Second-generation PLINK: rising to the challenge of larger and richer datasets
Christopher C. Chang,Carson C. Chow,Laurent C. A. M. Tellier,Shashaank Vattikuti,Shaun Purcell,James J. Lee +5 more
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PLINK as discussed by the authors is a C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics, which has been widely used in the literature.Abstract:
PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for even faster and more scalable implementations of key functions. In addition, GWAS and population-genetic data now frequently contain probabilistic calls, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1's primary data format.
To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O(sqrt(n))-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. This will be followed by PLINK 2.0, which will introduce (a) a new data format capable of efficiently representing probabilities, phase, and multiallelic variants, and (b) extensions of many functions to account for the new types of information.
The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.read more
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Journal ArticleDOI
The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease
William J. Astle,Heather Elding,Heather Elding,Tao Jiang,Dave Allen,Dace Ruklisa,Dace Ruklisa,Alice L. Mann,Daniel Mead,Heleen J. Bouman,Fernando Riveros-Mckay,Myrto Kostadima,Myrto Kostadima,Myrto Kostadima,John J. Lambourne,John J. Lambourne,Suthesh Sivapalaratnam,Suthesh Sivapalaratnam,Kate Downes,Kate Downes,Kousik Kundu,Kousik Kundu,Lorenzo Bomba,Kim Berentsen,John Bradley,John Bradley,Louise C. Daugherty,Louise C. Daugherty,Olivier Delaneau,Kathleen Freson,Stephen F. Garner,Stephen F. Garner,Luigi Grassi,Luigi Grassi,Jose A. Guerrero,Jose A. Guerrero,Matthias Haimel,Eva M. Janssen-Megens,Anita Kaan,Mihir A Kamat,Bowon Kim,Amit Mandoli,Jonathan Marchini,Jonathan Marchini,Joost H.A. Martens,Stuart Meacham,Stuart Meacham,Karyn Megy,Karyn Megy,Jared O'Connell,Jared O'Connell,Romina Petersen,Romina Petersen,Nilofar Sharifi,S.M. Sheard,James R Staley,Salih Tuna,Martijn van der Ent,Klaudia Walter,Shuang-Yin Wang,Eleanor Wheeler,Steven P. Wilder,Valentina Iotchkova,Valentina Iotchkova,Carmel Moore,Jennifer G. Sambrook,Jennifer G. Sambrook,Hendrik G. Stunnenberg,Emanuele Di Angelantonio,Emanuele Di Angelantonio,Emanuele Di Angelantonio,Stephen Kaptoge,Stephen Kaptoge,Taco W. Kuijpers,Enrique Carrillo-de-Santa-Pau,David Juan,Daniel Rico,Alfonso Valencia,Lu Chen,Lu Chen,Bing Ge,Louella Vasquez,Tony Kwan,Diego Garrido-Martín,Stephen Watt,Ying Yang,Roderic Guigó,Stephan Beck,Dirk S. Paul,Dirk S. Paul,Tomi Pastinen,David Bujold,Guillaume Bourque,Mattia Frontini,Mattia Frontini,Mattia Frontini,John Danesh,David J. Roberts,David J. Roberts,Willem H. Ouwehand,Adam S. Butterworth,Adam S. Butterworth,Adam S. Butterworth,Nicole Soranzo +103 more
TL;DR: A genome-wide association analysis in the UK Biobank and INTERVAL studies is performed, providing evidence of shared genetic pathways linking blood cell indices with complex pathologies, including autoimmune diseases, schizophrenia, and coronary heart disease and evidence suggesting previously reported population associations betweenBlood cell indices and cardiovascular disease may be non-causal.
