential molecular correlates of in vivo evidence of altered prefrontal-hippocampal functional coherence in schizophrenia. These results underscore the complexity and regional heterogeneity of the transcriptional correlates of schizophrenia and offer new insights into potentially causative biology.

Published
2019

23. Author Correction: Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function

Author

Peter W. Schofield, Dan Rujescu, Gail Davies, Vidar M. Steen, Ahmad R. Hariri, Sara Hägg, Lars Nyberg, Dimitrios Avramopoulos, Nikolaos Smyrnis, Gerardo Heiss, Pamela DeRosse, Russell A. Poldrack, Jingyun Yang, Evangelos Evangelou, Katri Räikkönen, Fred W. Sabb, B. Gwen Windham, Aiden Corvin, Peter R. Schofield, Teemu Palviainen, André G. Uitterlinden, Anders Lundquist, Henry Brodaty, Aarno Palotie, Gary Donohoe, Elisabeth Widen, Teresa Lee, Cornelia M. van Duijn, Harry Campbell, Caroline Hayward, Rebecca F. Gottesman, Shuo Li, Steffi G. Riedel-Heller, M. Arfan Ikram, Sudha Seshadri, Jari Lahti, Joshua C. Bis, Panos Bitsios, Nikos C. Stefanis, Bettina Konte, Steven T. Turner, Edith Hofer, Vilmundur Gudnason, Michael Gill, P. Eline Slagboom, Ozren Polasek, Ida K. Karlsson, Christopher Oldmeadow, Michael Griswold, Ulman Lindenberger, Eric Boerwinkle, Saskia P. Hagenaars, Ingrid Melle, Alfredo Ramirez, Janie Corley, Rodney J. Scott, Sven J. van der Lee, Mika Kähönen, Alison D. Murray, Daniel R. Weinberger, Neil Pendleton, J. Wouter Jukema, Suvi P. Rovio, Wei Zhao, Muralidharan Sargurupremraj, Raha Pazoki, Matthias Schmid, Ina Giegling, Grant W. Montgomery, Daniel E. Gustavson, Jerome I. Rotter, Dan E. Arking, Oscar L. Lopez, David J. Stott, Julian N. Trollor, Chandra A. Reynolds, Tobias Luck, Andrea Christoforou, David J. Porteous, Kent D. Taylor, Simon R. Cox, Yasaman Saba, Matthew A. Scult, Astri J. Lundervold, Aicha Soumare, Antony Payton, Stella Trompet, W. David Hill, Shu-Chen Li, Robert M. Bilder, Eero Vuoksimaa, Jennifer A. Smith, Katherine E. Burdick, Deborah K. Attix, Sudheer Giddaluru, David C. Glahn, Edythe D. London, Stephanie Le Hellard, Terho Lehtimäki, Markus Leber, Katja Petrovic, James F. Wilson, Dwight Dickinson, Elizabeth T. Cirulli, Christophe Tzourio, Panos Roussos, Amelia A. Assareh, Markus Scholz, Alex Hatzimanolis, Tamara B. Harris, Stéphanie Debette, Alison Pattie, Thomas Espeseth, John M. Starr, William E R Ollier, Nicola J. Armstrong, Kjetil Sundet, Michael Wagner, Ian Ford, Simone Reppermund, Qiong Yang, Albert V. Smith, Nicole A. Kochan, Riccardo E. Marioni, Anu Loukola, Igor Rudan, Nicholas G. Martin, Jan Bressler, Tian Liu, K. Hoyan Wen, Natalie Terzikhan, Emma Knowles, Raymond Noordam, Joey W. Trampush, John Attia, Nancy L. Pedersen, Claudia L. Satizabal, Anne C. Böhmer, Chloe Fawns-Ritchie, Adele M. Taylor, Bruce M. Psaty, Paul Elliott, David R. Weir, Catharine R. Gale, Ioanna Tzoulaki, Leonie Weinhold, Anbupalam Thalamuthu, Anders M. Dale, Helena Schmidt, Annette M. Hartmann, Ole A. Andreassen, Ian J. Deary, Arno Villringer, Andrew M. McIntosh, Srdjan Djurovic, Najaf Amin, David C. Liewald, Nathan A. Gillespie, Ivar Reinvang, Thomas H. Mosley, Veronique Vitart, Michelle Luciano, Robert Karlsson, Lenore J. Launer, Eliza Congdon, Karen A. Mather, Marisa Koini, Tyrone D. Cannon, Elizabeth G. Holliday, Goran Papenberg, Reinhold Schmidt, Philippe Amouyel, Holger Wagner, Todd Lencz, Margaret J. Wright, Leo-Pekka Lyytikäinen, Emily Drabant Conley, David A. Bennett, William S. Kremen, M. Kamran Ikram, Catriona L. K. Barnes, Stella G. Giakoumaki, Scott D. Gordon, Johan G. Eriksson, Perminder S. Sachdev, Olli T. Raitakari, Judith A. Okely, Aristotle N. Voineskos, Max Lam, Sarah E. Harris, Luca Kleineidam, Jaakko Kaprio, Derek W. Morris, Sharon L.R. Kardia, Peter K. Joshi, Erin B. Ware, Lars Bertram, Philip L. De Jager, Anna C. Need, Abbas Dehghan, Jin Yu, Jessica D. Faul, N Freimer, Matthew C. Keller, John B.J. Kwok, Anil K. Malhotra, Will Longstreth, Hieab H.H. Adams, Richard J. Rose, Annette L. Fitzpatrick, Richard E. Straub, Christina M. Lill, David Ames, Patricia A. Boyle, David S. Knopman, He Gao, Narelle K. Hansell, Ornit Chiba-Falek, Danielle M. Dick, Stuart J. Ritchie, Ari Ahola-Olli, and Jeannette Simino

Subjects
0301 basic medicine, Science, MEDLINE, General Physics and Astronomy, 02 engineering and technology, computer.software_genre, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, lcsh:Science, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Multidisciplinary, business.industry, Published Erratum, Cognition, General Chemistry, 021001 nanoscience & nanotechnology, 030104 developmental biology, Correction study, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, lcsh:Q, Artificial intelligence, ddc:500, 0210 nano-technology, Psychology, business, computer, Natural language processing
Abstract

Christina M. Lill, who contributed to analysis of data, was inadvertently omitted from the author list in the originally published version of this article. This has now been corrected in both the PDF and HTML versions of the article.

Published
2019

24. BrainSeq: Neurogenomics to Drive Novel Target Discovery for Neuropsychiatric Disorders

Author

Patricio O'Donnell, Christian Schubert, Tony Kam-Thong, Wayne C. Drevets, Amy Deep-Soboslay, Nicholas J. Brandon, David C. Airey, Andrew E. Jaffe, Laurent Essioux, James E. Scherschel, Mitsuyuki Matsumoto, Thomas M. Hyde, David A. Collier, Philip J. Ebert, Hartmuth C. Kolb, Michael Didriksen, Yushi Liu, Hui-Rong Qian, Alan J. Cross, Joo Heon Shin, Daniel R. Weinberger, Qi Wang, Kalpana M. Merchant, Laura Nisenbaum, Jens R. Wendland, Hualin S. Xi, Maura L. Furey, Richard E. Straub, John N. Calley, Ryan M. Smith, Cara L. Ruble, Jie Quan, Enrico Domenici, Ashley R. Winslow, Joel E. Kleinman, Husseini K. Manji, Takeshi Saito, Brian J. Eastwood, Hong Wang, and Yankai Jia

Subjects
Neurogenomics, medicine.medical_specialty, Mood Disorders, Mental Disorders, General Neuroscience, Genomic data, Brain, Computational biology, Medical research, medicine.disease, Epigenesis, Genetic, Mood disorders, Drug Discovery, Gene Targeting, medicine, Animals, Humans, Psychiatry, Psychology
Abstract

We outline an ambitious project to characterize the genetic and epigenetic regulation of multiple facets of transcription in distinct brain regions across the human lifespan in samples of major neuropsychiatric disorders and controls. Initially focused on schizophrenia and mood disorders, the goal of this consortium is to elucidate the underlying molecular mechanisms of genetic associations with the goal of identifying novel therapeutic targets. The consortium currently consists of seven pharmaceutical companies and a not-for-profit medical research institution working as a precompetitive team to generate and analyze publicly available archival brain genomic data related to neuropsychiatric illness.

Published
2015

25. iPSC-derived homogeneous populations of developing schizophrenia cortical interneurons have compromised mitochondrial function

Author

Sangmi Chung, James M. Park, Weihua Huang, Hae-Young Kim, Joseph T. Coyle, Daniel R. Weinberger, Donna L. McPhie, Richard E. Straub, Zhicheng Shao, Peiyan Ni, Bruce M. Cohen, Sophy Yu, Joy S. Park, Haneul Noh, Gun Hoo Park, Changhong Yin, and Youxin Guan

Subjects
0301 basic medicine, Male, Psychosis, medicine.medical_treatment, Induced Pluripotent Stem Cells, Oxidative phosphorylation, Biology, Article, Cell Line, Pathogenesis, 03 medical and health sciences, Cellular and Molecular Neuroscience, Glutamatergic, 0302 clinical medicine, Neurodevelopmental disorder, Interneurons, medicine, Humans, Antipsychotic, Molecular Biology, medicine.disease, Mitochondria, Psychiatry and Mental health, 030104 developmental biology, Schizophrenia, Neuroscience, 030217 neurology & neurosurgery, Function (biology)
Abstract

Schizophrenia (SCZ) is a neurodevelopmental disorder. Thus, studying pathogenetic mechanisms underlying SCZ requires studying the development of brain cells. Cortical interneurons (cINs) are consistently observed to be abnormal in SCZ postmortem brains. These abnormalities may explain altered gamma oscillation and cognitive function in patients with SCZ. Of note, currently used antipsychotic drugs ameliorate psychosis, but they are not very effective in reversing cognitive deficits. Characterizing mechanisms of SCZ pathogenesis, especially related to cognitive deficits, may lead to improved treatments. We generated homogeneous populations of developing cINs from 15 healthy control (HC) iPSC lines and 15 SCZ iPSC lines. SCZ cINs, but not SCZ glutamatergic neurons, show dysregulated Oxidative Phosphorylation (OxPhos) related gene expression, accompanied by compromised mitochondrial function. The OxPhos deficit in cINs could be reversed by Alpha Lipoic Acid/Acetyl-L-Carnitine (ALA/ALC) but not by other chemicals previously identified as increasing mitochondrial function. The restoration of mitochondrial function by ALA/ALC was accompanied by a reversal of arborization deficits in SCZ cINs. OxPhos abnormality, even in the absence of any circuit environment with other neuronal subtypes, appears to be an intrinsic deficit in SCZ cINs.

Published
2018

26. Publisher Correction: Variations in Dysbindin-1 are associated with cognitive response to antipsychotic drug treatment

Author

Gianfranco Spalletta, Rosa Mastrogiacomo, Emiliana Borrelli, Sanne S Kaalund, Sara Sannino, Francesca Managò, Genny Orso, Carlo Caltagirone, Fabrizio Piras, Francesco Papaleo, Diego Scheggia, Daniel R. Weinberger, Joel E. Kleinman, Fengyu Zhang, Richard E. Straub, Stefano Vicari, Maria Antonietta De Luca, Simone Guadagna, Maria Pontillo, Marco Armando, Thomas M. Hyde, and Maddalena Mereu

Subjects
Multidisciplinary, Science, Published Erratum, Section (typography), General Physics and Astronomy, General Chemistry, Dysbindin-1, Article, General Biochemistry, Genetics and Molecular Biology, 030227 psychiatry, 03 medical and health sciences, 0302 clinical medicine, lcsh:Q, Antipsychotic drug, lcsh:Science, Psychology, 030217 neurology & neurosurgery, Cognitive response, Cognitive psychology
Abstract

Antipsychotics are the most widely used medications for the treatment of schizophrenia spectrum disorders. While such drugs generally ameliorate positive symptoms, clinical responses are highly variable in terms of negative symptoms and cognitive impairments. However, predictors of individual responses have been elusive. Here, we report a pharmacogenetic interaction related to a core cognitive dysfunction in patients with schizophrenia. We show that genetic variations reducing dysbindin-1 expression can identify individuals whose executive functions respond better to antipsychotic drugs, both in humans and in mice. Multilevel ex vivo and in vivo analyses in postmortem human brains and genetically modified mice demonstrate that such interaction between antipsychotics and dysbindin-1 is mediated by an imbalance between the short and long isoforms of dopamine D2 receptors, leading to enhanced presynaptic D2 function within the prefrontal cortex. These findings reveal one of the pharmacodynamic mechanisms underlying individual cognitive response to treatment in patients with schizophrenia, suggesting a potential approach for improving the use of antipsychotic drugs., Patients with schizophrenia show varied response to antipsychotics. Here, the authors demonstrate in patients under antipsychotics treatment that a haplotype associated with lower dysbindin-1 expression correlated with better executive functions, providing further mechanistic support from mouse models.

Published
2018

27. Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs

Author

Amritha Jaishankar, Brady J. Maher, Alana Lescure, Kamel Shibbani, Ronald D.G. McKay, Leonardo Collado-Torres, Daniel J Hiler, William S Ulrich, Thomas M. Hyde, Alan J. Cross, Jose A. Apud, Josh G. Chenoweth, Gregory R. Hamersky, Nicola Micali, Keri Martinowich, Emily E. Burke, Stephanie Cerceo Page, Nicholas J. Brandon, Suel Kee Kim, BaDoi N. Phan, Stephen A. Semick, Anandita Rajpurohit, Joel E. Kleinman, Richard E. Straub, Andrew E. Jaffe, Yanhong Wang, Huei Ying Chen, Amanda J. Price, Daniel J. Hoeppner, Daniel R. Weinberger, Joo Heon Shin, James C. Barrow, Cristian Valencia, Roland Bürli, and Karen F. Berman

Subjects
Transcriptome, Corticogenesis, medicine.anatomical_structure, Precursor cell, Cell, Gene regulatory network, medicine, Human brain, Cell sorting, Biology, Induced pluripotent stem cell, Cell biology
Abstract

SummaryHuman induced pluripotent stem cells (hiPSCs) are a powerful model of neural differentiation and maturation. We present a hiPSC transcriptomics resource on corticogenesis from 5 iPSC donor and 13 subclonal lines across nine time points over 5 broad conditions: self-renewal, early neuronal differentiation, neural precursor cells (NPCs), assembled rosettes, and differentiated neuronal cells that were validated using electrophysiology. We identified widespread changes in the expression of individual transcript features and their splice variants, gene networks, and global patterns of transcription. We next demonstrated that co-culturing human NPCs with rodent astrocytes resulted in mutually synergistic maturation, and that cell type-specific expression data can be extracted using only sequencing read alignments without potentially disruptive cell sorting. We lastly developed and validated a computational tool to estimate the relative neuronal maturity of iPSC-derived neuronal cultures and human brain tissue, which were maturationally heterogeneous but contained subsets of cells most akin to adult human neurons.

