Gene expression elucidates functional impact of polygenic risk for schizophrenia
Menachem Fromer,Panos Roussos,Solveig K. Sieberts,Jessica S. Johnson,David H. Kavanagh,Thanneer M. Perumal,Douglas M. Ruderfer,Edwin C. Oh,Aaron Topol,Hardik Shah,Lambertus Klei,Robin Kramer,Dalila Pinto,Zeynep H. Gümüş,A. Ercument Cicek,Kristen K. Dang,Andrew W. Browne,Cong Lu,Lu Xie,Ben Readhead,Eli A. Stahl,Jianqiu Xiao,Mahsa Parvisi,Tymor Hamamsy,John F. Fullard,Ying-Chih Wang,Milind Mahajan,Jonathan M. J. Derry,Joel T. Dudley,Scott E. Hemby,Benjamin A. Logsdon,Konrad Talbot,Towfique Raj,Towfique Raj,David A. Bennett,Philip L. De Jager,Philip L. De Jager,Jun Zhu,Bin Zhang,Patrick F. Sullivan,Patrick F. Sullivan,Andrew Chess,Shaun Purcell,Leslie A. Shinobu,Lara M. Mangravite,Hiroyoshi Toyoshiba,Raquel E. Gur,Chang-Gyu Hahn,David A. Lewis,Vahram Haroutunian,Mette A. Peters,Barbara K. Lipska,Joseph D. Buxbaum,Eric E. Schadt,Keisuke Hirai,Kathryn Roeder,Kristen J. Brennand,Nicholas Katsanis,Enrico Domenici,Bernie Devlin,Pamela Sklar +60 more
TLDR
It is shown that schizophrenia is polygenic and the utility of this resource of gene expression and its genetic regulation for mechanistic interpretations of genetic liability for brain diseases is highlighted.Abstract:
Over 100 genetic loci harbor schizophrenia associated variants, yet how these variants confer liability is uncertain. The CommonMind Consortium sequenced RNA from dorsolateral prefrontal cortex of schizophrenia cases (N = 258) and control subjects (N = 279), creating a resource of gene expression and its genetic regulation. Using this resource, ~20% of schizophrenia loci have variants that could contribute to altered gene expression and liability. In five loci, only a single gene was involved: FURIN, TSNARE1, CNTN4, CLCN3, or SNAP91. Altering expression of FURIN, TSNARE1, or CNTN4 changes neurodevelopment in zebrafish; knockdown of FURIN in human neural progenitor cells yields abnormal migration. Of 693 genes showing significant case/control differential expression, their fold changes are ≤ 1.33, and an independent cohort yields similar results. Gene co-expression implicates a network relevant for schizophrenia. Our findings show schizophrenia is polygenic and highlight the utility of this resource for mechanistic interpretations of genetic liability for brain diseases.read more
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Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Jason Ernst,Angela Yen,Pouya Kheradpour,Zhizhuo Zhang,Jianrong Wang,Lucas D. Ward,Abhishek Sarkar,Gerald Quon,Matthew L. Eaton,Yi-Chieh Wu,Andreas R. Pfenning,Xinchen Wang,Melina Claussnitzer,Yaping Liu,Mukul S. Bansal,Soheil Feizi-Khankandi,Ah Ram Kim,Richard C Sallari,Nicholas A Sinnott-Armstrong,Laurie A. Boyer,Elizabeta Gjoneska,Li-Huei Tsai,Manolis Kellis +24 more
TL;DR: In this article, the authors describe the integrative analysis of 111 reference human epigenomes generated as part of the NIH Roadmap Epigenomics Consortium, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression.