Genome-wide association study identifies 74 loci associated with educational attainment
Aysu Okbay,Jonathan P. Beauchamp,Mark Alan Fontana,James J. Lee,Tune H. Pers,Cornelius A. Rietveld,Patrick Turley,Guo-Bo Chen,Valur Emilsson,S. Fleur W. Meddens,Sven Oskarsson,Joseph K. Pickrell,Kevin Thom,Pascal Timshel,Ronald de Vlaming,Abdel Abdellaoui,Tarunveer S. Ahluwalia,Jonas Bacelis,Clemens Baumbach,Gyda Bjornsdottir,Johannes H. Brandsma,Maria Pina Concas,Jaime Derringer,Nicholas A. Furlotte,Tessel E. Galesloot,Giorgia Girotto,Richa Gupta,Leanne M. Hall,Sarah E. Harris,Edith Hofer,Momoko Horikoshi,Jennifer E. Huffman,Kadri Kaasik,Ioanna P. Kalafati,Robert Karlsson,Augustine Kong,Jari Lahti,Sven J. van der Lee,Christiaan de Leeuw,Penelope A. Lind,Karl-Oskar Lindgren,Tian Liu,Massimo Mangino,Jonathan Marten,Evelin Mihailov,Michael B. Miller,Peter J. van der Most,Christopher Oldmeadow,Antony Payton,Natalia Pervjakova,Wouter J. Peyrot,Yong Qian,Olli T. Raitakari,Rico Rueedi,Erika Salvi,Brge Schmidt,Katharina E. Schraut,Jianxin Shi,Albert V. Smith,Raymond A. Poot,Beate St Pourcain,Alexander Teumer,Gudmar Thorleifsson,Niek Verweij,Dragana Vuckovic,Juergen Wellmann,Harm-Jan Westra,Jingyun Yang,Wei Zhao,Zhihong Zhu,Behrooz Z. Alizadeh,Najaf Amin,Andrew Bakshi,Sebastian E. Baumeister,Ginevra Biino,Klaus Bønnelykke,Patricia A. Boyle,Harry Campbell,Francesco P. Cappuccio,Gail Davies,Jan-Emmanuel De Neve,Panos Deloukas,Ilja Demuth,Jun Ding,Peter Eibich,Lewin Eisele,Niina Eklund,David M. Evans,Jessica D. Faul,Mary F. Feitosa,Andreas J. Forstner,Ilaria Gandin,Bjarni Gunnarsson,Bjarni V. Halldorsson,Tamara B. Harris,Andrew C. Heath,Lynne J. Hocking,Elizabeth G. Holliday,Georg Homuth,Michael A. Horan,Jouke-Jan Hottenga,Philip L. De Jager,Peter K. Joshi,Astanand Jugessur,Marika Kaakinen,Mika Kähönen,Stavroula Kanoni,Liisa Keltigangas-Jarvinen,Lambertus A. Kiemeney,Ivana Kolcic,Seppo Koskinen,Aldi T. Kraja,Martin Kroh,Zoltán Kutalik,Antti Latvala,Lenore J. Launer,Maël Lebreton,Douglas F. Levinson,Paul Lichtenstein,Peter Lichtner,David C. Liewald,Anu Loukola,Pamela A. F. Madden,Reedik Mägi,Tomi Mäki-Opas,Riccardo E. Marioni,Pedro Marques-Vidal,Gerardus A. Meddens,George McMahon,Christa Meisinger,Thomas Meitinger,Y. Milaneschi,Lili Milani,Grant W. Montgomery,Ronny Myhre,Christopher P. Nelson,Dale R. Nyholt,William E R Ollier,Aarno Palotie,Lavinia Paternoster,Nancy L. Pedersen,K. Petrovic,David J. Porteous,Katri Räikkönen,Susan M. Ring,Antonietta Robino,Olga Rostapshova,Igor Rudan,Aldo Rustichini,Veikko Salomaa,Alan R. Sanders,Antti-Pekka Sarin,Helena Schmidt,Rodney J. Scott,Blair H. Smith,Jennifer A. Smith,Jan A. Staessen,Elisabeth Steinhagen-Thiessen,Konstantin