Published
2018
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28. Multi-Trait Analysis of GWAS and Biological Insights Into Cognition: A Response to Hill (2018)

Author

Neil Pendleton, Tyrone D. Cannon, Panos Bitsios, Nikos C. Stefanis, Kjetil Sundet, Matthew C. Keller, Deborah K. Attix, Gary Donohoe, Aarno Palotie, Pamela DeRosse, Elisabeth Widen, Panos Roussos, Emma Knowles, Russell A. Poldrack, Antony Payton, Stella G. Giakoumaki, Anna C. Need, Nikolaos Smyrnis, Todd Lencz, Dwight Dickinson, Elizabeth T. Cirulli, Emily Drabant Conley, Ina Giegling, Ornit Chiba-Falek, Anil K. Malhotra, Joey W. Trampush, Jari Lahti, Thomas Espeseth, Bettina Konte, Astri J. Lundervold, Derek W. Morris, Jin Yu, Alex Hatzimanolis, William Ollier, Edythe D. London, Ingrid Melle, Max Lam, Andrea Christoforou, Matthew A. Scult, Katri Räikkönen, Ole A. Andreassen, Robert M. Bilder, Ivar Reinvang, Katherine E. Burdick, Aiden Corvin, Dan E. Arking, Aristotle N. Voineskos, Eliza Congdon, Srdjan Djurovic, Dan Rujescu, Johan G. Eriksson, Fred W. Sabb, Vidar M. Steen, Nelson A. Freimer, Michael Gill, David C. Glahn, Stephanie Le Hellard, Richard E. Straub, Daniel R. Weinberger, Ahmad R. Hariri, and Dimitrios Avramopoulos

Subjects
0301 basic medicine, False discovery rate, Empirical data, cerebellum, Clinical Sciences, Genome-wide association study, Polymorphism, Single Nucleotide, Paediatrics and Reproductive Medicine, 03 medical and health sciences, nootropics, Cognition, immune system diseases, synapse, hemic and lymphatic diseases, Multi trait, Genetics, 2.1 Biological and endogenous factors, Humans, GWAS, Genetic Predisposition to Disease, Polymorphism, Aetiology, Genetics (clinical), Nootropic Agents, Cognitive science, Genetics & Heredity, neurodevelopment, Human Genome, Obstetrics and Gynecology, Single Nucleotide, Articles, bacterial infections and mycoses, Twin study, Human genetics, general cognitive ability, 030104 developmental biology, Mental Health, Pediatrics, Perinatology and Child Health, gene expression, Cognitive Sciences, lipids (amino acids, peptides, and proteins), calcium channel, Psychology, Genome-Wide Association Study, potassium channel
Abstract

Hill (Twin Research and Human Genetics, Vol. 21, 2018, 84–88) presented a critique of our recently published paper in Cell Reports entitled ‘Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets’ (Lam et al., Cell Reports, Vol. 21, 2017, 2597–2613). Specifically, Hill offered several interrelated comments suggesting potential problems with our use of a new analytic method called Multi-Trait Analysis of GWAS (MTAG) (Turley et al., Nature Genetics, Vol. 50, 2018, 229–237). In this brief article, we respond to each of these concerns. Using empirical data, we conclude that our MTAG results do not suffer from ‘inflation in the FDR [false discovery rate]’, as suggested by Hill (Twin Research and Human Genetics, Vol. 21, 2018, 84–88), and are not ‘more relevant to the genetic contributions to education than they are to the genetic contributions to intelligence’.

Published
2018

29. Variations in Dysbindin-1 are associated with cognitive response to antipsychotic drug treatment

Author

Stefano Vicari, Sara Sannino, Rosa Mastrogiacomo, Emiliana Borrelli, Daniel R. Weinberger, Marco Armando, Fabrizio Piras, Genny Orso, Thomas M. Hyde, Carlo Caltagirone, Joel E. Kleinman, Fengyu Zhang, Richard E. Straub, Gianfranco Spalletta, Maria Antonietta De Luca, Maddalena Mereu, Maria Pontillo, Diego Scheggia, Francesca Managò, Francesco Papaleo, Simone Guadagna, and Sanne S Kaalund

Subjects
0301 basic medicine, Male, Genetics and Molecular Biology (all), medicine.medical_treatment, General Physics and Astronomy, Biochemistry, ddc:616.89, Executive Function, Mice, 0302 clinical medicine, Cognition, Adolescent, Adult, Aged, Animals, Antipsychotic Agents/pharmacology, Brain/drug effects, Brain/metabolism, Cognition/drug effects, Cognition/physiology, Dysbindin/deficiency, Dysbindin/genetics, Dysbindin/metabolism, Executive Function/drug effects, Executive Function/physiology, Genetic Variation, Humans, Mice, Inbred C57BL, Mice, Knockout, Middle Aged, Prefrontal Cortex/drug effects, Prefrontal Cortex/metabolism, Receptors, Dopamine D2/metabolism, Risperidone/pharmacology, Schizophrenia/drug therapy, Schizophrenia/genetics, Schizophrenia/metabolism, Schizophrenic Psychology, Young Adult, Prefrontal cortex, lcsh:Science, Multidisciplinary, Dysbindin, Chemistry (all), Brain, Executive functions, Risperidone, Publisher Correction, 3. Good health, Schizophrenia, medicine.drug, Antipsychotic Agents, Science, Prefrontal Cortex, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Physics and Astronomy (all), Dopamine receptor D2, medicine, Antipsychotic, business.industry, Receptors, Dopamine D2, General Chemistry, medicine.disease, 030104 developmental biology, lcsh:Q, Biochemistry, Genetics and Molecular Biology (all), business, Neuroscience, 030217 neurology & neurosurgery
Abstract

Antipsychotics are the most widely used medications for the treatment of schizophrenia spectrum disorders. While such drugs generally ameliorate positive symptoms, clinical responses are highly variable in terms of negative symptoms and cognitive impairments. However, predictors of individual responses have been elusive. Here, we report a pharmacogenetic interaction related to a core cognitive dysfunction in patients with schizophrenia. We show that genetic variations reducing dysbindin-1 expression can identify individuals whose executive functions respond better to antipsychotic drugs, both in humans and in mice. Multilevel ex vivo and in vivo analyses in postmortem human brains and genetically modified mice demonstrate that such interaction between antipsychotics and dysbindin-1 is mediated by an imbalance between the short and long isoforms of dopamine D2 receptors, leading to enhanced presynaptic D2 function within the prefrontal cortex. These findings reveal one of the pharmacodynamic mechanisms underlying individual cognitive response to treatment in patients with schizophrenia, suggesting a potential approach for improving the use of antipsychotic drugs.

Published
2018

30. Schizophrenia risk variants influence multiple classes of transcripts of sorting nexin 19 (SNX19)

Author

Liang, Ma, Stephen A, Semick, Qiang, Chen, Chao, Li, Ran, Tao, Amanda J, Price, Joo Heon, Shin, Yankai, Jia, Nicholas J, Brandon, Alan J, Cross, Thomas M, Hyde, Joel E, Kleinman, Andrew E, Jaffe, Daniel R, Weinberger, and Richard E, Straub

Subjects
Adult, Male, Genotype, Quantitative Trait Loci, Brain, Chromosome Mapping, Gene Expression, Exons, DNA Methylation, Middle Aged, Polymorphism, Single Nucleotide, Chromatin, Gene Frequency, Risk Factors, Schizophrenia, Humans, Female, Genetic Predisposition to Disease, Autopsy, Sorting Nexins, Alleles, Genome-Wide Association Study
Abstract

Genome-wide association studies (GWAS) have identified many genomic loci associated with risk for schizophrenia, but unambiguous identification of the relationship between disease-associated variants and specific genes, and in particular their effect on risk conferring transcripts, has proven difficult. To better understand the specific molecular mechanism(s) at the schizophrenia locus in 11q25, we undertook cis expression quantitative trait loci (cis-eQTL) mapping for this 2 megabase genomic region using postmortem human brain samples. To comprehensively assess the effects of genetic risk upon local expression, we evaluated multiple transcript features: genes, exons, and exon-exon junctions in multiple brain regions-dorsolateral prefrontal cortex (DLPFC), hippocampus, and caudate. Genetic risk variants strongly associated with expression of SNX19 transcript features that tag multiple rare classes of SNX19 transcripts, whereas they only weakly affected expression of an exon-exon junction that tags the majority of abundant transcripts. The most prominent class of SNX19 risk-associated transcripts is predicted to be overexpressed, defined by an exon-exon splice junction between exons 8 and 10 (junc8.10) and that is predicted to encode proteins that lack the characteristic nexin C terminal domain. Risk alleles were also associated with either increased or decreased expression of multiple additional classes of transcripts. With RACE, molecular cloning, and long read sequencing, we found a number of novel SNX19 transcripts that further define the set of potential etiological transcripts. We explored epigenetic regulation of SNX19 expression and found that DNA methylation at CpG sites near the primary transcription start site and within exon 2 partially mediate the effects of risk variants on risk-associated expression. ATAC sequencing revealed that some of the most strongly risk-associated SNPs are located within a region of open chromatin, suggesting a nearby regulatory element is involved. These findings indicate a potentially complex molecular etiology, in which risk alleles for schizophrenia generate epigenetic alterations and dysregulation of multiple classes of SNX19 transcripts.

Published
2018

31. Identification and prioritization of gene sets associated with schizophrenia risk by co-expression network analysis in human brain

Author

Eugenia, Radulescu, Andrew E, Jaffe, Richard E, Straub, Qiang, Chen, Joo Heon, Shin, Thomas M, Hyde, Joel E, Kleinman, and Daniel R, Weinberger

Subjects
Adult, Aged, 80 and over, Male, Multifactorial Inheritance, Brain, Prefrontal Cortex, Genomics, Middle Aged, White People, Schizophrenia, Humans, Female, Gene Regulatory Networks, Genetic Predisposition to Disease, Autopsy, Transcriptome, Aged, Genome-Wide Association Study
Abstract

Schizophrenia polygenic risk is plausibly manifested by complex transcriptional dysregulation in the brain, involving networks of co-expressed and functionally related genes. The main purpose of this study was to identify and prioritize co-expressed gene sets in a hierarchical manner, based on the strength of the relationships with clinical diagnosis and with polygenic risk for schizophrenia. Weighted Gene Co-expression Network Analysis (WGCNA) was applied to RNA-quality-adjusted DLPFC RNA-Seq data from the LIBD Postmortem Human Brain Repository (90 controls, 74 schizophrenia cases; all Caucasians) to construct co-expression networks and detect "modules" of co-expressed genes. After multiple internal and external validation procedures, modules of selected interest were tested for enrichment in biological ontologies, for association with schizophrenia polygenic risk scores (PRSs) and with diagnosis, and also for enrichment in genes within the significant GWAS loci reported by the Psychiatric Genomic Consortium (PGC2). The association between schizophrenia genetic signals and modules of co-expression converged on one module showing not only a significant association with both diagnosis and PRS but also significant overlap with 36 PGC2 loci genes, deemed the strongest candidates for drug targets. This module contained many genes involved in synaptic signaling and neuroplasticity. Fifty-three PGC2 genes were in modules associated only with diagnosis and 59 in modules unrelated to diagnosis or PRS. Our study highlights complex relationships between gene co-expression networks in the brain and clinical state and polygenic risk for SCZ and provides a strategy for using this information in selecting and prioritizing potentially targetable gene sets for therapeutic drug development.

Published
2018

32. Identification and prioritization of gene sets associated with schizophrenia risk by co-expression network analysis in human brain

Author

Richard E. Straub, Daniel R. Weinberger, Qiang Chen, Eugenia Radulescu, Andrew E. Jaffe, Thomas M. Hyde, Joel E. Kleinman, and Joo Heon Shin

Subjects
0301 basic medicine, Schizophrenia (object-oriented programming), Genome-wide association study, Computational biology, Human brain, Biology, 03 medical and health sciences, Cellular and Molecular Neuroscience, Psychiatry and Mental health, 030104 developmental biology, 0302 clinical medicine, medicine.anatomical_structure, Drug development, Tier 2 network, Neuroplasticity, medicine, Identification (biology), Synaptic signaling, Molecular Biology, Gene, 030217 neurology & neurosurgery, Network analysis
Abstract

Schizophrenia polygenic risk is plausibly manifested by complex transcriptional dysregulation in the brain, involving networks of co-expressed and functionally related genes. The main purpose of this study was to identify and prioritize co-expressed gene sets in a hierarchical manner, based on the strength of the relationships with clinical diagnosis and with polygenic risk for schizophrenia. Weighted Gene Co-expression Network Analysis (WGCNA) was applied to RNA-quality-adjusted DLPFC RNA-Seq data from the LIBD Postmortem Human Brain Repository (90 controls, 74 schizophrenia cases; all Caucasians) to construct co-expression networks and detect “modules” of co-expressed genes. After multiple internal and external validation procedures, modules of selected interest were tested for enrichment in biological ontologies, for association with schizophrenia polygenic risk scores (PRSs) and with diagnosis, and also for enrichment in genes within the significant GWAS loci reported by the Psychiatric Genomic Consortium (PGC2). The association between schizophrenia genetic signals and modules of co-expression converged on one module showing not only a significant association with both diagnosis and PRS but also significant overlap with 36 PGC2 loci genes, deemed the strongest candidates for drug targets. This module contained many genes involved in synaptic signaling and neuroplasticity. Fifty-three PGC2 genes were in modules associated only with diagnosis and 59 in modules unrelated to diagnosis or PRS. Our study highlights complex relationships between gene co-expression networks in the brain and clinical state and polygenic risk for SCZ and provides a strategy for using this information in selecting and prioritizing potentially targetable gene sets for therapeutic drug development.