Journal ArticleDOI
Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression
Naomi R. Wray,Stephan Ripke,Stephan Ripke,Stephan Ripke,Manuel Mattheisen,Maciej Trzaskowski,Enda M. Byrne,Abdel Abdellaoui,Mark Adams,Esben Agerbo,Esben Agerbo,Tracy Air,Till M.F. Andlauer,Silviu Alin Bacanu,Marie Bækvad-Hansen,Marie Bækvad-Hansen,Aartjan F.T. Beekman,Tim B. Bigdeli,Elisabeth B. Binder,Elisabeth B. Binder,Douglas Blackwood,Julien Bryois,Henriette N. Buttenschøn,Henriette N. Buttenschøn,Jonas Bybjerg-Grauholm,Jonas Bybjerg-Grauholm,Na Cai,Na Cai,Enrique Castelao,Jane H. Christensen,Jane H. Christensen,Toni-Kim Clarke,Jonathan I.R. Coleman,Lucía Colodro-Conde,Baptiste Couvy-Duchesne,Nicholas John Craddock,Gregory E. Crawford,Cheynna A. Crowley,Hassan S. Dashti,Hassan S. Dashti,Gail Davies,Ian J. Deary,Franziska Degenhardt,Eske M. Derks,Nese Direk,Nese Direk,Conor V. Dolan,Erin C. Dunn,Erin C. Dunn,Thalia C. Eley,Nicholas Eriksson,Valentina Escott-Price,Farnush Hassan Farhadi Kiadeh,Hilary K. Finucane,Hilary K. Finucane,Andreas J. Forstner,Josef Frank,Helena Gaspar,Michael Gill,Paola Giusti-Rodríguez,Fernando S. Goes,Scott D. Gordon,Jakob Grove,Lynsey S. Hall,Lynsey S. Hall,Eilis Hannon,Christine Søholm Hansen,Christine Søholm Hansen,Thomas Hansen,Thomas Hansen,Stefan Herms,Stefan Herms,Ian B. Hickie,Per Hoffmann,Per Hoffmann,Georg Homuth,Carsten Horn,Jouke-Jan Hottenga,David M. Hougaard,David M. Hougaard,Ming Hu,Craig L. Hyde,Marcus Ising,Rick Jansen,Fulai Jin,Eric Jorgenson,James A. Knowles,Isaac S. Kohane,Isaac S. Kohane,Isaac S. Kohane,Julia Kraft,Warren W. Kretzschmar,Jesper Krogh,Zoltán Kutalik,Zoltán Kutalik,Jacqueline M. Lane,Jacqueline M. Lane,Yihan Li,Yun Li,Penelope A. Lind,Xiaoxiao Liu,Leina Lu,Donald J. MacIntyre,Dean F. MacKinnon,Robert Maier,Wolfgang Maier,Jonathan Marchini,Hamdi Mbarek,Patrick J. McGrath,Peter McGuffin,Sarah E. Medland,Divya Mehta,Divya Mehta,Christel M. Middeldorp,Christel M. Middeldorp,Evelin Mihailov,Yuri Milaneschi,Lili Milani,Jonathan Mill,Francis M. Mondimore,Grant W. Montgomery,Sara Mostafavi,Niamh Mullins,Matthias Nauck,Bernard Ng,Michel G. Nivard,Dale R. Nyholt,Paul F. O'Reilly,Hogni Oskarsson,Michael John Owen,Jodie N. Painter,Carsten Bøcker Pedersen,Carsten Bøcker Pedersen,Marianne Giørtz Pedersen,Marianne Giørtz Pedersen,Roseann E. Peterson,Erik Pettersson,Wouter J. Peyrot,Giorgio Pistis,Danielle Posthuma,Shaun Purcell,Jorge A. Quiroz,Per Qvist,Per Qvist,John P. Rice,Brien P. Riley,Margarita Rivera,Margarita Rivera,Saira Saeed Mirza,Richa Saxena,Richa Saxena,Robert A. Schoevers,Eva C. Schulte,Ling Shen,Jianxin Shi,Stanley I. Shyn,Engilbert Sigurdsson,Grant Sinnamon,Johannes H. Smit,Daniel J. Smith,Hreinn Stefansson,Stacy Steinberg,Craig A. Stockmeier,Fabian Streit,Jana Strohmaier,Katherine E. Tansey,Henning Teismann,Alexander Teumer,Wesley K. Thompson,Pippa A. Thomson,Thorgeir E. Thorgeirsson,Chao Tian,Matthew Traylor,Jens Treutlein,Vassily Trubetskoy,André G. Uitterlinden,Daniel Umbricht,Sandra Van der Auwera,Albert M. van