LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis
Jie Zheng,A. Mesut Erzurumluoglu,Benjamin Elsworth,John P. Kemp,Laurence J. Howe,Philip C Haycock,Gibran Hemani,Katherine E. Tansey,Charles Laurin,Early Genetics,Beate St Pourcain,Nicole M. Warrington,Hilary K. Finucane,Hilary K. Finucane,Alkes L. Price,Alkes L. Price,Brendan Bulik-Sullivan,Verneri Anttila,Lavinia Paternoster,Tom R. Gaunt,Tom R. Gaunt,David M. Evans,David M. Evans,Benjamin M. Neale,Benjamin M. Neale +24 more
TLDR
The proposed LD Hub database and accompanying web interface will ensure maximal uptake of the LD score regression methodology, provide a useful database for the public dissemination of GWAS results, and provide a method for easily screening hundreds of traits for overlapping genetic aetiologies.Abstract:
Motivation: LD score regression is a reliable and efficient method of using genome-wide association
study (GWAS) summary-level results data to estimate the SNP heritability of complex traits
and diseases, partition this heritability into functional categories, and estimate the genetic correlation
between different phenotypes. Because the method relies on summary level results data, LD
score regression is computationally tractable even for very large sample sizes. However, publicly
available GWAS summary-level data are typically stored in different databases and have different
formats, making it difficult to apply LD score regression to estimate genetic correlations across
many different traits simultaneously.
Results: In this manuscript, we describe LD Hub - a centralized database of summary-level GWAS results
for 173 diseases/traits from different publicly available resources/consortia and a web interface
that automates the LD score regression analysis pipeline. To demonstrate functionality and validate
our software, we replicated previously reported LD score regression analyses of 49 traits/diseases
using LD Hub; and estimated SNP heritability and the genetic correlation across the different phenotypes.
We also present new results obtained by uploading a recent atopic dermatitis GWAS meta-analysis to examine the genetic correlation between the condition and other potentially related traits.
In response to the growing availability of publicly accessible GWAS summary-level results data, our
database and the accompanying web interface will ensure maximal uptake of the LD score regression
methodology, provide a useful database for the public dissemination of GWAS results, and provide a
method for easily screening hundreds of traits for overlapping genetic aetiologiesread more
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10 Years of GWAS Discovery: Biology, Function, and Translation
Peter M. Visscher,Naomi R. Wray,Qian Zhang,Pamela Sklar,Mark I. McCarthy,Matthew A. Brown,Jian Yang +6 more
TL;DR: The remarkable range of discoveriesGWASs has facilitated in population and complex-trait genetics, the biology of diseases, and translation toward new therapeutics are reviewed.
Journal ArticleDOI
The MR-Base platform supports systematic causal inference across the human phenome
Gibran Hemani,Jie Zheng,Benjamin Elsworth,Kaitlin H Wade,Valeriia Haberland,Denis Baird,Charles Laurin,Stephen Burgess,Jack Bowden,Ryan Langdon,Vanessa Y Tan,James Yarmolinsky,Hashem A Shihab,Nicholas J. Timpson,David M. Evans,David M. Evans,Caroline L Relton,Richard M. Martin,George Davey Smith,Tom R. Gaunt,Philip C Haycock +20 more
TL;DR: MR-Base is a platform that integrates a curated database of complete GWAS results (no restrictions according to statistical significance) with an application programming interface, web app and R packages that automate 2SMR, and includes several sensitivity analyses for assessing the impact of horizontal pleiotropy and other violations of assumptions.
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.