Published
2018
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33. T57IDENTIFYING CAUSAL GENETIC VARIANTS IN PSYCHIATRIC DISORDERS USING SUMMARY DATA BASED MENDELIAN RANDOMIZATION

Author

Daniel R. Weinberger, Eugenia Radulescu, Andrew E. Jaffe, Qiang Chen, Joo Heon Shin, Vijay Sadashivaiah, Joel E. Kleinman, Richard E. Straub, Thomas M. Hyde, and Giulio Pergola

Subjects
Pharmacology, Genetics, Psychiatry and Mental health, Neurology, Summary data, Mendelian randomization, Genetic variants, Pharmacology (medical), Neurology (clinical), Biology, Biological Psychiatry
Published
2019

34. Correction: iPSC-derived homogeneous populations of developing schizophrenia cortical interneurons have compromised mitochondrial function

Author

Sangmi Chung, Joseph T. Coyle, Donna L. McPhie, Gun Hoo Park, Sophy Yu, Richard E. Straub, Zhicheng Shao, Bruce M. Cohen, James M. Park, Peiyan Ni, Changhong Yin, Weihua Huang, Hae-Young Kim, Daniel R. Weinberger, Haneul Noh, Joy S. Park, and Youxin Guan

Subjects
Cellular and Molecular Neuroscience, Psychiatry and Mental health, Homogeneous, Schizophrenia (object-oriented programming), Biology, Molecular Biology, Neuroscience, Function (biology)
Published
2019

35. DIFFERENTIAL DISTRIBUTION OF SCHIZOPHRENIA RISK GENES WITHIN GENE CO-EXPRESSION NETWORKS CONSTRUCTED FROM RNA-SEQ DATA (POSTMORTEM DLPFC) OF AFFECTED AND UNAFFECTED INDIVIDUALS

Author

Richard E. Straub, Andrew E. Jaffe, Eugenia Radulescu, Qiang Chen, Joo Heon Shin, and Daniel R. Weinberger

Subjects
Pharmacology, RNA-Seq, Genome-wide association study, Chemical synaptic transmission, Computational biology, PTPRF, Biology, Axonogenesis, Psychiatry and Mental health, Neurology, Gene expression, Transcriptional regulation, Pharmacology (medical), Neurology (clinical), Gene, Biological Psychiatry
Abstract

Background Schizophrenia polygenic risk is plausibly manifested by complex transcriptional dysregulation in the brain, involving networks of co-expressed and functionally related genes. Methods 1. Samples: DLPFC gene expression (RNA-Seq) abundance was quantified (RPKM) in postmortem human brains from the LIBD Postmortem Human Brain Repository (90 controls- CTRL, 76 schizophrenia- SCZ, Caucasians, age: 16–80, RIN≥7). Common Mind Consortium (CMC) RNA-Seq postmortem DLPFC (125 CTRL, 109 SCZ, Caucasians, age, RIN as above) was used for replication of LIBD co-expression networks. 2. Expression measures/ quality control: only genes with median RPKM≥0.1 (N=23132 genes; LIBD samples) were used. Expression data was normalized by log2 transformation and adjusted for RNA quality measures (RIN, PMI, total gene assignment, proportion of mitochondrial RNA) by empirical Bayesian models. 3. Data analysis: WGCNA was applied to the adjusted expression data to construct co-expression networks, separately for LIBD- CTRL and LIBD- SCZ. Modules of co-expressed genes were detected by dynamic tree cutting method and summarized as “module eigengenes” for further analyses. 4. Modules of LIBD (CTRL; SCZ) were tested for enrichment in PGC2 genes within the 108 loci associated with the schizophrenia risk in the latest GWAS. 5. Composite module preservation statistics- median rank and Zsummary was used for assessing the preservation of LIBD SCZ modules in LIBD CTRL network and for replication of LIBD co-expression modules in the CMC independent data sets. Gene enrichment analyses for testing modules’ enrichment in Gene Ontology (GO) biological processes (BP) was performed with AmiGO/ PANTHER. Results 17 co-expression modules were identified in each LIBD group. Module preservation analysis showed a good preservation of co-expression modules between LIBD CTRL and SCZ networks, with all but one SCZ module showing evidence for strong preservation (Zsummary≥10). PGC2 genes were overrepresented in two CTRL modules (p=0.001973, p=0.028297) enriched for GO-BP such as translation, ATP synthesis, oxidative phosphorylation, homophilic cell adhesion via plasma membrane adhesion molecules, chemical synaptic transmission, axonogenesis, and in one SCZ module (p=0.000519) enriched for RNA processing, nervous system development and modulation of synaptic transmission. 58 PGC2 genes overlapped with the SCZ module (e.g., DRD2, FURIN, TSNARE1), whereas 48 + 17 PGC2 genes were overrepresented in the two CTRL modules (e.g., CACNA1C, CHRM4, CACNA1I, TCF20). Of note, only 9 overrepresented PGC2 genes were shared by CTRL and SCZ: AMBRA1, ANKRD63, HSPA9, LRP1, PRR12, PTPRF, RERE, TOM1L2, ZDHHC5. Replication of co-expression LIBD networks in CMC data set showed evidence of weak to strong preservation (Zsummary>2, respectively ≥10) for 16/ 17 modules for each LIBD group. Discussion Our results illustrate the complexity of SCZ risk distribution within the DLPFC co-expression networks in postmortem brains of affected and unaffected individuals. Importantly, not the same PGC2 genes are members of co-expression modules in CTRL and SCZ, nor do they aggregate in similar modules. These observations may be explained by differential transcriptional regulation due to pleiotropy, epistasis, epigenetic dysregulation, or even hidden RNA quality artifacts. Future studies are necessary to elucidate the participation of SCZ risk genes in brain co-expression networks.

Published
2019

36. SA59POLYGENIC RISK SCORE INCREASES SCHIZOPHRENIA LIABILITY THROUGH COGNITION-RELEVANT PATHWAYS

Author

Daniel R. Weinberger, Stacey Cherny, Timothea Toulopoulou, Richard E. Straub, Pak C. Sham, Xiaowei Zhang, Karen F. Berman, and Dwight Dickinson

Subjects
Pharmacology, Framingham Risk Score, business.industry, Schizophrenia (object-oriented programming), Liability, Cognition, Psychiatry and Mental health, Neurology, Medicine, Pharmacology (medical), Neurology (clinical), business, Biological Psychiatry, Clinical psychology
Published
2019

37. Independent evidence for an association between general cognitive ability and a genetic locus for educational attainment

Author

Ole A. Andreassen, Anil K. Malhotra, Masashi Ikeda, Andrea Christoforou, Jari Lahti, Matthew A. Scult, Bettina Konte, Matthew C. Keller, Gary Donohoe, Dwight Dickinson, Neil Pendleton, Semanti Mukherjee, Stella G. Giakoumaki, Emma Knowles, William Ollier, Dan Rujescu, Joey W. Trampush, Vidar M. Steen, Pamela DeRosse, Stephanie Le Hellard, Saurav Guha, Ingrid Melle, Astri J. Lundervold, Nakao Iwata, Katri Räikkönen, Itsik Pe'er, Aarno Palotie, Elisabeth Widen, Panos Bitsios, Panos Roussos, Ivar Reinvang, Aiden Corvin, Michael A Horan, Johan G. Eriksson, Ina Giegling, Ian J. Deary, Srdjan Djurovic, Derek W. Morris, David C. Liewald, Thomas Espeseth, Todd Lencz, Richard E. Straub, Daniel R. Weinberger, Gail Davies, Ahmad R. Hariri, Majnu John, David C. Glahn, Michael Gill, Ariel Darvasi, Katherine E. Burdick, Antony Payton, John M. Starr, and Kjetil Sundet

Subjects
Genetics, education.field_of_study, Population, Locus (genetics), Genome-wide association study, Cognition, Quantitative trait locus, Educational attainment, Cellular and Molecular Neuroscience, Psychiatry and Mental health, SNP, Psychology, education, Neurocognitive, Genetics (clinical), Clinical psychology
Abstract

Cognitive deficits and reduced educational achievement are common in psychiatric illness; understanding the genetic basis of cognitive and educational deficits may be informative about the etiology of psychiatric disorders. A recent, large genome-wide association study (GWAS) reported a genome-wide significant locus for years of education, which subsequently demonstrated association to general cognitive ability (“g”) in overlapping cohorts. The current study was designed to test whether GWAS hits for educational attainment are involved in general cognitive ability in an independent, large-scale collection of cohorts. Using cohorts in the Cognitive Genomics Consortium (COGENT; up to 20,495 healthy individuals), we examined the relationship between g and variants associated with educational attainment. We next conducted meta-analyses with 24,189 individuals with neurocognitive data from the educational attainment studies, and then with 53,188 largely independent individuals from a recent GWAS of cognition. A SNP (rs1906252) located at chromosome 6q16.1, previously associated with years of schooling, was significantly associated with g (P = 1.47 × 10−4) in COGENT. The first joint analysis of 43,381 non-overlapping individuals for this a priori-designated locus was strongly significant (P = 4.94 × 10−7), and the second joint analysis of 68,159 non-overlapping individuals was even more robust (P = 1.65 × 10−9). These results provide independent replication, in a large-scale dataset, of a genetic locus associated with cognitive function and education. As sample sizes grow, cognitive GWAS will identify increasing numbers of associated loci, as has been accomplished in other polygenic quantitative traits, which may be relevant to psychiatric illness. © 2015 Wiley Periodicals, Inc.

Published
2015

38. Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores

Author

Bjarni J. Vilhjálmsson, Jian Yang, Hilary K. Finucane, Alexander Gusev, Sara Lindström, Stephan Ripke, Giulio Genovese, Po-Ru Loh, Gaurav Bhatia, Ron Do, Tristan Hayeck, Hong-Hee Won, Sekar Kathiresan, Michele Pato, Carlos Pato, Rulla Tamimi, Eli Stahl, Noah Zaitlen, Bogdan Pasaniuc, Gillian Belbin, Eimear E. Kenny, Mikkel H. Schierup, Philip De Jager, Nikolaos A. Patsopoulos, Steve McCarroll, Mark Daly, Shaun Purcell, Daniel Chasman, Benjamin Neale, Michael Goddard, Peter M. Visscher, Peter Kraft, Nick Patterson, Alkes L. Price, Benjamin M. Neale, Aiden Corvin, James T.R. Walters, Kai-How Farh, Peter A. Holmans, Phil Lee, Brendan Bulik-Sullivan, David A. Collier, Hailiang Huang, Tune H. Pers, Ingrid Agartz, Esben Agerbo, Margot Albus, Madeline Alexander, Farooq Amin, Silviu A. Bacanu, Martin Begemann, Richard A. Belliveau, Judit Bene, Sarah E. Bergen, Elizabeth Bevilacqua, Tim B. Bigdeli, Donald W. Black, Richard Bruggeman, Nancy G. Buccola, Randy L. Buckner, William Byerley, Wiepke Cahn, Guiqing Cai, Dominique Campion, Rita M. Cantor, Vaughan J. Carr, Noa Carrera, Stanley V. Catts, Kimberly D. Chambert, Raymond C.K. Chan, Ronald Y.L. Chen, Eric Y.H. Chen, Wei Cheng, Eric F.C. Cheung, Siow Ann Chong, C. Robert Cloninger, David Cohen, Nadine Cohen, Paul Cormican, Nick Craddock, 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, Naser Durmishi, Peter Eichhammer, Johan Eriksson, Valentina Escott-Price, Laurent Essioux, Ayman H. Fanous, Martilias S. Farrell, Josef Frank, Lude Franke, Robert Freedman, Nelson B. Freimer, Marion Friedl, Joseph I. Friedman, Menachem Fromer, Lyudmila Georgieva, Elliot S. Gershon, Ina Giegling, Paola Giusti-Rodrguez, Stephanie Godard, Jacqueline I. Goldstein, Vera Golimbet, Srihari Gopal, Jacob Gratten, Jakob Grove, Lieuwe de Haan, Christian Hammer, 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, Masashi Ikeda, Inge Joa, Antonio Julia, Rene S. Kahn, Luba Kalaydjieva, Sena Karachanak-Yankova, Juha Karjalainen, David Kavanagh, Matthew C. Keller, Brian J. Kelly, James L. Kennedy, Andrey Khrunin, Yunjung Kim, Janis Klovins, James A. Knowles, Bettina Konte, Vaidutis Kucinskas, Zita Ausrele Kucinskiene, Hana Kuzelova-Ptackova, Anna K. Kahler, Claudine Laurent, Jimmy Lee Chee Keong, S. Hong Lee, Sophie E. Legge, Bernard Lerer, Miaoxin Li, Tao Li, Kung-Yee Liang, Jeffrey Lieberman, Svetlana Limborska, Carmel M. Loughland, Jan Lubinski, Jouko Lnnqvist, Milan Macek, Patrik K.E. Magnusson, Brion S. Maher, Wolfgang Maier, Jacques Mallet, Sara Marsal, Manuel Mattheisen, Morten Mattingsdal, Robert W. McCarley, Colm McDonald, Andrew M. McIntosh, Sandra Meier, Carin J. Meijer, Bela Melegh, Ingrid Melle, Raquelle I. Mesholam-Gately, Andres Metspalu, Patricia T. Michie, Lili Milani, Vihra Milanova, Younes Mokrab, Derek W. Morris, Ole Mors, Preben B. Mortensen, Kieran C. Murphy, Robin M. Murray, Inez Myin-Germeys, Bertram Mller-Myhsok, Mari Nelis, Igor Nenadic, Deborah A. Nertney, Gerald Nestadt, Kristin K. Nicodemus, Liene Nikitina-Zake, Laura Nisenbaum, Annelie Nordin, Eadbhard O’Callaghan, Colm O’Dushlaine, F. Anthony O’Neill, Sang-Yun Oh, Ann Olincy, Line Olsen, Jim Van Os, Christos Pantelis, George N. Papadimitriou, Sergi Papiol, Elena Parkhomenko, Michele T. Pato, Tiina Paunio, Milica Pejovic-Milovancevic, Diana O. Perkins, Olli Pietilinen, 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, Chris C.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 Sderman, Srinivas Thirumalai, Draga Toncheva, Paul A. Tooney, 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 H.M. Wong, Brandon K. Wormley, Jing Qin Wu, Hualin Simon Xi, Clement C. Zai, Xuebin Zheng, Fritz Zimprich, Naomi R. Wray, Kari Stefansson, Rolf Adolfsson, Ole A. Andreassen, Douglas H.R. Blackwood, Elvira Bramon, Joseph D. Buxbaum, Anders D. Børglum, Sven Cichon, Ariel Darvasi, Enrico Domenici, Hannelore Ehrenreich, Tonu Esko, Pablo V. Gejman, Michael Gill, Hugh Gurling, Christina M. Hultman, Nakao Iwata, Assen V. Jablensky, Erik G. Jonsson, 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, Bryan J. Mowry, Markus M. Nthen, 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, David J. Hunter, Muriel Adank, Habibul Ahsan, Kristiina Aittomäki, Laura Baglietto, Sonja Berndt, Carl Blomquist, Federico Canzian, Jenny Chang-Claude, Stephen J. Chanock, Laura Crisponi, Kamila Czene, Norbert Dahmen, Isabel dos Santos Silva, Douglas Easton, A. Heather Eliassen, Jonine Figueroa, Olivia Fletcher, Montserrat Garcia-Closas, Mia M. Gaudet, Lorna Gibson, Christopher A. Haiman, Per Hall, Aditi Hazra, Rebecca Hein, Brian E. Henderson, Albert Hofman, John L. Hopper, Astrid Irwanto, Mattias Johansson, Rudolf Kaaks, Muhammad G. Kibriya, Peter Lichtner, Eiliv Lund, Enes Makalic, Alfons Meindl, Hanne Meijers-Heijboer, Bertram Müller-Myhsok, Taru A. Muranen, Heli Nevanlinna, Petra H. Peeters, Julian Peto, Ross L. Prentice, Nazneen Rahman, María José Sánchez, Daniel F. Schmidt, Rita K. Schmutzler, Melissa C. Southey, Ruth Travis, Clare Turnbull, Andre G. Uitterlinden, Rob B. van der Luijt, Quinten Waisfisz, Zhaoming Wang, Alice S. Whittemore, Rose Yang, Wei Zheng, ANS - Amsterdam Neuroscience, Adult Psychiatry, Other departments, CCA -Cancer Center Amsterdam, ARD - Amsterdam Reproduction and Development, Human Genetics, Grove, Jakob, Complex Trait Genetics, Neuroscience Campus Amsterdam - Neurobiology of Mental Health, Vilhjalmsson, Bjarni J, Yang, Jian, Finucane, Hilary K, Gusev, Alexander, Lee, SH, Price, Alkes L, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) study, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) Study, Psychosis Endophenotype International Consortium, Wellcome Trust Case Control Consortium, Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON), Human genetics, NCA - Brain mechanisms in health and disease, CCA - Oncogenesis, CCA - Quality of life, CCA - Cancer biology and immunology, Psychiatry, Department of Technology and Operations Management, Department of Organisation and Personnel Management, Child and Adolescent Psychiatry / Psychology, Clinical Genetics, Cell biology, and Internal Medicine