Hemert,Alexander Viktorin,Peter M. Visscher,Yunpeng Wang,Yunpeng Wang,Yunpeng Wang,Bradley T. Webb,Shantel Weinsheimer,Shantel Weinsheimer,Jürgen Wellmann,Gonneke Willemsen,Stephanie H. Witt,Yang Wu,Hualin S. Xi,Jian Yang,Futao Zhang,Volker Arolt,Bernhard T. Baune,Klaus Berger,Dorret I. Boomsma,Sven Cichon,Udo Dannlowski,E. C.J. De Geus,J. Raymond DePaulo,Enrico Domenici,Katharina Domschke,Tõnu Esko,Tõnu Esko,Hans J. Grabe,Steven P. Hamilton,Caroline Hayward,Andrew C. Heath,David A. Hinds,Kenneth S. Kendler,Stefan Kloiber,Stefan Kloiber,Stefan Kloiber,Glyn Lewis,Qingqin S. Li,Susanne Lucae,Pamela F.A. Madden,Patrik K. E. Magnusson,Nicholas G. Martin,Andrew M. McIntosh,Andres Metspalu,Ole Mors,Ole Mors,Preben Bo Mortensen,Bertram Müller-Myhsok,Bertram Müller-Myhsok,Merete Nordentoft,Merete Nordentoft,Markus M. Nöthen,Michael Conlon O'Donovan,Sara A. Paciga,Nancy L. Pedersen,Brenda W.J.H. Penninx,Roy H. Perlis,David J. Porteous,James B. Potash,Martin Preisig,Marcella Rietschel,Catherine Schaefer,Thomas G. Schulze,Jordan W. Smoller,Jordan W. Smoller,Kari Stefansson,Kari Stefansson,Henning Tiemeier,Rudolf Uher,Henry Völzke,Myrna M. Weissman,Myrna M. Weissman,Thomas Werge,Thomas Werge,Thomas Werge,Ashley R. Winslow,Ashley R. Winslow,Cathryn M. Lewis,Douglas F. Levinson,Gerome Breen,Anders D. Børglum,Anders D. Børglum,Patrick F. Sullivan,Patrick F. Sullivan +262 more
TL;DR: A genome-wide association meta-analysis of individuals with clinically assessed or self-reported depression identifies 44 independent and significant loci and finds important relationships of genetic risk for major depression with educational attainment, body mass, and schizophrenia.
Journal ArticleDOI
Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer's disease risk.
Iris E. Jansen,Jeanne E. Savage,Kyoko Watanabe,Julien Bryois,Dylan M. Williams,Stacy Steinberg,Julia Sealock,Ida K. Karlsson,Ida K. Karlsson,Sara Hägg,Lavinia Athanasiu,Lavinia Athanasiu,Nicola Voyle,Petroula Proitsi,Aree Witoelar,Sven Stringer,Dag Aarsland,Dag Aarsland,Ina S. Almdahl,Ina S. Almdahl,Ina S. Almdahl,Fred Andersen,Sverre Bergh,Francesco Bettella,Sigurbjorn Bjornsson,Anne Brækhus,Geir Bråthen,Christiaan de Leeuw,Rahul S. Desikan,Srdjan Djurovic,Srdjan Djurovic,Logan Dumitrescu,Tormod Fladby,Tormod Fladby,Timothy J. Hohman,Palmi V. Jonsson,Steven J. Kiddle,Arvid Rongve,Ingvild Saltvedt,Sigrid Botne Sando,Geir Selbæk,Maryam Shoai,Nathan G. Skene,Nathan G. Skene,Jon Snaedal,Eystein Stordal,Eystein Stordal,Ingun Ulstein,Yunpeng Wang,Linda R. White,John Hardy,Jens Hjerling-Leffler,Patrick F. Sullivan,Patrick F. Sullivan,Wiesje M. van der Flier,Richard Dobson,Lea K. Davis,Hreinn Stefansson,Kari Stefansson,Nancy L. Pedersen,Stephan Ripke,Stephan Ripke,Stephan Ripke,Ole A. Andreassen,Danielle Posthuma,Danielle Posthuma +65 more
TL;DR: A large genome-wide association study of clinically diagnosed AD and AD-by-proxy identifies new loci and functional pathways that contribute to AD risk and adds novel insights into the neurobiology of AD.