Hundreds of variants clustered in genomic loci and biological pathways affect human height
Hana Lango Allen,Karol Estrada,Guillaume Lettre,Sonja I. Berndt,Michael N. Weedon,Fernando Rivadeneira,Cristen J. Willer,Anne U. Jackson,Sailaja Vedantam,Soumya Raychaudhuri,Teresa Ferreira,Andrew R. Wood,Robert J. Weyant,Ayellet V. Segrè,Elizabeth K. Speliotes,Eleanor Wheeler,Nicole Soranzo,Ju-Hyun Park,Jian Yang,Daniel F. Gudbjartsson,Nancy L. Heard-Costa,Joshua C. Randall,Lu Qi,Albert V. Smith,Reedik Maegi,Tomi Pastinen,Liming Liang,Iris M. Heid,Jian'an Luan,Gudmar Thorleifsson,Thomas W. Winkler,Michael E. Goddard,Ken Sin Lo,Cameron D. Palmer,Tsegaselassie Workalemahu,Yurii S. Aulchenko,Åsa Johansson,M. Carola Zillikens,Mary F. Feitosa,Tõnu Esko,Toby Johnson,Shamika Ketkar,Peter Kraft,Massimo Mangino,Inga Prokopenko,Devin Absher,Eva Albrecht,Florian Ernst,Nicole L. Glazer,Caroline Hayward,Jouke-Jan Hottenga,Kevin B. Jacobs,Joshua W. Knowles,Zoltán Kutalik,Keri L. Monda,Ozren Polasek,Michael Preuss,Nigel W. Rayner,Neil R. Robertson,Valgerdur Steinthorsdottir,Jonathan Tyrer,Benjamin F. Voight,Fredrik Wiklund,Jianfeng Xu,Jing Hua Zhao,Dale R. Nyholt,Niina Pellikka,Markus Perola,John R. B. Perry,Ida Surakka,Mari-Liis Tammesoo,Elizabeth L. Altmaier,Najaf Amin,Thor Aspelund,Tushar Bhangale,Gabrielle Boucher,Daniel I. Chasman,Constance Chen,Lachlan J. M. Coin,Mark E. Cooper,Anna L. Dixon,Quince Gibson,Elin Grundberg,Ke Hao,M. Juhani Junttila,Lee M. Kaplan,Johannes Kettunen,Inke R. Koenig,Tony Kwan,Robert Lawrence,Douglas F. Levinson,Mattias Lorentzon,Barbara McKnight,Andrew P. Morris,Martina Mueller,Julius S. Ngwa,Shaun Purcell,Suzanne Rafelt,Rany M. Salem,Erika Salvi,Serena Sanna,Jianxin Shi,Ulla Sovio,John R. Thompson,Michael C. Turchin,Liesbeth Vandenput,Dominique J. Verlaan,Veronique Vitart,Charles C. White,Andreas Ziegler,Peter Almgren,Anthony J. Balmforth,Harry Campbell,Lorena Citterio,Alessandro De Grandi,Anna F. Dominiczak,Jubao Duan,Paul Elliott,Roberto Elosua,Johan G. Eriksson,Nelson B. Freimer,Eco J. C. de Geus,Nicola Glorioso,Shen Haiqing,Anna-Liisa Hartikainen,Aki S. Havulinna,Andrew A. Hicks,Jennie Hui,Wilmar Igl,Thomas Illig,Antti Jula,Eero Kajantie,Tuomas O. Kilpelaeinen,Markku Koiranen,Ivana Kolcic,Seppo Koskinen,Peter Kovacs,Jaana Laitinen,Jianjun Liu,Marja-Liisa Lokki,Ana Marušić,Andrea Maschio,Thomas Meitinger,Antonella Mulas,Guillaume Paré,Alex N. Parker,John F. Peden,Astrid Petersmann,Irene Pichler,Kirsi H. Pietiläinen,Anneli Pouta,Martin Riddertrale,Jerome I. Rotter,Jennifer G. Sambrook,Alan R. Sanders,Carsten Oliver Schmidt,Juha Sinisalo,Jan Smit,Heather M. Stringham,G. Bragi Walters,Elisabeth Widen,Sarah H. Wild,Gonneke Willemsen,Laura Zagato,Lina Zgaga,Paavo Zitting,Helene Alavere,Martin Farrall,Wendy L. McArdle,Mari Nelis,Marjolein Peters,Samuli Ripatti,Joyce B. J. vVan Meurs,Katja K.H. Aben,Kristin G. Ardlie,Jacques S. Beckmann,John Beilby,Richard N. Bergman,Sven Bergmann,Francis S. Collins,Daniele Cusi,Martin den Heijer,Gudny Eiriksdottir,Pablo V. Gejman,Alistair S. Hall,Anders Hamsten,Heikki V. Huikuri,Carlos Iribarren,Mika Kähönen,Jaakko Kaprio,Sekar Kathiresan,Lambertus A. Kiemeney,Thomas D. Kocher,Lenore J. Launer,Terho Lehtimäki,Olle Melander,Thomas H. Mosley,Arthur W. Musk,Markku S. Nieminen,Christopher J. O'Donnell,Claes Ohlsson,Ben A. Oostra,Lyle J. Palmer,Olli T. Raitakari,Paul M. Ridker,John D. Rioux,Aila Rissanen,Carlo Rivolta,Heribert Schunkert,Alan R. Shuldiner,David S. Siscovick,Michael Stumvoll,Anke Toenjes,Jaakko Tuomilehto,Gert-Jan B. van Ommen,Jorma Viikari,Andrew C. Heath,Nicholas G. Martin,Grant W. Montgomery,Michael A. Province,Manfred Kayser,Alice M. Arnold,Larry D. Atwood,Eric Boerwinkle,Stephen J. Chanock,Panos Deloukas,Christian Gieger,Henrik Grönberg,Per Hall,Andrew T. Hattersley,Christian Hengstenberg,Wolfgang Hoffman,G. Mark Lathrop,Veikko Salomaa,Stefan Schreiber,Manuela Uda,Dawn M. Waterworth,Alan F. Wright,Themistocles L. Assimes,Inês Barroso,Albert Hofman,Karen L. Mohlke,Dorret I. Boomsma,Mark J. Caulfield,L. Adrienne Cupples,Jeanette Erdmann,Caroline S. Fox,Vilmundur Gudnason,Ulf Gyllensten,Tamara B. Harris,Richard B. Hayes,Marjo-Ritta Jarvelin,Vincent Mooser,Patricia B. Munroe,Willem H. Ouwehand,Brenda W.J.H. Penninx,Peter P. Pramstaller,Thomas Quertermous,Igor Rudan,Nilesh J. Samani,Tim D. Spector,Henry Voelzke,Hugh Watkins,James F. Wilson,Leif Groop,Talin Haritunians,Frank B. Hu,Robert C. Kaplan,Andres Metspalu,Kari E. North,David Schlessinger,Nicholas J. Wareham,David J. Hunter,Jeffrey R. O'Connell,David P. Strachan,H. Erich Schadt,Unnur Thorsteinsdottir,Leena Peltonen,André G. Uitterlinden,Peter M. Visscher,Nilanjan Chatterjee,Ruth J. F. Loos,Michael Boehnke,Mark I. McCarthy,Erik Ingelsson,Cecilia M. Lindgren,Gonçalo R. Abecasis,Kari Stefansson,Timothy M. Frayling,Joel N. Hirschhorn +289 more
TL;DR: In this paper, the authors show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait, revealing patterns with important implications for genetic studies of common human diseases and traits.