Subjects
Multifactorial Inheritance, Linkage disequilibrium, Complex disease, heritability, Bioinformatics, Medical and Health Sciences, Linkage Disequilibrium, 0302 clinical medicine, Theoretical, External reference, Models, Statistics, GWAS, Genetics(clinical), Genetics (clinical), Mathematics, Genetics & Heredity, Schizophrenia Working Group of the Psychiatric Genomics Consortium, 0303 health sciences, Single Nucleotide, Biological Sciences, Serious Mental Illness, Prognosis, Thresholding, Regression, Mental Health, Phenotype, polygenic risk scores, Mixed model, Multiple Sclerosis, Genotype, Quantitative Trait Loci, polygenic risk score, schizophrenia, GWAS, Discovery, Quantitative trait locus, Biology, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Genetics, Humans, p-value, Pruning (decision trees), Polymorphism, Genome-Wide Association Study, Schizophrenia, Models, Theoretical, 030304 developmental biology, genome-wide association study, and Risk of Inherited Variants in Breast Cancer (DRIVE) study, Brain Disorders, Data set, schizophrenia, Sample size determination, polygenic risk score, Polygenic risk score, 030217 neurology & neurosurgery, linkage disequilibrium
Abstract

Polygenic risk scores have shown great promise in predicting complex disease risk and will become more accurate as training sample sizes increase. The standard approach for calculating risk scores involves linkage disequilibrium (LD)-based marker pruning and applying a p value threshold to association statistics, but this discards information and can reduce predictive accuracy. We introduce LDpred, a method that infers the posterior mean effect size of each marker by using a prior on effect sizes and LD information from an external reference panel. Theory and simulations show that LDpred outperforms the approach of pruning followed by thresholding, particularly at large sample sizes. Accordingly, predicted R-2 increased from 20.1% to 25.3% in a large schizophrenia dataset and from 9.8% to 12.0% in a large multiple sclerosis dataset. A similar relative improvement in accuracy was observed for three additional large disease datasets and for non-European schizophrenia samples. The advantage of LDpred over existing methods will grow as sample sizes increase. Refereed/Peer-reviewed

Published
2015

39. Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis

Author

Alan J. Cross, Leonardo Collado Torres, Hualin S. Xi, Richard E. Straub, Nicholas J. Brandon, Tony Kam-Thong, Joel E. Kleinman, Joo Heon Shin, Carlo Colantuoni, Yuan Gao, Brady J. Maher, Thomas M. Hyde, Jeffrey T. Leek, Daniel R. Weinberger, Jie Quan, Ran Tao, Qiang Chen, Amy Deep-Soboslay, William S Ulrich, and Andrew E. Jaffe

Subjects
0301 basic medicine, Adult, Male, Adolescent, Genotype, Sequence analysis, Prefrontal Cortex, Biology, Polymorphism, Single Nucleotide, Article, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, RNA degradation, Pregnancy, Genetic variation, Databases, Genetic, medicine, Humans, Genetic Predisposition to Disease, Child, Gene, Genetic association, Genetics, Regulation of gene expression, human postmortem brain, Sequence Analysis, RNA, General Neuroscience, Gene Expression Regulation, Developmental, Genetic Variation, Infant, RNA sequencing, medicine.disease, 3. Good health, schizophrenia, 030104 developmental biology, Schizophrenia, differential expression analysis, Child, Preschool, Expression quantitative trait loci, Chronic Disease, Female, Autopsy, Neuroscience, functional genomics, 030217 neurology & neurosurgery
Abstract

Summary: GWAS have identified 108 schizophrenia risk loci, but risk mechanisms for individual loci are largely unknown. Using developmental, genetic, and illness-based RNA sequencing expression analysis in human brain, we characterized the human brain transcriptome around these loci and found enrichment for developmentally regulated genes with novel examples of shifting isoform usage across pre- and post-natal life. Across the genome, we found widespread expression quantitative trait loci (eQTLs), including many with transcript specificity and previously unannotated sequence that were independently replicated. We leveraged this general eQTL database to show that 48.1% of risk variants for schizophrenia associated with nearby expression. We lastly found 237 genes significantly differentially expressed between patients and controls which replicated in an independent dataset, implicated synaptic processes and were strongly regulated in early development. These findings together offer genetic- and diagnosis-related targets for better modeling schizophrenia risk. This publicly-available resource is available at: http://eqtl.brainseq.org/phase1

Published
2017

40. Estimation of Genetic Correlation via Linkage Disequilibrium Score Regression and Genomic Restricted Maximum Likelihood

Author

Guiyan Ni, Gerhard Moser, Naomi R. Wray, S. Hong Lee, Stephan Ripke, Benjamin M. Neale, Aiden Corvin, James T.R. Walters, Kai-How Farh, Peter A. Holmans, Phil Lee, Brendan Bulik-Sullivan, David A. Collier, Hailiang Huang, Tune H. Pers, Ingrid Agartz, Esben Agerbo, Margot Albus, Madeline Alexander, Farooq Amin, Silviu A. Bacanu, Martin Begemann, Richard A. Belliveau, Judit Bene, Sarah E. Bergen, Elizabeth Bevilacqua, Tim B. Bigdeli, Donald W. Black, Richard Bruggeman, Nancy G. Buccola, Randy L. Buckner, William Byerley, Wiepke Cahn, Guiqing Cai, Dominique Campion, Rita M. Cantor, Vaughan J. Carr, Noa Carrera, Stanley V. Catts, Kimberly D. Chambert, Raymond C.K. Chan, Ronald Y.L. Chen, Eric Y.H. Chen, Wei Cheng, Eric F.C. Cheung, Siow Ann Chong, C. Robert Cloninger, David Cohen, Nadine Cohen, Paul Cormican, Nick Craddock, James J. Crowley, David Curtis, Michael Davidson, Kenneth L. Davis, Franziska Degenhardt, Jurgen Del Favero, Ditte Demontis, Dimitris Dikeos, Timothy Dinan, Srdjan Djurovic, Gary Donohoe, Elodie Drapeau, Jubao Duan, Frank Dudbridge, Naser Durmishi, Peter Eichhammer, Johan Eriksson, Valentina Escott-Price, Laurent Essioux, Ayman H. Fanous, Martilias S. Farrell, Josef Frank, Lude Franke, Robert Freedman, Nelson B. Freimer, Marion Friedl, Joseph I. Friedman, Menachem Fromer, Giulio Genovese, Lyudmila Georgieva, Ina Giegling, Paola Giusti-Rodríguez, Stephanie Godard, Jacqueline I. Goldstein, Vera Golimbet, Srihari Gopal, Jacob Gratten, Lieuwe de Haan, Christian Hammer, 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, Masashi Ikeda, Inge Joa, Antonio Juliá, René S. Kahn, Luba Kalaydjieva, Sena Karachanak-Yankova, Juha Karjalainen, David Kavanagh, Matthew C. Keller, James L. Kennedy, Andrey Khrunin, Yunjung Kim, Janis Klovins, James A. Knowles, Bettina Konte, Vaidutis Kucinskas, Zita Ausrele Kucinskiene, Hana Kuzelova-Ptackova, Anna K. Kähler, Claudine Laurent, Jimmy Lee Chee Keong, Sophie E. Legge, Bernard Lerer, Miaoxin Li, Tao Li, Kung-Yee Liang, Jeffrey Lieberman, Svetlana Limborska, Carmel M. Loughland, Jan Lubinski, Jouko Lönnqvist, Milan Macek, Patrik K.E. Magnusson, Brion S. Maher, Wolfgang Maier, Jacques Mallet, Sara Marsal, Manuel Mattheisen, Morten Mattingsda, Robert W. McCarley, Colm McDonald, Andrew M. McIntosh, Sandra Meier, Carin J. Meijer, Bela Melegh, Ingrid Melle, Raquelle I. Mesholam-Gately, Andres Metspalu, Patricia T. Michie, Lili Milani, Vihra Milanova, Younes Mokrab, Derek W. Morris, Ole Mors, Kieran C. Murphy, Robin M. Murray, Inez Myin-Germeys, Bertram Müller-Myhsok, Mari Nelis, Igor Nenadic, Deborah A. Nertney, Gerald Nestadt, Kristin K. Nicodemus, Liene Nikitina-Zake, Laura Nisenbaum, Annelie Nordin, Eadbhard O’Callaghan, Colm O’Dushlaine, F. Anthony O’Neill, Sang-Yun Oh, Ann Olinc, Line Olsen, Jim Van Os, Christos Pantelis, George N. Papadimitriou, Sergi Papio, Elena Parkhomenko, Michele T. Pato, Tiina Paunio, Milica Pejovic-Milovancevic, Diana O. Perkins, Olli Pietiläinenl, 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, Chris C.A. Spencer, Eli A. Stah, 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 H.M. Wong, Brandon K. Wormley, Hualin Simon Xi, Clement C. Zai, Xuebin Zheng, Fritz Zimprich, Kari Stefansson, Peter M. Visscher, Rolf Adolfsson, Ole A. Andreassen, Douglas H.R. 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. McCarrol, 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 Rietsche, 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, APH - Mental Health, ANS - Complex Trait Genetics, Adult Psychiatry, Ni, Guiyan, Moser, Gerhard, Wray, Naomi R, Lee, S Hong, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Amsterdam Neuroscience - Complex Trait Genetics, Complex Trait Genetics, Clinicum, Department of Psychiatry, and HUS Psychiatry

Subjects
0301 basic medicine, Linkage disequilibrium, Schizophrenia/genetics, INFORMATION, Restricted maximum likelihood, Inheritance Patterns, linkage disequilibrium score regression, Bioinformatics, Medical and Health Sciences, 3124 Neurology and psychiatry, Linkage Disequilibrium, biasedness, 0302 clinical medicine, Statistics, Databases, Genetic, WIDE ASSOCIATION, Genetics(clinical), PARTITIONING HERITABILITY, Genetics (clinical), Genetics & Heredity, education.field_of_study, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Likelihood Functions, Genome, Body Height/genetics, accuracy, Regression analysis, Single Nucleotide, Biological Sciences, Polymorphism, Single Nucleotide/genetics, genetic correlation, Regression, STATISTICS, genomic restricted maximum likelihood, Mental Health, Phenotype, Regression Analysis, COMPLEX HUMAN TRAITS, Single Nucleotide/genetics, Human, Adult, SUSCEPTIBILITY LOCI, Genotype, SNP heritability, body mass index, genome-wide SNPs, height, schizophrenia, Population, Haplotypes/genetics, Biology, Genetic correlation, Polymorphism, Single Nucleotide, 03 medical and health sciences, Databases, Genetic, ddc:570, Report, Genetics, Humans, Linkage Disequilibrium/genetics, Computer Simulation, Polymorphism, education, linkage disequilibrium score regression (LDSC), Genome, Human, Human Genome, genetic architecture, Genetic architecture, Body Height, Brain Disorders, Inheritance Patterns/genetics, BODY-MASS INDEX, 030104 developmental biology, Haplotypes, Sample size determination, Schizophrenia, 3111 Biomedicine, HUMAN HEIGHT, 030217 neurology & neurosurgery
Abstract

J. Lönnqvist on työryhmän Psychiat Genomics Consortium jäsen. Genetic correlation is a key population parameter that describes the shared genetic architecture of complex traits and diseases. It can be estimated by current state-of-art methods, i.e., linkage disequilibrium score regression (LDSC) and genomic restricted maximum likelihood (GREML). The massively reduced computing burden of LDSC compared to GREML makes it an attractive tool, although the accuracy (i.e., magnitude of standard errors) of LDSC estimates has not been thoroughly studied. In simulation, we show that the accuracy of GREML is generally higher than that of LDSC. When there is genetic heterogeneity between the actual sample and reference data from which LD scores are estimated, the accuracy of LDSC decreases further. In real data analyses estimating the genetic correlation between schizophrenia (SCZ) and body mass index, we show that GREML estimates based on similar to 150,000 individuals give a higher accuracy than LDSC estimates based on similar to 400,000 individuals (from combinedmeta-data). A GREML genomic partitioning analysis reveals that the genetic correlation between SCZ and height is significantly negative for regulatory regions, which whole genome or LDSC approach has less power to detect. We conclude that LDSC estimates should be carefully interpreted as there can be uncertainty about homogeneity among combined meta-datasets. We suggest that any interesting findings from massive LDSC analysis for a large number of complex traits should be followed up, where possible, with more detailed analyses with GREML methods, even if sample sizes are lesser.