Journal ArticleDOI
Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection
Antonio F. Pardiñas,Peter Holmans,Andrew Pocklington,Valentina Escott-Price,Stephan Ripke,Stephan Ripke,Noa Carrera,Sophie E. Legge,Sophie Bishop,D. F. Cameron,Marian L. Hamshere,Jun Han,Leon Hubbard,Amy Lynham,Kiran Kumar Mantripragada,Elliott Rees,James H. MacCabe,Steven A. McCarroll,Bernhard T. Baune,Gerome Breen,Gerome Breen,Enda M. Byrne,Udo Dannlowski,Thalia C. Eley,Caroline Hayward,Nicholas G. Martin,Nicholas G. Martin,Andrew M. McIntosh,Robert Plomin,David J. Porteous,Naomi R. Wray,Armando Caballero,Daniel H. Geschwind,Laura M. Huckins,Douglas M. Ruderfer,Enrique Santiago,Pamela Sklar,Eli A. Stahl,Hyejung Won,Esben Agerbo,Esben Agerbo,Thomas Damm Als,Thomas Damm Als,Ole A. Andreassen,Ole A. Andreassen,Marie Bækvad-Hansen,Marie Bækvad-Hansen,Preben Bo Mortensen,Preben Bo Mortensen,Carsten Bøcker Pedersen,Carsten Bøcker Pedersen,Anders D. Børglum,Anders D. Børglum,Jonas Bybjerg-Grauholm,Jonas Bybjerg-Grauholm,Srdjan Djurovic,Srdjan Djurovic,Naser Durmishi,Marianne Giørtz Pedersen,Marianne Giørtz Pedersen,Vera Golimbet,Jakob Grove,David M. Hougaard,David M. Hougaard,Manuel Mattheisen,Manuel Mattheisen,Espen Molden,Ole Mors,Ole Mors,Merete Nordentoft,Merete Nordentoft,Milica Pejovic-Milovancevic,Engilbert Sigurdsson,Teimuraz Silagadze,Christine Søholm Hansen,Christine Søholm Hansen,Kari Stefansson,Hreinn Stefansson,Stacy Steinberg,Sarah Tosato,Thomas Werge,Thomas Werge,Thomas Werge,David A. Collier,David A. Collier,Dan Rujescu,Dan Rujescu,George Kirov,Michael J. Owen,Michael Conlon O'Donovan,James T.R. Walters +90 more
TL;DR: A new genome-wide association study of schizophrenia is reported, and through meta-analysis with existing data and integrating genomic fine-mapping with brain expression and chromosome conformation data, 50 novel associated loci and 145 loci are identified.