Strauch,Antonio Terracciano,Martin D. Tobin,Sheila Ulivi,Simona Vaccargiu,Lydia Quaye,Frank J. A. van Rooij,Cristina Venturini,Anna A. E. Vinkhuyzen,Uwe Völker,Henry Völzke,Judith M. Vonk,Diego Vozzi,Johannes Waage,Erin B. Ware,Gonneke Willemsen,John Attia,David A. Bennett,Klaus Berger,Lars Bertram,Hans Bisgaard,Dorret I. Boomsma,Ingrid B. Borecki,Ute Bültmann,Christopher F. Chabris,Francesco Cucca,Daniele Cusi,Ian J. Deary,George Dedoussis,Cornelia M. van Duijn,Johan G. Eriksson,Barbara Franke,Lude Franke,Paolo Gasparini,Pablo V. Gejman,Christian Gieger,Hans-Jörgen Grabe,Jacob Gratten,Patrick J. F. Groenen,Vilmundur Gudnason,Pim van der Harst,Caroline Hayward,David A. Hinds,Wolfgang Hoffmann,Elina Hyppnen,William G. Iacono,Bo Jacobsson,Marjo-Riitta Järvelin,Karl-Heinz Jöckel,Jaakko Kaprio,Sharon L.R. Kardia,Terho Lehtimäki,Steven F. Lehrer,Patrik K. E. Magnusson,Nicholas G. Martin,Matt McGue,Andres Metspalu,Neil Pendleton,Brenda W.J.H. Penninx,Markus Perola,Nicola Pirastu,Mario Pirastu,Ozren Polasek,Danielle Posthuma,Christine Power,Michael A. Province,Nilesh J. Samani,David Schlessinger,Reinhold Schmidt,Thorkild I. A. Sørensen,Tim D. Spector,Kari Stefansson,Unnur Thorsteinsdottir,Roy Thurik,Nicholas J. Timpson,Henning Tiemeier,Joyce Y. Tung,André G. Uitterlinden,Veronique Vitart,Peter Vollenweider,David R. Weir,James F. Wilson,Alan F. Wright,Dalton Conley,Robert F. Krueger,George Davey Smith,Albert Hofman,David Laibson,Sarah E. Medland,Michelle N. Meyer,Jian Yang,Magnus Johannesson,Peter M. Visscher,Tõnu Esko,Philipp Koellinger,David Cesarini,Daniel J. Benjamin +254 more
Journal ArticleDOI
Genomic atlas of the human plasma proteome.
Benjamin B. Sun,Joseph C. Maranville,James E. Peters,James E. Peters,David Stacey,James R Staley,James A. Blackshaw,Stephen Burgess,Tao Jiang,Ellie Paige,Ellie Paige,Praveen Surendran,Clare Oliver-Williams,Mihir A Kamat,Bram P. Prins,Sheri K. Wilcox,Erik S Zimmerman,An Chi,Narinder Bansal,Narinder Bansal,Sarah L. Spain,Angela M. Wood,Nicholas W. Morrell,Nicholas W. Morrell,John Bradley,Nebojsa Janjic,David J. Roberts,David J. Roberts,Willem H. Ouwehand,John A. Todd,Nicole Soranzo,Karsten Suhre,Dirk S. Paul,Caroline S. Fox,Robert M. Plenge,John Danesh,John Danesh,Heiko Runz,Adam S. Butterworth +38 more
TL;DR: The genetic architecture of the human plasma proteome in healthy blood donors from the INTERVAL study is characterized, and it is shown that protein quantitative trait loci overlap with gene expression quantitative traits, as well as with disease-associated loci, and evidence that protein biomarkers have causal roles in disease is found.
Journal ArticleDOI
Genetic mechanisms of critical illness in Covid-19.