Journal ArticleDOI
Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing
Cohorts for Heart,Genetic,Genetic,Genetic,Environmental Risk in Ad,Polygenic Defining Genetic,Perades +6 more
TL;DR: Pathway analysis implicates immunity, lipid metabolism, tau binding proteins, and amyloid precursor protein (APP) metabolism, showing that genetic variants affecting APP and Aβ processing are associated not only with early-onset autosomal dominant Alzheimer’s disease but also with LOAD.
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TL;DR: Associations at DRD2 and several genes involved in glutamatergic neurotransmission highlight molecules of known and potential therapeutic relevance to schizophrenia, and are consistent with leading pathophysiological hypotheses.
Journal ArticleDOI
GCTA: a tool for genome-wide complex trait analysis.
TL;DR: The GCTA software is a versatile tool to estimate and partition complex trait variation with large GWAS data sets and focuses on the function of estimating the variance explained by all the SNPs on the X chromosome and testing the hypotheses of dosage compensation.
Journal ArticleDOI
Common polygenic variation contributes to risk of schizophrenia and bipolar disorder
Shaun Purcell,Shaun Purcell,Naomi R. Wray,Jennifer Stone,Jennifer Stone,Peter M. Visscher,Michael Conlon O'Donovan,Patrick F. Sullivan,Pamela Sklar,Pamela Sklar,Douglas M. Ruderfer,Andrew McQuillin,Derek W. Morris,Colm O'Dushlaine,Aiden Corvin,Peter Holmans,Stuart MacGregor,Hugh Gurling,Douglas Blackwood,Nicholas John Craddock,Michael Gill,Christina M. Hultman,Christina M. Hultman,George Kirov,Paul Lichtenstein,Walter J. Muir,Michael John Owen,Carlos N. Pato,Edward M. Scolnick,Edward M. Scolnick,David St Clair,Nigel Williams,Lyudmila Georgieva,Ivan Nikolov,Nadine Norton,Hywel Williams,Draga Toncheva,Vihra Milanova,Emma Flordal Thelander,Patrick Sullivan,Elaine Kenny,Emma M. Quinn,Khalid Choudhury,Susmita Datta,Jonathan Pimm,Srinivasa Thirumalai,Vinay Puri,Robert Krasucki,Jacob Lawrence,Digby Quested,Nicholas Bass,Caroline Crombie,Gillian Fraser,Soh Leh Kuan,Nicholas Walker,Kevin A. McGhee,Ben S. Pickard,P. Malloy,Alan W Maclean,Margaret Van Beck,Michele T. Pato,Helena Medeiros,Frank A. Middleton,Célia Barreto Carvalho,Christopher P. Morley,Ayman H. Fanous,David V. Conti,James A. Knowles,Carlos Ferreira,António Macedo,M. Helena Azevedo,Andrew Kirby,Andrew Kirby,Manuel A. R. Ferreira,Manuel A. R. Ferreira,Mark J. Daly,Mark J. Daly,Kimberly Chambert,Finny G Kuruvilla,Stacey Gabriel,Kristin G. Ardlie,Jennifer L. Moran +81 more
TL;DR: The extent to which common genetic variation underlies the risk of schizophrenia is shown, using two analytic approaches, and the major histocompatibility complex is implicate, which is shown to involve thousands of common alleles of very small effect.
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Systemic lupus erythematosus
Jessica J Manson,Anisur Rahman +1 more
TL;DR: Systemic lupus erythematosus is a relapsing and remitting disease, and treatment aims are threefold: managing acute periods of potentially life-threatening ill health, minimizing the risk of flares during periods of relative stability, and controlling the less life- threatening, but often incapacitating day to day symptoms.