Published
2017

41. Age at first birth in women is genetically associated with increased risk of schizophrenia

Author

Fritz Zimprich, Manuel Mattheisen, Edward M. Scolnick, Ayman H. Fanous, Henrik B. Rasmussen, Steven A. McCarroll, Ingrid Agartz, Carmel M. Loughland, Aiden Corvin, Ann Olincy, Anders D. Børglum, F. Anthony O'Neill, T. Scott Stroup, Elizabeth Bevilacqua, Sandra Meier, Ulrich Schall, Jouko Lönnqvist, Jianxin Shi, C. Robert Cloninger, Judit Bene, Veikko Salomaa, George N. Papadimitriou, Milica Pejovic-Milovancevic, Béla Melegh, Kari Stefansson, Brendan Bulik-Sullivan, Janis Klovins, Enrico Domenici, Sibylle G. Schwab, Dai Wang, Assen Jablensky, Mari Nelis, Sang Yun Oh, Peter Holmans, Aaron R. Wolen, Hualin Simon Xi, Eric Strengman, Bryan J. Mowry, Michael Gill, Kung Yee Liang, William Byerley, Rolf Adolfsson, Hugh Gurling, Joseph I. Friedman, Andrew Pocklington, Brien P. Riley, Engilbert Sigurdsson, Benjamin M. Neale, Miaoxin Li, Michael Davidson, Bernard Lerer, Michele T. Pato, Xuebin Zheng, Patrick F. Sullivan, Frans Henskens, Madeline Alexander, Andrew M. McIntosh, Inez Myin-Germeys, Draga Toncheva, Liene Nikitina-Zake, Kenneth S. Kendler, Carin J. Meijer, Robin M. Murray, Richard E. Straub, Ann E. Pulver, Menachem Fromer, Derek W. Morris, Douglas M. Ruderfer, Mythily Subramaniam, Paul Cormican, Lyudmila Georgieva, Giulio Genovese, Brion S. Maher, Stanley V. Catts, David St Clair, Robert W. McCarley, David Cohen, Nancy G. Buccola, Dan Rujescu, Carlos N. Pato, Kristin K. Nicodemus, Josef Frank, Claudine Laurent, Dominique Campion, Guiyan Ni, James L. Kennedy, Sena Karachanak-Yankova, Nicholas John Craddock, Peter M. Visscher, Valentina Escott-Price, Jeffrey A. Lieberman, Deborah A. Nertney, Bertram Müller-Myhsok, Marcella Rietschel, Dimitris Dikeos, Stephanie Godard, Stephanie Williams, Andres Metspalu, John L. Waddington, Sophie E. Legge, Roel A. Ophoff, Jonathan Pimm, Richard Bruggeman, Tim B. Bigdeli, Gerald Nestadt, Mark Weiser, Kieran C. Murphy, Eric F.C. Cheung, Kang Sim, Jordan W. Smoller, David J. Kavanagh, Inge Joa, Jens R. Wendland, Thomas G. Schulze, Richard A. Belliveau, Sarah E. Bergen, Ditte Demontis, David Curtis, Todd Lencz, Danielle Posthuma, René S. Kahn, Lili Milani, Randy L. Buckner, Jianjun Liu, Petr Slominsky, Wiepke Cahn, Hana Kuzelova-Ptackova, Sergi Papiol, Tune H. Pers, Stephan Ripke, Rita M. Cantor, Ariel Darvasi, Christina M. Hultman, Larry J. Seidman, Eli A. Stahl, David A. Collier, Michael Conlon O'Donovan, Svetlana A. Limborska, James T.R. Walters, Farooq Amin, Noa Carrera, Ronald Y.L. Chen, Pablo V. Gejman, Joel N. Hirschhorn, Zita Ausrele Kucinskiene, Michael John Owen, Ina Giegling, Stephanie H. Witt, Timothy G. Dinan, Margot Albus, Wei Cheng, Marian L. Hamshere, Markus M. Nöthen, Thomas Werge, Guiqing Cai, Raquelle I. Mesholam-Gately, Annette M. Hartmann, Ingrid Melle, Ole A. Andreassen, Preben Bo Mortensen, Hannelore Ehrenreich, Tiina Paunio, James A. Knowles, Pak C. Sham, Marion Friedl, Teimuraz Silagadze, Dermot Walsh, Emily H. M. Wong, Igor Nenadic, Matthew C. Keller, John Powell, Naomi R. Wray, Patricia T. Michie, Bradley T. Webb, Lude Franke, Mark Hansen, Masashi Ikeda, Sven Cichon, Elvira Bramon, Frank Dudbridge, Erik G. Jönsson, Annelie Nordin, Wolfgang Maier, Peter Eichhammer, Christian R. Schubert, J. Mallet, Jacob Gratten, Andrey Khrunin, Jacqueline I. Goldstein, Panos Roussos, Pamela Sklar, Diana O. Perkins, Srdjan Djurovic, Phil Lee, Elodie Drapeau, Douglas F. Levinson, Nadine Cohen, Luba Kalaydjieva, Brandon Wormley, Tao Li, Tõnu Esko, Alexander Richards, Srihari Gopal, Jubao Duan, Anil K. Malhotra, Elisabeth Stögmann, Gary Donohoe, Kimberly Chambert, Sara Marsal, Hreinn Stefansson, Jo Knight, Ole Mors, Per Hoffmann, Dieter B. Wildenauer, James J. Crowley, Srinivas Thirumalai, Vahram Haroutunian, A. Hofman, Hailiang Huang, Thomas Hansen, Daniel R. Weinberger, Andrew McQuillin, Vaughan J. Carr, Vaidutis Kučinskas, Jimmy Lee Chee Keong, Digby Quested, Aarno Palotie, Robert Freedman, Hon-Cheong So, Jennifer L. Moran, Donald W. Black, Mark Reimers, Abraham Reichenberg, Jurgen Del Favero, Paola Giusti-Rodríguez, Tracey L. Petryshen, Olli Pietiläinen, Franziska Degenhardt, Laurent Essioux, Esben Agerbo, Qiang Wang, Jana Strohmaier, Siow Ann Chong, Johan G. Eriksson, Martin Begemann, Younes Mokrab, Colm McDonald, Silviu Alin Bacanu, Martilias S. Farrell, Christos Pantelis, Kai How Farh, Line Olsen, Naser Durmishi, Antonio Julià, Stefan Herms, Qingqin S. Li, Bettina Konte, George Kirov, Rodney J. Scott, Nelson B. Freimer, Mads V. Hollegaard, Shaun Purcell, Erik Söderman, Dragan M. Svrakic, Patrik K. E. Magnusson, Douglas Blackwood, Jin P. Szatkiewicz, Sang Hong Lee, Yunjung Kim, Colm O'Dushlaine, Morten Mattingsdal, Jim van Os, Sarah Tosato, Milan Macek, Joshua L. Roffman, Jan Lubinski, Eadbhard O'Callaghan, Juha Karjalainen, Vera Golimbet, Anna K. Kähler, Clement C. Zai, Nigel Williams, Joseph D. Buxbaum, Laura Nisenbaum, Eric Y.H. Chen, David M. Hougaard, Jaana Suvisaari, Chris C. A. Spencer, Alan R. Sanders, Alkes L. Price, Vihra Milanova, Juha Veijola, Christian Hammer, Raymond C.K. Chan, Stacy Steinberg, Nakao Iwata, Jeremy M. Silverman, Mark J. Daly, Elena Parkhomenko, Kenneth L. Davis, Lieuwe de Haan, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Human genetics, Amsterdam Neuroscience - Complex Trait Genetics, Amsterdam Reproduction & Development (AR&D), Kučinskas, Vaidutis, Kučinskienė, Zita Aušrelė, Ni, Guiyan, Gratten, Jacob, Wray, Naomi R, Lee, Sang Hong, Germeys, Inez, Complex Trait Genetics, Háskóli Íslands, University of Iceland, Child and Adolescent Psychiatry / Psychology, Research Programs Unit, Diabetes and Obesity Research Program, Johan Eriksson / Principal Investigator, Department of General Practice and Primary Health Care, University Management, Department of Psychiatry, Center for Population, Health and Society, Department of Public Health, Centre of Excellence in Complex Disease Genetics, Research Programme of Molecular Medicine, Aarno Palotie / Principal Investigator, Institute for Molecular Medicine Finland, and Genomics of Neurological and Neuropsychiatric Disorders

Subjects
0301 basic medicine, Multifactorial Inheritance, PATERNAL-AGE, 3124 Neurology and psychiatry, COMMON SNPS, fluids and secretions, 0302 clinical medicine, CHILD, Risk Factors, Pregnancy, 2.1 Biological and endogenous factors, Medicine, Aetiology, Pediatric, PROPORTION, Schizophrenia Working Group of the Psychiatric Genomics Consortium, 0303 health sciences, Multidisciplinary, PSYCHIATRIC-DISORDERS, BIPOLAR DISORDER, Biobank, 3. Good health, AFB, Mental Health, Schizophrenia, Female, Erfðarannsóknir, Psychosocial, TRAITS, schizophrenia, age at birth, AFB, Maternal Age, Adult, age at first birth in women, genetic association, Offspring, Science, Genetic correlation, Article, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Geðklofi, Genetics, age at birth, Humans, Genetic Predisposition to Disease, Bipolar disorder, General, Biology, Genetic association study, 030304 developmental biology, Genetic association, business.industry, Genetic heterogeneity, Prevention, average aged parents, Parturition, SCORE REGRESSION, bacterial infections and mycoses, medicine.disease, Mental health, Brain Disorders, respiratory tract diseases, schizophrenia, Good Health and Well Being, 030104 developmental biology, younger and older parents, DE-NOVO MUTATIONS, ddc:000, Human medicine, business, 030217 neurology & neurosurgery, Demography
Abstract

Publisher's version (útgefin grein), Previous studies have shown an increased risk for mental health problems in children born to both younger and older parents compared to children of average-aged parents. We previously used a novel design to reveal a latent mechanism of genetic association between schizophrenia and age at first birth in women (AFB). Here, we use independent data from the UK Biobank (N = 38,892) to replicate the finding of an association between predicted genetic risk of schizophrenia and AFB in women, and to estimate the genetic correlation between schizophrenia and AFB in women stratified into younger and older groups. We find evidence for an association between predicted genetic risk of schizophrenia and AFB in women (P-value = 1.12E-05), and we show genetic heterogeneity between younger and older AFB groups (P-value = 3.45E-03). The genetic correlation between schizophrenia and AFB in the younger AFB group is −0.16 (SE = 0.04) while that between schizophrenia and AFB in the older AFB group is 0.14 (SE = 0.08). Our results suggest that early, and perhaps also late, age at first birth in women is associated with increased genetic risk for schizophrenia in the UK Biobank sample. These findings contribute new insights into factors contributing to the complex bio-social risk architecture underpinning the association between parental age and offspring mental health., This research is supported by the Australian National Health and Medical Research Council (1080157, 1087889, 1103418, 1127440), and the Australian Research Council (DP160102126, FT160100229). This research has been conducted using the UK Biobank Resource. UK Biobank (http://www.ukbiobank.ac.uk) Research Ethics Committee (REC) approval number is 11/NW/0382. Our reference number approved by UK Biobank is 14575.