Journal ArticleDOI
Genome-wide association study identifies 30 loci associated with bipolar disorder
Eli A. Stahl,Eli A. Stahl,Gerome Breen,Andreas J. Forstner,Andrew McQuillin,Stephan Ripke,Stephan Ripke,Stephan Ripke,Vassily Trubetskoy,Manuel Mattheisen,Yunpeng Wang,Yunpeng Wang,Jonathan R. I. Coleman,Helena Gaspar,Christiaan de Leeuw,Stacy Steinberg,Jennifer M. Whitehead Pavlides,Maciej Trzaskowski,Enda M. Byrne,Tune H. Pers,Tune H. Pers,Peter Holmans,Alexander Richards,Liam Abbott,Esben Agerbo,Esben Agerbo,Huda Akil,Diego Albani,Ney Alliey-Rodriguez,Thomas Damm Als,Thomas Damm Als,Adebayo Anjorin,Verneri Antilla,Swapnil Awasthi,Judith A. Badner,Marie Bækvad-Hansen,Marie Bækvad-Hansen,Jack D. Barchas,Nicholas Bass,Michael Bauer,Richard A. Belliveau,Sarah E. Bergen,Carsten Bøcker Pedersen,Carsten Bøcker Pedersen,Erlend Bøen,Marco P. Boks,James Boocock,Monika Budde,William E. Bunney,Margit Burmeister,Jonas Bybjerg-Grauholm,Jonas Bybjerg-Grauholm,William Byerley,Miquel Casas,Felecia Cerrato,Pablo Cervantes,Kimberly Chambert,Alexander W. Charney,Danfeng Chen,Claire Churchhouse,Claire Churchhouse,Toni-Kim Clarke,William Coryell,David Craig,Cristiana Cruceanu,Cristiana Cruceanu,David Curtis,David Curtis,Piotr M. Czerski,Anders M. Dale,Simone de Jong,Franziska Degenhardt,Jurgen Del-Favero,J. Raymond DePaulo,Srdjan Djurovic,Srdjan Djurovic,Amanda Dobbyn,Ashley Dumont,Torbjørn Elvsåshagen,Valentina Escott-Price,Chun Chieh Fan,Sascha B. Fischer,Sascha B. Fischer,Matthew Flickinger,Tatiana Foroud,Liz Forty,Josef Frank,Christine Fraser,Nelson B. Freimer,Louise Frisén,Katrin Gade,Katrin Gade,Diane Gage,Julie Garnham,Claudia Giambartolomei,Marianne Giørtz Pedersen,Marianne Giørtz Pedersen,Jaqueline Goldstein,Scott D. Gordon,Katherine Gordon-Smith,Elaine K. Green,Melissa J. Green,Melissa J. Green,Tiffany A. Greenwood,Jakob Grove,Weihua Guan,Jose Guzman-Parra,Marian L. Hamshere,Martin Hautzinger,Urs Heilbronner,Stefan Herms,Stefan Herms,Stefan Herms,Maria Hipolito,Per Hoffmann,Per Hoffmann,Per Hoffmann,Dominic Holland,Laura M. Huckins,Stéphane Jamain,Stéphane Jamain,Jessica S. Johnson,Anders Juréus,Radhika Kandaswamy,Robert Karlsson,James L. Kennedy,Sarah Kittel-Schneider,James A. Knowles,Manolis Kogevinas,Anna C. Koller,Ralph W. Kupka,Catharina Lavebratt,Jacob Lawrence,William Lawson,Markus Leber,Phil Lee,Phil Lee,Shawn Levy,Jun Li,Chunyu Liu,Susanne Lucae,Anna Maaser,Donald J. MacIntyre,Pamela B. Mahon,Pamela B. Mahon,Wolfgang Maier,Lina Martinsson,Steve McCarroll,Steve McCarroll,Peter McGuffin,Melvin G. McInnis,James McKay,Helena Medeiros,Sarah E. Medland,Fan Meng,Fan Meng,Lili Milani,Grant W. Montgomery,Derek W. Morris,Derek W. Morris,Thomas W. Mühleisen,Thomas W. Mühleisen,Niamh Mullins,Hoang T. Nguyen,Caroline M. Nievergelt,Caroline M. Nievergelt,Annelie Nordin Adolfsson,Evaristus A. Nwulia,Claire O'Donovan,Loes M. Olde Loohuis,Anil P.S. Ori,Lilijana Oruc,Urban Ösby,Roy H. Perlis,Amy Perry,Andrea Pfennig,James B. Potash,Shaun Purcell,Shaun Purcell,Eline