Erola Pairo-Castineira,Erola Pairo-Castineira,Sara Clohisey,Lucija Klaric,Andrew D. Bretherick,Konrad Rawlik,Dorota Pasko,Susan P. Walker,Nicholas J. Parkinson,Max Head Fourman,Clark D Russell,James J Furniss,Anne Richmond,E. Gountouna,Nicola Wrobel,David A Harrison,B. Wang,Yang Wu,A. Meynert,Fiona Griffiths,Wilna Oosthuyzen,Athanasios Kousathanas,Loukas Moutsianas,Z. Yang,R. Zhai,Canbin Zheng,Graeme R. Grimes,Rupert Beale,Jonathan E Millar,Barbara Shih,Seán Keating,Marie Zechner,Chris Haley,David J. Porteous,Caroline Hayward,Jian Yang,Julian C. Knight,Charlotte Summers,Manu Shankar-Hari,Manu Shankar-Hari,Paul Klenerman,Lance Turtle,Antonia Ho,S. C. Moore,Charles J. Hinds,P. Horby,Alistair Nichol,Alistair Nichol,Alistair Nichol,David M. Maslove,Lowell Ling,Daniel F. McAuley,Hugh Montgomery,Timothy S. Walsh,Alexandre C. Pereira,Alessandra Renieri,C. Ponting,J. Meikle,P. Finernan,E. Mcmaster,E. Mcmaster,Andy Law,J. K. Baillie,T. Paterson,T. Wackett,Robert C. Armstrong,Robert C. Armstrong,R. Clark,A. Coutts,L. Donnelly,Tamara Gilchrist,K. Hafezi,K. Hafezi,L. Macgillivray,L. Macgillivray,Alan MacLean,Sarah McCafferty,Kirstie Morrice,J. Weaver,C. Boz,C. Boz,A. Golightly,Minghong Ward,H. Mal,H. Szoor-McElhinney,Anthony Brown,Ross Hendry,A. Stenhouse,L. Cullum,D. Law,S. Law,R. Law,Maaike C. Swets,N. Day,F. Taneski,Emma L. Duncan,David Collier,S. Wood,A. Zak,C. Borra,M. Matharu,P. May,Z. Alldis,O. Mitchelmore,R. Bowles,A. Easthope,F. Bibi,I. Lancoma-Malcolm,J. Gurasashvili,J. Pheby,J. Shiel,M. Bolton,Minal Patel,M. Taylor,O. Zongo,P. Ebano,P. Harding,R. Astin-Chamberlain,Y. Choudhury,Anna Cox,D. Kallon,M. Burton,R. Hall,S. Blowes,Z. Prime,J. Biddle,O. Prysyazhna,T. Newman,C. Tierney,J. Kassam,Marlies Ostermann,S. Campos,A. Bociek,R. Lim,N. Grau,T. O. Jones,C. Whitton,M. Marotti,Gill Arbane,S. Bonner,K. Hugill,J. Reid,Ingeborg Welters,V. Waugh,Katherine Williams,D. Shaw,J. F. Roman,M. L. Martinez,Elizabeth M. Johnson,A. Waite,B. Johnston,D. Hamilton,S. 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Turner-Bone,L. Wilding,A. Reddy,S. Whiteley,E. Wilby,C. Howcroft,A. Aspinwall,Sue Charlton,B. Ogg,Donna J. Menzies,Richard Pugh,E. Allan,R. Lean,F. Davies,J. Easton,X. Qiu,Shriya B. Kumar,K. Darlington,G. Houston,P. O'Brien,T. Geary,Jay Allan,A. Meikle,Grant L. Hughes,M. Balasubramaniam,S. Latham,E. McKenna,R. Flanagan,S. Sathe,Emma L. Davies,M. Chablani,A. Kirkby,K. Netherton,S. Archer,Bryan Yates,C. Ashbrook-Raby,Sarah Cole,M. Casey,L. Cabrelli,Stephen Chapman,A. Hutcheon,C. Whyte,C. Almaden-Boyle,Natalie Pattison,Claudina Cruz,A. Vochin,H. Kent,Adri A. M. Thomas,S. Murdoch,B. David,M. Penacerrada,G. Lubimbi,V. Bastion,R. Wulandari,Roberto Lorusso,J. Valentine,D. Clarke,A. Serrano-Ruiz,S. Hierons,C. Eckbad,L. Ramos,C. Demetriou,S. Mitchard,K. White,Nicholas