Published
2017

42. GWAS meta-analysis (N=279,930) identifies new genes and functional links to intelligence

Author

Lene Christiansen, Robert M. Bilder, Katherine E. Burdick, Tinca J. C. Polderman, Ana B. Muñoz-Manchado, Gary Donohoe, Matthew C. Keller, Stephan Ripke, Anil K. Malhotra, Delilah Zabaneh, Andrea Christoforou, Matthew A. Scult, Nikolaos Smyrnis, Scott I. Vrieze, Fred W. Sabb, Stella G. Giakoumaki, Nathan G. Skene, Ole A. Andreassen, Nicholas G. Martin, Jari Lahti, Anna C. Need, Philip R. Jansen, Todd Lencz, Emma Knowles, Peter B. Barr, Pamela DeRosse, Russell A. Poldrack, Henning Tiemeier, Sten Linnarsson, Hannah Young, Emily Drabant Conley, Dan E. Arking, Jin Yu, Grant W. Montgomery, Danielle Posthuma, Dwight Dickinson, Elizabeth T. Cirulli, Gerome Breen, Gunter Schumann, Michael Gill, Erin Burke Quinlan, Robert Plomin, Kyoko Watanabe, Joey W. Trampush, John M. Starr, Katri Räikkönen, Narelle K. Hansell, Eliza Congdon, Olav B. Smeland, Jens Hjerling-Leffler, Richard E. Straub, Aiden Corvin, Chandra A. Reynolds, Astri J. Lundervold, Bradley T. Webb, Gonçalo R. Abecasis, Jonathan R. I. Coleman, Srdjan Djurovic, Margaret J. Wright, Kjetil Sundet, Ivar Reinvang, Robert Karlsson, Deborah C. Koltai, Ina Giegling, Alex Hatzimanolis, David C. Liewald, William Ollier, Sophie van der Sluis, Edythe D. London, Tyrone D. Cannon, Thomas Espeseth, M. Arfan Ikram, Ian J. Deary, Christiaan de Leeuw, Daniel R. Weinberger, Neil Pendleton, Ornit Chiba-Falek, Jakob Kaminski, Danielle M. Dick, Panos Bitsios, Nikos C. Stefanis, Tonya White, Bettina Konte, Ida K. Karlsson, Mats Nagel, Derek W. Morris, Anke R. Hammerschlag, Swapnil Awasthi, Antony Payton, Julien Bryois, Nelson A. Freimer, Nancy L. Pedersen, Panos Roussos, Andreas Heinz, Johan G. Eriksson, Marianne Nygaard, Birgit Debrabant, Aarno Palotie, Elisabeth Widen, Aristotle N. Voineskos, Patrick Sullivan, Ingrid Melle, Dan Rujescu, Vidar M. Steen, Eva Krapohl, Katrina L. Grasby, Max Lam, Stephanie Le Hellard, Kenneth S. Kendler, Jeanne E. Savage, Sarah E. Medland, Sven Stringer, David C. Glahn, Gail Davies, Ahmad R. Hariri, Sara Hägg, and Dimitrios Avramopoulos

Subjects
Genetics, Nonsynonymous substitution, 0303 health sciences, Genome-wide association study, Biology, 03 medical and health sciences, 0302 clinical medicine, Pleiotropy, Mendelian randomization, Expression quantitative trait loci, Neuron differentiation, Gene, 030217 neurology & neurosurgery, 030304 developmental biology, Genetic association
Abstract

Intelligence is highly heritable1 and a major determinant of human health and well-being2. Recent genome-wide meta-analyses have identified 24 genomic loci linked to intelligence3–7, but much about its genetic underpinnings remains to be discovered. Here, we present the largest genetic association study of intelligence to date (N=279,930), identifying 206 genomic loci (191 novel) and implicating 1,041 genes (963 novel) via positional mapping, expression quantitative trait locus (eQTL) mapping, chromatin interaction mapping, and gene-based association analysis. We find enrichment of genetic effects in conserved and coding regions and identify 89 nonsynonymous exonic variants. Associated genes are strongly expressed in the brain and specifically in striatal medium spiny neurons and cortical and hippocampal pyramidal neurons. Gene-set analyses implicate pathways related to neurogenesis, neuron differentiation and synaptic structure. We confirm previous strong genetic correlations with several neuropsychiatric disorders, and Mendelian Randomization results suggest protective effects of intelligence for Alzheimer’s dementia and ADHD, and bidirectional causation with strong pleiotropy for schizophrenia. These results are a major step forward in understanding the neurobiology of intelligence as well as genetically associated neuropsychiatric traits.

Published
2017
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43. Convergence of placenta biology and genetic risk for schizophrenia

Author

Giancarlo Maddalena, Marina Mitjans, Annamaria Porcelli, Joshua F. Robinson, Jan Seidel, Martin Begemann, Ryota Hashimoto, Dan Rujescu, Qiang Chen, Alessandro Bertolino, Giuseppe Blasi, Karen F. Berman, Stefano Marenco, Carlo Colantuoni, Hannelore Ehrenreich, Andrew E. Jaffe, Daniel R. Weinberger, Gianluca Ursini, Michael F. Egan, Emily G. Hamilton, Giovanna Punzi, Hidenaga Yanamori, and Richard E. Straub

Subjects
0301 basic medicine, Male, Multifactorial Inheritance, Offspring, Placenta, Context (language use), Genome-wide association study, Biology, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Life Change Events, 03 medical and health sciences, 0302 clinical medicine, Pregnancy, Risk Factors, Cellular stress response, medicine, Humans, Genetic Predisposition to Disease, Gene, Regulation of gene expression, Genetics, Sex Characteristics, Genome, Human, Case-control study, General Medicine, medicine.disease, 030104 developmental biology, Gene Expression Regulation, Schizophrenia, Case-Control Studies, Female, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

Defining the environmental context in which genes enhance disease susceptibility can provide insight into the pathogenesis of complex disorders. We report that the intra-uterine environment modulates the association of schizophrenia with genomic risk (in this study, genome-wide association study–derived polygenic risk scores (PRSs)). In independent samples from the United States, Italy, and Germany, the liability of schizophrenia explained by PRS is more than five times greater in the presence of early-life complications (ELCs) compared with their absence. Patients with ELC histories have significantly higher PRS than patients without ELC histories, which is confirmed in additional samples from Germany and Japan. The gene set composed of schizophrenia loci that interact with ELCs is highly expressed in placenta, is differentially expressed in placentae from complicated in comparison with normal pregnancies, and is differentially upregulated in placentae from male compared with female offspring. Pathway analyses reveal that genes driving the PRS-ELC interaction are involved in cellular stress response; genes that do not drive such interaction implicate orthogonal biological processes (for example, synaptic function). We conclude that a subset of the most significant genetic variants associated with schizophrenia converge on a developmental trajectory sensitive to events that affect the placental response to stress, which may offer insights into sex biases and primary prevention.

Published
2017

44. Ninety-nine independent genetic loci influencing general cognitive function include genes associated with brain health and structure (N = 280,360)

Author

Nancy L. Pedersen, John M. Starr, Kjetil Sundet, Qiong Yang, Nicole A. Kochan, Beverly Gwen Windham, Ida K. Karlsson, Daniel E. Gustavson, Jerome I. Rotter, Antony Payton, M. Arfan Ikram, Alison D. Murray, Edith Hofer, Ozren Polasek, Markus Leber, Will Longstreth, Stephanie Le Hellard, Peter W. Schofield, Raha Pazoki, Janie Corley, Max Lam, Deborah K. Attix, Hieab H.H. Adams, Tobias Luck, Ian J. Deary, Panos Roussos, Amelia A. Assareh, Katja Petrovic, Dwight Dickinson, Elizabeth T. Cirulli, Thomas Espeseth, Richard J. Rose, Annette L. Fitzpatrick, Robert M. Bilder, Rodney J. Scott, Katherine E. Burdick, William S. Kremen, Christophe Tzourio, Richard E. Straub, Thomas H. Mosley, Michael Griswold, Ulman Lindenberger, Peter R. Schofield, Riccardo E. Marioni, Stéphanie Debette, Jennifer A. Smith, M. Kamran Ikram, Pamela DeRosse, Russell A. Poldrack, Teemu Palviainen, Panos Bitsios, Nikos C. Stefanis, Anu Loukola, Nikolaos Smyrnis, Todd Lencz, Michelle Luciano, Robert Karlsson, Bettina Konte, Dan Rujescu, Mika Kähönen, James F. Wilson, Steven T. Turner, David A. Bennett, Jingyun Yang, Cornelia M. van Duijn, David S. Knopman, Harry Campbell, R. F. Gottesman, Vidar M. Steen, Nicola J. Armstrong, Alfredo Ramirez, Ina Giegling, Jari Lahti, Marisa Koini, Tyrone D. Cannon, Gerardo Heiss, Ian Ford, Vilmundur Gudnason, Alex Hatzimanolis, Joshua C. Bis, Albert V. Smith, David Ames, Jan Bressler, Catriona L. K. Barnes, Emily Drabant Conley, Raymond Noordam, Ornit Chiba-Falek, Michael Gill, Simone Reppermund, Katri Räikkönen, Christopher Oldmeadow, Kent D. Taylor, Holger Wagner, Claudia L. Satizabal, Chandra A. Reynolds, Tian Liu, Daniel R. Weinberger, Neil Pendleton, Scott D. Gordon, Eric Boerwinkle, Saskia P. Hagenaars, Andrew M. McIntosh, Igor Rudan, Joey W. Trampush, John Attia, Michael Wagner, K. Hoyan Wen, Judith A. Okely, Aristotle N. Voineskos, Patricia A. Boyle, Danielle M. Dick, Anna C. Need, Markus Scholz, Luca Kleineidam, Aiden Corvin, Ingrid Melle, Margaret J. Wright, Helena Schmidt, Leo-Pekka Lyytikäinen, Natalie Terzikhan, Stuart J. Ritchie, He Gao, Anne C. Böhmer, Dan E. Arking, Narelle K. Hansell, Nicholas G. Martin, Fred W. Sabb, Nathan A. Gillespie, Evangelos Evangelou, Bruce M. Psaty, Anders Lundquist, Oscar L. Lopez, Emma Knowles, Matthew C. Keller, Henry Brodaty, Julian N. Trollor, Gary Donohoe, Ivar Reinvang, Ari Ahola-Olli, Tamara B. Harris, André G. Uitterlinden, David R. Weir, Abbas Dehghan, Sarah E. Harris, P. Eline Slagboom, Chloe Fawns-Ritchie, Paul Elliott, William Ollier, Edythe D. London, Anders M. Dale, Jaakko Kaprio, Catharine R. Gale, Karen A. Mather, Aarno Palotie, Stella G. Giakoumaki, Sven J. van der Lee, Jeannette Simino, Elisabeth Widen, Teresa Lee, Sudheer Giddaluru, Anil K. Malhotra, Philippe Amouyel, Caroline Hayward, Shuo Li, Goran Papenberg, Steffi G. Riedel-Heller, Wei Zhao, Nelson A. Freimer, Simon R. Cox, Yasaman Saba, Andrea Christoforou, Johan G. Eriksson, Eliza Congdon, David J. Porteous, Matthew A. Scult, Eero Vuoksimaa, Veronique Vitart, Derek W. Morris, Sharon L.R. Kardia, Elizabeth G. Holliday, Peter K. Joshi, Suvi P. Rovio, Astri J. Lundervold, J. Wouter Jukema, Aicha Soumare, Stella Trompet, Annette M. Hartmann, Ole A. Andreassen, Erin B. Ware, Matthias Schmid, Perminder S. Sachdev, Grant W. Montgomery, Lars Bertram, Philip L. De Jager, Olli T. Raitakari, Terho Lehtimäki, Arno Villringer, Srdjan Djurovic, David C. Liewald, Sudha Seshadri, Gail Davies, Ahmad R. Hariri, Sara Hägg, Lars Nyberg, Dimitrios Avramopoulos, Muralidharan Sargurupremraj, W. David Hill, Shu-Chen Li, Leonie Weinhold, David J. Stott, David C. Glahn, John B.J. Kwok, Ioanna Tzoulaki, Reinhold Schmidt, Najaf Amin, Lenore J. Launer, Jin Yu, Jessica D. Faul, Adele M. Taylor, Anbupalam Thalamuthu, and Alison Pattie

Subjects
Genetics, 0303 health sciences, media_common.quotation_subject, Longevity, Genetic data, Cognition, Heritability, Significant snps, Biology, Biobank, 03 medical and health sciences, 0302 clinical medicine, Trait, Gene, 030217 neurology & neurosurgery, 030304 developmental biology, media_common
Abstract

General cognitive function is a prominent human trait associated with many important life outcomes1,2, including longevity3. The substantial heritability of general cognitive function is known to be polygenic, but it has had little explication in terms of the contributing genetic variants4,5,6. Here, we combined cognitive and genetic data from the CHARGE and COGENT consortia, and UK Biobank (total N=280,360; age range = 16 to 102). We found 9,714 genome-wide significant SNPs (P−8) in 99 independent loci. Most showed clear evidence of functional importance. Among many novel genes associated with general cognitive function wereSGCZ,ATXN1,MAPT,AUTS2, andP2RY6. Within the novel genetic loci were variants associated with neurodegenerative disorders, neurodevelopmental disorders, physical and psychiatric illnesses, brain structure, and BMI. Gene-based analyses found 536 genes significantly associated with general cognitive function; many were highly expressed in the brain, and associated with neurogenesis and dendrite gene sets. Genetic association results predicted up to 4% of general cognitive function variance in independent samples. There was significant genetic overlap between general cognitive function and information processing speed, as well as many health variables including longevity.