J. Regeer,Andreas Reif,Céline S. Reinbold,Céline S. Reinbold,John P. Rice,Fabio Rivas,Margarita Rivera,Margarita Rivera,Panos Roussos,Douglas M. Ruderfer,Euijung Ryu,Cristina Sánchez-Mora,Cristina Sánchez-Mora,Alan F. Schatzberg,William A. Scheftner,Nicholas J. Schork,Cynthia Shannon Weickert,Cynthia Shannon Weickert,Tatyana Shehktman,Paul D. Shilling,Engilbert Sigurdsson,Claire Slaney,Olav B. Smeland,Olav B. Smeland,Janet L. Sobell,Christine Søholm Hansen,Christine Søholm Hansen,Anne T. Spijker,David St Clair,Michael Steffens,John Strauss,John Strauss,Fabian Streit,Jana Strohmaier,Szabolcs Szelinger,Robert C. Thompson,Thorgeir E. Thorgeirsson,Jens Treutlein,Helmut Vedder,Weiqing Wang,Stanley J. Watson,Thomas W. Weickert,Thomas W. Weickert,Stephanie H. Witt,Simon Xi,Wei Xu,Wei Xu,Allan H. Young,Peter P. Zandi,Peng Zhang,Sebastian Zöllner,Rolf Adolfsson,Ingrid Agartz,Ingrid Agartz,Martin Alda,Martin Alda,Lena Backlund,Bernhard T. Baune,Bernhard T. Baune,Frank Bellivier,Wade H. Berrettini,Joanna M. Biernacka,Douglas Blackwood,Michael Boehnke,Anders D. Børglum,Anders D. Børglum,Aiden Corvin,Nicholas John Craddock,Mark J. Daly,Mark J. Daly,Udo Dannlowski,Tõnu Esko,Bruno Etain,Mark A. Frye,Janice M. Fullerton,Janice M. Fullerton,Elliot S. Gershon,Michael Gill,Fernando S. Goes,Maria Grigoroiu-Serbanescu,Joanna Hauser,David M. Hougaard,David M. Hougaard,Christina M. Hultman,Ian Jones,Lisa Jones,René S. Kahn,George Kirov,Mikael Landén,Mikael Landén,Marion Leboyer,Marion Leboyer,Cathryn M. Lewis,Qingqin S. Li,Jolanta Lissowska,Nicholas G. Martin,Nicholas G. Martin,Fermín Mayoral,Susan L. McElroy,Andrew M. McIntosh,Francis J. McMahon,Ingrid Melle,Andres Metspalu,Philip B. Mitchell,Gunnar Morken,Ole Mors,Ole Mors,Preben Bo Mortensen,Preben Bo Mortensen,Bertram Müller-Myhsok,Bertram Müller-Myhsok,Richard M. Myers,Benjamin M. Neale,Benjamin M. Neale,Vishwajit L. Nimgaonkar,Merete Nordentoft,Merete Nordentoft,Markus M. Nöthen,Michael Conlon O'Donovan,Ketil J. Oedegaard,Michael John Owen,Sara A. Paciga,Carlos N. Pato,Michele T. Pato,Danielle Posthuma,Josep Antoni Ramos-Quiroga,Marta Ribasés,Marta Ribasés,Marcella Rietschel,Guy A. Rouleau,Guy A. Rouleau,Martin Schalling,Peter R. Schofield,Peter R. Schofield,Thomas G. Schulze,Alessandro Serretti,Jordan W. Smoller,Jordan W. Smoller,Hreinn Stefansson,Kari Stefansson,Kari Stefansson,Eystein Stordal,Patrick F. Sullivan,Patrick F. Sullivan,Gustavo Turecki,Arne E. Vaaler,Eduard Vieta,John B. Vincent,Thomas Werge,Thomas Werge,Thomas Werge,John I. Nurnberger,Naomi R. Wray,Arianna Di Florio,Arianna Di Florio,Howard J. Edenberg,Sven Cichon,Roel A. Ophoff,Laura J. Scott,Ole A. Andreassen,Ole A. Andreassen,John R. Kelsoe,Pamela Sklar,Pamela Sklar +342 more
TL;DR: Genome-wide analysis identifies 30 loci associated with bipolar disorder, allowing for comparisons of shared genes and pathways with other psychiatric disorders, including schizophrenia and depression.
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