PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
Shaun Purcell,Shaun Purcell,Benjamin M. Neale,Benjamin M. Neale,Kathe Todd-Brown,Lori Thomas,Manuel A. R. Ferreira,David Bender,David Bender,Julian Maller,Julian Maller,Pamela Sklar,Pamela Sklar,Paul I.W. de Bakker,Paul I.W. de Bakker,Mark J. Daly,Mark J. Daly,Pak C. Sham +17 more
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TLDR
This work introduces PLINK, an open-source C/C++ WGAS tool set, and describes the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation, which focuses on the estimation and use of identity- by-state and identity/descent information in the context of population-based whole-genome studies.Abstract:
Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis.read more
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Identification of new susceptibility loci for osteoarthritis (arcOGEN): A genome-wide association study
Eleftheria Zeggini,Kalliope Panoutsopoulou,Lorraine Southam,Lorraine Southam,N W Rayner,Aaron G. Day-Williams,M C Lopes,M C Lopes,Vesna Boraska,Tõnu Esko,Evangelos Evangelou,A Hoffman,Jeanine J. Houwing-Duistermaat,Thorvaldur Ingvarsson,Ingileif Jonsdottir,Ingileif Jonsdottir,H Jonnson,Hanneke J. M. Kerkhof,Margreet Kloppenburg,Steffan D. Bos,Massimo Mangino,Sarah Metrustry,P E Slagboom,Gudmar Thorleifsson,Raine Eva.,Madhushika Ratnayake,Michelle Ricketts,C Beazley,Hannah Blackburn,Suzannah Bumpstead,K S Elliott,Sarah E. Hunt,Simon C. Potter,Shin S-Y.,Vijay K. Yadav,Guangju Zhai,K Sherburn,K Dixon,E Arden,N Aslam,Battley P-K.,I Carluke,Sally Doherty,Allan Gordon,J Joseph,Richard Keen,N Koller,Sheryl Mitchell,F O'Neill,E Paling,Mike R. Reed,Fernando Rivadeneira,D Swift,K Walker,Bridget Watkins,M. Wheeler,Fraser Birrell,Ioannidis Jpa.,Ingrid Meulenbelt,Andres Metspalu,Ashok Rai,Donald Salter,K. Stefansson,U Stykarsdottir,A.G. Uitterlinden,van Meurs Jbj.,Karen E. Chapman,Panagiotis Deloukas,Ollier Wer.,Gillian A. Wallis,Nigel K Arden,Andrew Carr,Michael Doherty,Andrew McCaskie,J M Willkinson,Stuart Ralston,Ana M. Valdes,Tim D. Spector,John Loughlin +78 more
TL;DR: One of the signals close to genome-wide significance was within the FTO gene, which is involved in regulation of bodyweight—a strong risk factor for osteoarthritis.
Journal ArticleDOI
Life-threatening influenza and impaired interferon amplification in human IRF7 deficiency
Michael J. Ciancanelli,Sarah X.L. Huang,Priya Luthra,Hannah Garner,Yuval Itan,Stefano Volpi,Stefano Volpi,Fabien G. Lafaille,Céline Trouillet,Mirco Schmolke,Randy A. Albrecht,Elisabeth Israelsson,Hye Kyung Lim,Melina Casadio,Tamar Hermesh,Lazaro Lorenzo,Lazaro Lorenzo,Lawrence W. Leung,Vincent Pedergnana,Vincent Pedergnana,Bertrand Boisson,Satoshi Okada,Satoshi Okada,Capucine Picard,Benedicte Ringuier,Françoise Troussier,Damien Chaussabel,Damien Chaussabel,Laurent Abel,Laurent Abel,Laurent Abel,Isabelle Pellier,Luigi D. Notarangelo,Adolfo García-Sastre,Christopher F. Basler,Frederic Geissmann,Shen-Ying Zhang,Shen-Ying Zhang,Shen-Ying Zhang,Hans-Willem Snoeck,Jean-Laurent Casanova +40 more
TL;DR: It is suggested that IRF7-dependent amplification of type I and III IFNs is required for protection against primary infection by influenza virus in humans and that severe influenza may result from single-gene inborn errors of immunity.