Published
2017

45. Placental gene expression mediates the interaction between obstetrical history and genetic risk for schizophrenia

Author

Giancarlo Maddalena, Martin Begemann, Annamaria Porcelli, Giovanna Punzi, Jan Seidel, Giuseppe Blasi, Hannelore Ehrenreich, Karen F. Berman, Daniel R. Weinberger, Andrew E. Jaffe, Emily G. Hamilton, Michael F. Egan, Hidenaga Yanamori, Joshua F. Robinson, Qiang Chen, Carlo Colantuoni, Dan Rujescu, Alessandro Bertolino, Stefano Marenco, Marina Mitjans, Gianluca Ursini, Ryota Hashimoto, and Richard E. Straub

Subjects
Genetics, 0303 health sciences, Offspring, Placentation, Context (language use), Genome-wide association study, Biology, medicine.disease, 3. Good health, Pathogenesis, 03 medical and health sciences, 0302 clinical medicine, medicine.anatomical_structure, Schizophrenia, Placenta, medicine, Gene, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

Defining the environmental context in which genes enhance susceptibility can provide insight into the pathogenesis of complex disorders, like schizophrenia. Here we show that the intrauterine and perinatal environment modulates the association of schizophrenia with genomic risk, as measured with polygenic risk scores (PRS) based primarily on GWAS significant variants. Genomic risk interacts with intrauterine and perinatal complications (Early Life Complications, ELCs) in each of three independent samples from USA, Italy and Germany (overall n= 1693, p= 6e-05). In each sample, the liability of schizophrenia explained by PRS is nominally more than five times greater in the presence of a history of ELCs compared with its absence. In each sample, patients with positive ELC histories have higher PRS than patients without ELCs, which is further confirmed in two additional patient samples from Germany and Japan (overall n=2038, p= 1e-04). The gene set based on the schizophrenia loci interacting with ELCs is highly expressed in multiple placental compartments and dynamically regulated in placenta from complicated in comparison with normal pregnancies. The same genes are differentially up-regulated in placentae from male compared with female offspring. The interaction between genomic risk and ELCs is mainly driven by GWAS significant loci enriched for genes highly expressed in the various placenta samples. Molecular pathway analyses based on the genes not driving this interaction reflect previous analyses about schizophrenia risk-genes, while genes highly and differentially expressed in placentae implicate an orthogonal biology involving cellular stress. These results suggest that the most significant genetic variants detected by current schizophrenia GWAS contribute to risk in part by converging on a developmental trajectory sensitive to events affecting placentation, which may underlie the male preponderance of schizophrenia and offer new insights into primary prevention.

Published
2017

46. Developmental and genetic regulation of the human cortex transcriptome in schizophrenia

Author

Amy Deep-Soboslay, Richard E. Straub, Leonardo Collado Torres, Thomas M. Hyde, Yuan Gao, Qiang Chen, Joo Heon Shin, William S Ulrich, Carlo Colantuoni, Ran Tao, Daniel R. Weinberger, Jie Quan, Tony Kam-Thong, Joel E. Kleinman, Brady J. Maher, Jeffrey T. Leek, Andrew E. Jaffe, Alan J. Cross, Hualin S. Xi, and Nicholas J. Brandon

Subjects
Gene isoform, Genetics, 0303 health sciences, RNA, Genome-wide association study, Human brain, Biology, medicine.disease, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, medicine.anatomical_structure, Schizophrenia, medicine, Directionality, Gene, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

SummaryGWAS have identified 108 loci that confer risk for schizophrenia, but risk mechanisms for individual loci are largely unknown. Using developmental, genetic, and illness-based RNA sequencing expression analysis, we characterized the human brain transcriptome around these loci and found enrichment for developmentally regulated genes with novel examples of shifting isoform usage across pre- and post-natal life. We found widespread expression quantitative trait loci (eQTLs), including many with transcript specificity and previously unannotated sequence that were independently replicated. We leveraged this eQTL database to show that 48.1% of risk variants for schizophrenia associated with nearby expression. Within patients and controls, we implemented a novel algorithm for RNA quality adjustment, and identified 237 genes significantly associated with diagnosis that replicated in an independent case-control dataset. These genes implicated synaptic processes and were strongly regulated in early development (p < 10-20). These data offer new targets for modeling schizophrenia risk in cellular systems.

Published
2017

47. Genetic correlation between amyotrophic lateral sclerosis and schizophrenia

Author

Cristina Cereda, Jurjen J. Luykx, Sandra Meier, Derek W. Morris, Douglas M. Ruderfer, Mythily Subramaniam, Paul Cormican, Lyudmila Georgieva, John Landers, Silvana Penco, Marian L. Hamshere, Frank Dudbridge, Mari Nelis, Dick Schijven, Jimmy Lee, Sarah E. Bergen, Alessandro Padovani, Nicholas W. Wood, Meraida Polak, Hannelore Ehrenreich, Nancy G. Buccola, Noa Carrera, Stefan Herms, Panos Roussos, Marion Friedl, Teimuraz Silagadze, Jim van Os, Annette M. Hartmann, Ole A. Andreassen, R. Jeroen Pasterkamp, Sibylle G. Schwab, Aleksey Shatunov, Eli A. Stahl, David A. Collier, Farooq Amin, Michael Conlon O'Donovan, Guiqing Cai, Kung-Yee Liang, Denis C. Bauer, Charles Curtis, Brion S. Maher, Ashley R. Jones, Sara L. Pulit, Sarah Tosato, Milan Macek, Vivianna M. Van Deerlin, Vincenzo Silani, Pietro Fratta, Bettina Konte, Rosanna Tortelli, Dan Rujescu, T. Scott Stroup, Elizabeth Bevilacqua, Christian Lunetta, Bradley T. Webb, Christophe Tzourio, Patrick Vourc'h, Joel N. Hirschhorn, Gilbert Bensimon, Timothy G. Dinan, Thomas G. Schulze, Richard A. Belliveau, Daniel R. Weinberger, Andrew McQuillin, Qingqin S. Li, Orla Hardiman, Claudine Laurent, Masashi Ikeda, Tim Kahlke, Rodney J. Scott, Frans Henskens, Tune H. Pers, Wolfgang Lieb, Christian Hammer, Elvira Bramon, Hana Kuzelova-Ptackova, Raquelle I. Mesholam-Gately, Ingrid Melle, Nadine Cohen, David Cohen, Nazli Basak, Elisabeth Stögmann, Nelson B. Freimer, Peter Eichhammer, J. Mallet, Preben Bo Mortensen, Robert H. Brown, Wouter van Rheenen, Roberto Del Bo, Dai Wang, Laurent Essioux, Larry J. Seidman, Hreinn Stefansson, Erik G. Jönsson, Mads V. Hollegaard, Raymond C.K. Chan, Susana Pinto, Alexander Richards, Jubao Duan, Peter Holmans, George Kirov, Pablo V. Gejman, Philippe Amouyel, Stephanie Godard, Dieter B. Wildenauer, Martina Wiedau-Pazos, Stacy Steinberg, Ole Mors, Andres Metspalu, Rolf Adolfsson, Shaun Purcell, Hugh Gurling, Joseph I. Friedman, Erik Söderman, Mark Weiser, Giacomo P. Comi, James A. Knowles, Peter M. Andersen, Brien P. Riley, Nakao Iwata, Jeremy M. Silverman, Mark J. Daly, Elena Parkhomenko, Digby Quested, Srinivas Thirumalai, Ulrich Schall, Jan Lubinski, Dragan M. Svrakic, Aaron R. Wolen, S. Hong Lee, Andrew Pocklington, Bernard Lerer, Vahram Haroutunian, Matthew C. Kiernan, Kenneth L. Davis, Assen Jablensky, William Byerley, Karol Estrada, Aarno Palotie, Cinzia Tiloca, Eadbhard O'Callaghan, Perry T.C. van Doormaal, Colm McDonald, Federico Casale, Thomas Meitinger, Robert Freedman, Gerome Breen, Milena Blagojevic-Radivojkov, Ian P. Blair, Ann E. Pulver, Jan H. Veldink, Giancarlo Logroscino, Miaoxin Li, Abraham Reichenberg, Esben Agerbo, Siddharthan Chandran, Patrik K. E. Magnusson, Andrew M. McIntosh, Gianni Sorarù, Maura Brunetti, Xuebin Zheng, Madeline Alexander, James L. Kennedy, Douglas Blackwood, Menachem Fromer, Martilias S. Farrell, Alan R. Sanders, Dominic B. Rowe, Alexis Brice, Jonathan Pimm, Emily H. M. Wong, Jana Strohmaier, André G. Uitterlinden, Andrea Calvo, Carsten Drepper, John Q. Trojanowski, Marcella Rietschel, Siow Ann Chong, Karen E. Morrison, Sang-Yun Oh, Laura Nisenbaum, Margaret O'Brien, Alkes L. Price, Carin J. Meijer, Michael Davidson, John Powell, Petr Slominsky, Wiepke Cahn, Cinzia Gellera, Vihra Milanova, Peter M. Visscher, Patricia T. Michie, Dimitris Dikeos, Jianxin Shi, Veikko Salomaa, Philip Van Damme, James J. Crowley, Younes Mokrab, Valentina Escott-Price, Jesus S. Mora, Stanley V. Catts, David St Clair, Bernhard Landwehrmeyer, John Hardy, Kristin K. Nicodemus, Dominique Campion, Juha Veijola, Wim Robberecht, Thomas Meyer, Peter Lichtner, Christos Pantelis, Markus Weber, Nilo Riva, Jin P. Szatkiewicz, Michele T. Pato, Cinzia Bertolin, Frank P. Diekstra, Simon Arcuti, Bryan J. Mowry, Hon-Cheong So, Adriano Chiò, Viviana Pensato, Yunjung Kim, Jean-François Dartigues, Zita Ausrele Kucinskiene, Inez Myin-Germeys, Jaana Suvisaari, Sophie E. Legge, Roel A. Ophoff, Philippe Corcia, Gerald Nestadt, Stephan Ripke, Kuang Lin, Paola Giusti-Rodríguez, Michael John Owen, Chris C. A. Spencer, Safa Saker-Delye, Robert W. McCarley, Kimberley D. Chambert, Brandon Wormley, Isabella Fogh, Mamede de Carvalho, Pamela J. Shaw, Tõnu Esko, Ronald Y. L. Chan, Jianjun Liu, Tim B. Bigdeli, Christian R. Andres, David M. Hougaard, Michael Gill, Ammar Al-Chalabi, Colm O'Dushlaine, Rick A.A. van der Spek, Gary Donohoe, Tao Li, Jonathan D. Glass, Christopher Shaw, Draga Toncheva, Leonard H. van den Berg, Liene Nikitina-Zake, Morten Mattingsdal, François Salachas, Andrey Khrunin, Line Olsen, Jochen H. Weishaupt, Jo Knight, Katie Sidle, Filip Eftimov, Massimiliano Filosto, Russell L. McLaughlin, Pak C. Sham, Joshua L. Roffman, Thomas Hansen, Naser Durmishi, Deborah A. Nertney, Juha Karjalainen, Robert Swingler, Ditte Demontis, Vaidutis Kučinskas, Jennifer L. Moran, Leo McCluskey, Donald W. Black, Eric F.C. Cheung, Qiang Wang, Olli Pietilainen, Vera Golimbet, Anna K. Kähler, Clement C. Zai, Nigel Williams, Annelie Nordin, Wolfgang Maier, Bradley N. Smith, Ettore Beghi, Rosa Capozzo, Garth A. Nicholson, Markus M. Nöuthen, Jordan W. Smoller, Eric Y.H. Chen, Joseph D. Buxbaum, Letizia Mazzini, Andrea Malaspina, Antonio Julià, Stephanie Williams, Tracey L. Petryshen, Christine Payan, Johan G. Eriksson, Carmel M. Loughland, Elodie Drapeau, Lieuwe de Haan, Martin Begemann, Lukas Tittmann, Franziska Degenhardt, Mark Reimers, Jurgen Del Favero, Jacqueline I. Goldstein, Annelot M. Dekker, Sergi Papiol, Svetlana A. Limborska, René S. Kahn, Shuna Colville, Kelly L. Williams, Pamela Sklar, Diana O. Perkins, Lili Milani, Ayman H. Fanous, Nicola Ticozzi, Fernando Rivadeneira, Marianne de Visser, P. Nigel Leigh, James T.R. Walters, Josef Frank, Aiden Corvin, Silviu Alin Bacanu, John L. Waddington, Stephanie H. Witt, Tiina Paunio, Margot Albus, Catherine Lomen-Hoerth, Sara Marsal, Per Hoffmann, David Curtis, Cindy Maurel, Todd Lencz, Orietta Pansarasa, Manuel Mattheisen, Anneke J. van der Kooi, A. Hofman, Dermot Walsh, Hailiang Huang, Ann Olincy, Anders D. Børglum, Ricardo Rojas-García, William Sproviero, Albert C. Ludolph, Edward M. Scolnick, Danielle Posthuma, George N. Papadimitriou, Michael A. van Es, Fritz Zimprich, F. Anthony O'Neill, Lude Franke, Jouko Lönnqvist, Daniel G. Bradley, Sven Cichon, Susanna Abdulla, Kristel R. van Eijk, Ingrid Agartz, Elisabetta Pupillo, Milica Pejovic-Milovancevic, Antonia Ratti, Henrik B. Rasmussen, Kari Stefansson, Brendan Bulik-Sullivan, Béla Melegh, Stéphanie Millecamps, Janis Klovins, Enrico Domenici, Michael Sendtner, Kai-How Farh, Randy L. Buckner, Albert Hofman, Benjamin M. Neale, Naomi R. Wray, An Goris, Kang Sim, Lauren Elman, Giulio Genovese, Jens R. Wendland, Rita M. Cantor, Ariel Darvasi, Christina M. Hultman, Sandra D'Alfonso, Cristina Moglia, Carlos N. Pato, Sena Karachanak-Yankova, Nicholas John Craddock, Richard W. Orrell, Richard Bruggeman, Kenneth S. Kendler, Alan M. Pittman, Robin M. Murray, Richard E. Straub, Cathryn M. Lewis, Srdjan Djurovic, Vincent Meininger, Jeffrey A. Lieberman, Bertram Müller-Myhsok, Phil Lee, David J. Kavanagh, Srihari Gopal, Igor Nenadic, Matthew C. Keller, Christian R. Schubert, Jacob Gratten, Alexandra Durr, Roger Pamphlett, Douglas F. Levinson, Luba Kalaydjieva, Chiara Zecca, Anil K. Malhotra, Andre Franke, Vaughan J. Carr, Steven A. McCarroll, C. Robert Cloninger, Judit Bene, Ina Giegling, Wei Cheng, Hualin Simon Xi, Thomas Werge, Eric Strengman, Susanne Petri, Engilbert Sigurdsson, Mark Hansen, Patrick F. Sullivan, Kieran C. Murphy, Inge Joa, Complex Trait Genetics, McLaughlin, Russell L, Schijven, Dick, Van Rheenen, Wouter, Van Eijk, Kristel R, O'Brien, Margaret, Kahn, René S, Ophoff, Roel A, Goris, An, Bradley, Daniel G, Al-Chalabi, Ammar, Van Den Berg, Leonard H, Luykx, Jurjen J, Hardiman, Orla, Veldink, Jan H, Lee, S Hong, Project MinE GWAS Consortium, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Centre of Excellence in Complex Disease Genetics, Aarno Palotie / Principal Investigator, Institute for Molecular Medicine Finland, Genomics of Neurological and Neuropsychiatric Disorders, Kučinskas, Vaidutis, Kučinskienė, Zita Aušrelė, Other departments, Neurology, APH - Mental Health, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, Adult Psychiatry, Schizophrenia Working Group of the Psychiatric Genomics Consortiumz, Germeys, Inez, Robberecht, Wim, and Van Damme, Philip