Journal ArticleDOI
Genome-wide association study results for educational attainment aid in identifying genetic heterogeneity of schizophrenia
Vikas Bansal,Marina Mitjans,Casper A.P. Burik,Casper A.P. Burik,Richard Karlsson Linnér,Richard Karlsson Linnér,Aysu Okbay,Cornelius A. Rietveld,Martin Begemann,Stefan Bonn,Stefan Bonn,Stephan Ripke,Stephan Ripke,Stephan Ripke,Ronald de Vlaming,Michel G. Nivard,Hannelore Ehrenreich,Philipp Koellinger,Philipp Koellinger +18 more
TL;DR: Strong genetic dependence between EA and SZ is found that cannot be explained by chance, linkage disequilibrium, or assortative mating, and multiple genes have pleiotropic effects on both without a systematic pattern of sign concordance.
Journal ArticleDOI
Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus
Timothy R D J Radstake,Olga Y. Gorlova,Blanca Rueda,Jose Ezequiel Martin,Behrooz Z. Alizadeh,Rogelio Palomino-Morales,Marieke J H Coenen,Madelon C. Vonk,Alexandre E. Voskuyl,Annemie J. Schuerwegh,Jasper C A Broen,Piet L. C. M. van Riel,Ruben van 't Slot,Annet Italiaander,Roel A. Ophoff,Roel A. Ophoff,Gabriela Riemekasten,Nico Hunzelmann,Carmen P. Simeon,Norberto Ortego-Centeno,Miguel A. Gonzalez-Gay,María Francisca González-Escribano,Paolo Airò,Jaap M van Laar,Ariane L. Herrick,Jane Worthington,Roger Hesselstrand,Vanessa Smith,Filip De Keyser,Fredric Houssiau,Meng May Chee,Rajan Madhok,Paul G. Shiels,Rene Westhovens,Alexander Kreuter,Hans P. Kiener,Elfride De Baere,Torsten Witte,Leonid Padykov,Lars Klareskog,Lorenzo Beretta,Rafaella Scorza,Benedicte A. Lie,Anna Maria Hoffmann-Vold,Patricia Carreira,John Varga,Monique Hinchcliff,Peter K. Gregersen,Annette Lee,Jun Ying,Younghun Han,Shih-Feng Weng,Christopher I. Amos,Fredrick M. Wigley,Laura K. Hummers,J. Lee Nelson,Sandeep K. Agarwal,Shervin Assassi,Pravitt Gourh,Filemon K. Tan,Bobby P. C. Koeleman,Frank C. Arnett,Javier Martín,Maureen D. Mayes +63 more
TL;DR: The first genome-wide association study in a population of European ancestry including a total of 2,296 individuals with SSc and 5,171 controls identified a new susceptibility locus for systemic sclerosis at CD247 (1q22–23, rs2056626).
Journal ArticleDOI
Largest GWAS of PTSD (N=20 070) yields genetic overlap with schizophrenia and sex differences in heritability
Laramie E. Duncan,Andrew Ratanatharathorn,Allison E. Aiello,Lynn M. Almli,Amstadter Ab,Allison E. Ashley-Koch,Dewleen G. Baker,Jean C. Beckham,Laura J. Bierut,Jonathan Ian Bisson,Bekh Bradley,Chia-Yen Chen,Shareefa Dalvie,Lindsay A. Farrer,Sandro Galea,Melanie E. Garrett,Joel Gelernter,Guia Guffanti,Michael A. Hauser,Eric O. Johnson,Ronald C. Kessler,Nathan A. Kimbrel,Nathan A. Kimbrel,Anthony P. King,Nastassja Koen,Nastassja Koen,Henry R. Kranzler,Mark W. Logue,Adam X. Maihofer,Alicia R. Martin,Mark W. Miller,Mark W. Miller,Rajendra A. Morey,Nicole R. Nugent,John P. Rice,Stephan Ripke,Stephan Ripke,Stephan Ripke,Andrea L. Roberts,Nancy L. Saccone,Jordan W. Smoller,Jordan W. Smoller,Dan J. Stein,Dan J. Stein,Murray B. Stein,Murray B. Stein,Jennifer A. Sumner,Monica Uddin,Robert J. Ursano,Derek E. Wildman,Rachel Yehuda,Hongyu Zhao,Mark J. Daly,Mark J. Daly,Israel Liberzon,Kerry J. Ressler,Kerry J. Ressler,Caroline M. Nievergelt,Caroline M. Nievergelt,Karestan C. Koenen,Karestan C. Koenen +60 more
TL;DR: The results demonstrate genetic influences on the development of PTSD, identify shared genetic risk between PTSD and other psychiatric disorders and highlight the importance of multiethnic/racial samples.
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