Subjects
0301 basic medicine, Oncology, Genetics and Molecular Biology (all), Linkage disequilibrium, Multifactorial Inheritance, General Physics and Astronomy, Genome-wide association study, Comorbidity, VARIANTS, Neurodegenerative, Biochemistry, DISEASE, 3124 Neurology and psychiatry, Linkage Disequilibrium, Cohort Studies, 0302 clinical medicine, Genetics research, Odds Ratio, 2.1 Biological and endogenous factors, Amyotrophic lateral sclerosis, Aetiology, ARCHITECTURE, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Multidisciplinary, Chemistry (all), Motor neuron disease, Schizophrenia, BIPOLAR DISORDER, Single Nucleotide, Serious Mental Illness, 3. Good health, Mental Health, RC0346, motor neuron disease, Project MinE GWAS Consortium, medicine.medical_specialty, SUSCEPTIBILITY LOCI, Science, European Continental Ancestry Group, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Article, White People, 03 medical and health sciences, Physics and Astronomy (all), Rare Diseases, SDG 3 - Good Health and Well-being, Clinical Research, Internal medicine, MD Multidisciplinary, mental disorders, medicine, Genetics, Journal Article, Humans, Genetic Predisposition to Disease, Family, Bipolar disorder, GENOME-WIDE ASSOCIATION, Polymorphism, Biology, METAANALYSIS, business.industry, Amyotrophic Lateral Sclerosis, Human Genome, Case-control study, 3112 Neurosciences, Neurosciences, General Chemistry, Odds ratio, medicine.disease, R1, Brain Disorders, 030104 developmental biology, genetics research, Case-Control Studies, RC0321, Linear Models, PLEIOTROPY, Human medicine, 3111 Biomedicine, Biochemistry, Genetics and Molecular Biology (all), ALS, business, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

We have previously shown higher-than-expected rates of schizophrenia in relatives of patients with amyotrophic lateral sclerosis (ALS), suggesting an aetiological relationship between the diseases. Here, we investigate the genetic relationship between ALS and schizophrenia using genome-wide association study data from over 100,000 unique individuals. Using linkage disequilibrium score regression, we estimate the genetic correlation between ALS and schizophrenia to be 14.3% (7.05–21.6; P=1 × 10−4) with schizophrenia polygenic risk scores explaining up to 0.12% of the variance in ALS (P=8.4 × 10−7). A modest increase in comorbidity of ALS and schizophrenia is expected given these findings (odds ratio 1.08–1.26) but this would require very large studies to observe epidemiologically. We identify five potential novel ALS-associated loci using conditional false discovery rate analysis. It is likely that shared neurobiological mechanisms between these two disorders will engender novel hypotheses in future preclinical and clinical studies., Relatives of patients with amyotrophic lateral sclerosis have an unexpectedly high incidence of schizophrenia. Here, the authors show a genetic link between the two conditions, suggesting shared neurobiological mechanisms.

Published
2017

48. GWAS meta-analysis reveals novel loci and genetic correlates for general cognitive function: a report form the COGENT consortium

Author

Anna C. Need, Katri Räikkönen, Edythe D. London, Jari Lahti, Aiden Corvin, Antony Payton, Russell A. Poldrack, Nikolaos Smyrnis, Matthew C. Keller, Ian J. Deary, Aarno Palotie, Deborah K. Attix, Srdjan Djurovic, Elisabeth Widen, John M. Starr, Fred W. Sabb, Kjetil Sundet, Stella G. Giakoumaki, David C. Liewald, Daniel R. Weinberger, Neil Pendleton, Panos Bitsios, Jin Yu, Ole A. Andreassen, Bettina Konte, Alex Hatzimanolis, William E R Ollier, Johan G. Eriksson, Ina Giegling, Emma Knowles, Dwight Dickinson, Elizabeth T. Cirulli, David C. Glahn, Nelson A. Freimer, Panos Roussos, Aristotle N. Voineskos, Thomas Espeseth, Joey W. Trampush, Dan E. Arking, Gary Davies, Nicholas C. Stefanis, Dan Rujescu, Derek W. Morris, Gary Donohoe, Vidar M. Steen, S. Le Hellard, Anil K. Malhotra, Astri J. Lundervold, Todd Lencz, Ornit Chiba-Falek, Andrea Christoforou, Matthew A. Scult, Emily Drabant Conley, Michael A Horan, Ingrid Melle, M. Gill, Robert M. Bilder, Katherine E. Burdick, Ivar Reinvang, M. L. Z. Yang, Eliza Congdon, Tyrone D. Cannon, Richard E. Straub, Pamela DeRosse, Ahmad R. Hariri, Dimitrios Avramopoulos, Medicum, Behavioural Sciences, Institute for Molecular Medicine Finland, Elisabeth Ingrid Maria Widen / Principal Investigator, Clinicum, Aarno Palotie / Principal Investigator, Department of Medical and Clinical Genetics, Johan Eriksson / Principal Investigator, Department of General Practice and Primary Health Care, Helsinki Collegium for Advanced Studies, Developmental Psychology Research Group, Genomics of Neurological and Neuropsychiatric Disorders, and Genomic Discoveries and Clinical Translation

Subjects
0301 basic medicine, Male, Multifactorial Inheritance, Genome-wide association study, Cathie Marsh Institute, Medical and Health Sciences, 3124 Neurology and psychiatry, 0302 clinical medicine, Cognition, Gene Frequency, 2.1 Biological and endogenous factors, provides insights, Aetiology, Genetics, Psychiatry, scottish mental survey, 11 Medical And Health Sciences, Single Nucleotide, Biological Sciences, Middle Aged, educational-attainment, developmental delay, Psychiatry and Mental health, uk biobank n=112151, Mental Health, intellectual disability, Female, Psychology, Corrigendum, Biotechnology, Adult, ability, 515 Psychology, human intelligence, European Continental Ancestry Group, Neurocognitive Disorders, Single-nucleotide polymorphism, Basic Behavioral and Social Science, Polymorphism, Single Nucleotide, White People, 17 Psychology And Cognitive Sciences, 03 medical and health sciences, Cellular and Molecular Neuroscience, Clinical Research, Behavioral and Social Science, Journal Article, SNP, Humans, Genetic Predisposition to Disease, Allele, Polymorphism, Molecular Biology, Allele frequency, Alleles, Genetic Association Studies, Genetic association, Prevention, Human Genome, Psychology and Cognitive Sciences, Genetic Variation, 06 Biological Sciences, Minor allele frequency, 030104 developmental biology, executive function, Genetic Loci, ResearchInstitutes_Networks_Beacons/cathie_marsh_institute, genome-wide association, 1182 Biochemistry, cell and molecular biology, Immediate Communication, Neurocognitive, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract

The complex nature of human cognition has resulted in cognitive genomics lagging behind many other fields in terms of gene discovery using genome-wide association study (GWAS) methods. In an attempt to overcome these barriers, the current study utilized GWAS meta-analysis to examine the association of common genetic variation (~8M single-nucleotide polymorphisms (SNP) with minor allele frequency ⩾1%) to general cognitive function in a sample of 35 298 healthy individuals of European ancestry across 24 cohorts in the Cognitive Genomics Consortium (COGENT). In addition, we utilized individual SNP lookups and polygenic score analyses to identify genetic overlap with other relevant neurobehavioral phenotypes. Our primary GWAS meta-analysis identified two novel SNP loci (top SNPs: rs76114856 in the CENPO gene on chromosome 2 and rs6669072 near LOC105378853 on chromosome 1) associated with cognitive performance at the genome-wide significance level (P−8). Gene-based analysis identified an additional three Bonferroni-corrected significant loci at chromosomes 17q21.31, 17p13.1 and 1p13.3. Altogether, common variation across the genome resulted in a conservatively estimated SNP heritability of 21.5% (s.e.=0.01%) for general cognitive function. Integration with prior GWAS of cognitive performance and educational attainment yielded several additional significant loci. Finally, we found robust polygenic correlations between cognitive performance and educational attainment, several psychiatric disorders, birth length/weight and smoking behavior, as well as a novel genetic association to the personality trait of openness. These data provide new insight into the genetics of neurocognitive function with relevance to understanding the pathophysiology of neuropsychiatric illness.

Published
2017

49. Incomplete penetrance of NRXN1 deletions in families with schizophrenia

Author

Richard E. Straub, Radhakrishna Vakkalanka, Ningping Feng, Chao Li, Daniel R. Weinberger, Alessandro Bertolino, Bhaskar Kolachana, and Giovanna Todarello

Subjects
Adult, Male, Adolescent, Genotype, Cell Adhesion Molecules, Neuronal, Neurexin, Nerve Tissue Proteins, Penetrance, Biology, Young Adult, medicine, Humans, Genetic Predisposition to Disease, In patient, Copy-number variation, Neural Cell Adhesion Molecules, Biological Psychiatry, Sequence Deletion, Family Health, Genetics, Calcium-Binding Proteins, Comparative Genome Hybridization, Unaffected sibling, Middle Aged, medicine.disease, Psychiatry and Mental health, Real-time polymerase chain reaction, Schizophrenia, Female
Abstract

Neurexin 1 (NRXN1) is a presynaptic neuronal adhesion molecule that interacts with postsynaptic neuroligins in both glutamatergic and GABAergic synapses and is important in synaptic formation and function. NRXN1 deletions increase the risk of schizophrenia, so our aims were to explore this in our family sample, to distinguish de novo from inherited mutations, to examine transmission to affected and unaffected siblings and to estimate penetrance. We performed copy number analyses in NRXN1 using data from Illumina BeadArrays from 635 subjects with schizophrenia (276 in genotyped families), 487 of their unaffected parents and 309 unaffected siblings as well as 635 normal controls, all from the CBDB/NIMH Genetic Study of Schizophrenia. Deletions called by software were confirmed by quantitative PCR and comparative genome hybridization. There were deletions in 15 individuals in 11 families, including de novo exonic deletions in one case and one unaffected sibling. We observed no deletions in controls, 7 deletions in cases (1.10%), and an unexpectedly high deletion frequency in parents (n = 5, 1.02%) and siblings (n = 3, 0.97%). Three families showed inheritance from an unaffected parent, and in two families an unaffected parent did not transmit to the affected offspring. Thus we have added to the evidence that NRXN1 deletions are more frequent in patients with schizophrenia than in healthy individuals. However, the presence of de novo deletions in unaffected relatives and transmission from and to unaffected family members demonstrated that while the deletions may well have been necessary for some carriers to develop schizophrenia, they were not always sufficient.

Published
2014

50. Characteristics of the Cation Cotransporter NKCC1 in Human Brain: Alternate Transcripts, Expression in Development, and Potential Relationships to Brain Function and Schizophrenia

Author

Daniel R. Weinberger, Joseph H. Callicott, Amanda J. Law, Dwight Dickinson, Lauren R. Testa, Joel E. Kleinman, Barbara K. Lipska, Michelle I. Mighdoll, Tianzhang Ye, Yukitaka Morita, Ran Tao, Richard E. Straub, Bhaskar Kolachana, Qiang Chen, and Thomas M. Hyde

Subjects
Adult, Male, medicine.medical_specialty, Adolescent, Genotype, DNA, Recombinant, Prefrontal Cortex, Biology, Inhibitory postsynaptic potential, Cohort Studies, Young Adult, chemistry.chemical_compound, Fetus, Internal medicine, medicine, Humans, Solute Carrier Family 12, Member 2, Allele, Child, Neurotransmitter, Aged, Psychiatric Status Rating Scales, Working memory, General Neuroscience, Infant, Newborn, Gene Expression Regulation, Developmental, Infant, Articles, Human brain, Middle Aged, Phenotype, Oxygen, Minor allele frequency, HEK293 Cells, medicine.anatomical_structure, Endocrinology, chemistry, Child, Preschool, Postmortem Changes, Mutation, Schizophrenia, Excitatory postsynaptic potential, Female, Cognition Disorders, Neuroscience
Abstract

Early in development, GABA, an inhibitory neurotransmitter in adults, is excitatory. NKCC1 (SLC12A2) encodes one of two cation chloride cotransporters mediating the conversion of GABA from excitatory to inhibitory. Using 3′ and 5′ RACE and PCR, we verified previously characterized alternative transcripts of NKCC1a (1–27) and NKCC1b (1–27(Δ21)), identified new NKCC1 transcripts, and explored their expression patterns during human prefrontal cortical development. A novel ultra-short transcript (1–2a) was expressed preferentially in the fetus. Expression of NKCC1b and 1–2a were decreased in schizophrenia compared with controls (NKCC1b: 0.8-fold decrease,p= 0.013; 1–2a: 0.8-fold decrease,p= 0.006). Furthermore, the expression of NKCC1b was associated with NKCC1 polymorphism rs3087889. The minor allele at rs3087889, associated with reduced NKCC1b expression (homozygous for major allele:N= 37; homozygous for minor allele:N= 15; 1.5-fold decrease;p< 0.01), was also associated with a modest increase in schizophrenia risk in a case-control sample (controls:N= 435; cases:N= 397, OR = 1.5). This same allele was then found associated with cognitive (n= 369) and fMRI (n= 313) intermediate phenotypes associated with schizophrenia—working memory (Cohen's d = 0.35), global cognition org(d = 0.18), and prefrontal inefficiency (d = 0.36) as measured by BOLD fMRI during a working memory task. Together, these preclinical and clinical results suggest that variation in NKCC1 may increase risk for schizophrenia via alterations of mRNA expression at the molecular level and impairment of optimal prefrontal function at the macro or systems level.

Published
2014

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