J. White,Steven J. Pitts,D. Branney,J. Frankham,M. Watters,H. Langton,Rachel Prout,V. Page,T. Varghes,A. Cowton,A. Kay,K. Potts,M. Birt,Matthew Peter Kent,A. Wilkinson,E. B. Jude,V. Turner,H. Savill,J. McCormick,M. Coulding,S. Siddiqui,O. Mercer,H. Rehman,D. Potla,N. Capps,David S. Donaldson,H. Button,Terry Martin,K. Hard,A. Agasou,L. Tonks,T. Arden,Patricia A. Boyle,M. Carnahan,J. Strickley,Christopher M. Adams,D. Childs,R. Rikunenko,M. Leigh,M. Breekes,R. Wilcox,A. Bowes,H. Tiveran,F. Hurford,J. Summers,Austin Carter,Y. Hussain,L. Ting,A. Javaid,N. Motherwell,H. Moore,H. Millward,S. Jose,N. Schunki,A. Noakes,C. Clulow,G. Sadera,Reni Jacob,Chris Jones,M. Blunt,Z. Coton,H. Curgenven,S. M. Ally,K. Beaumont,M. Elsaadany,K. Fernandes,I. Ali Mohamed Ali,H. Rangarajan,V. Sarathy,S. Selvanayagam,D. Vedage,M. White,N. Truman,Srikanth Chukkambotla,S. Keith,J. Cockerill-Taylor,J. Ryan-Smith,R. Bolton,P. Springle,J. Dykes,Jo Thomas,Muzamil Majid Khan,M. T. Hijazi,E. Massey,G. Croston,Henrik Reschreiter,Julie Camsooksai,S. Patch,S. Jenkins,C. Humphrey,B. Wadams,M. Msiska,O. Adanini,B. Attwood,P. Parsons,Kate Tatham,S. Jhanji,E. Black,A. Dela Rosa,R. Howle,B. Thomas,T. Bemand,R. Raobaikady,R. Saha,Nikki Staines,A. Daniel,J. Finn,J. Hutter,P. Doble,C. Shovelton,C. Pawley,T. Kannan,Michael Hill,E. Combes,S. Monnery,T. Joefield,M. Popescu,M. Thankachen,M. Oblak,Jeff Little,S. McIvor,A. Brady,H. Whittle,H. Prady,R. Chan,A. Ahmed,Andrew D. Morris,C. Gibson,E. Gordon,S. Keenan,H. Quinn,S. Benyon,S. Marriott,L. Zitter,L. Park,K. Baines,M. Lyons,M. Holland,N. Keenan,M. Young,S. Garrioch,J. Dawson,M. Tolson,B. Scholefield,R. Bi,Neil Richardson,N. Schumacher,T. Cosier,G. Millen,A. Higham,S. Turki,L. Allen,N. Crisp,T. Hazleton,A. Knight,J. Deery,C. Price,S. Turney,S. Tilbey,E. Beranova,Derek W. Wright,L. George,S. Twiss,S. Wadd,K. Postlethwaite,P. Gondo,B. Masunda,A. Kayani,B. Hadebe,J. Whiteside,N. Clarke,Phil Donnison,F. Trim,I. Leadbitter,D. Butcher,S. O'Sullivan,B. Purewal,Scott C. Bell,V. Rivers,R. O'Leary,J. Birch,E. Collins,Stephen K. Anderson,K. Hammerton,E. Andrews,K. Burns,I. Edmond,A. Todd,J. Donnachie,P. Turner,L. Prentice,L. Symon,N. Runciman,F. Auld,M. Halkes,P. Mercer,L. Thornton,G. Debreceni,J. Wilkins,V. Crickmore,G. Subramanian,Robert Marshall,C. Jennings,M. Latif,L. Bunni,M. Spivey,S. Bean,K. Burt,Vanessa Linnett,J. Ritzema,A. Sanderson,W. McCormick,M. Bokhari,R. Kapoor,D. Loader,A. Ayers,W. Harrison,J. North,Z. Belagodu,R. Paramsothy,O. Olufuwa,A. Gherman,B. Fuller,C. Stuart,O. Kelsall,Carrie A. Davis,L. Wild,Henry Wood,Jessica Thrush,A. Durie,K. Austin,K. Archer,P. Anderson,C. Vigurs,C. Thorpe,E. Knights,N. Boyle,Alkes L. Price,A. Kubisz-Pudelko,D. Wood,Amy Lewis,S. Board,L. Pippard,John R. B. Perry,K. Beesley,A. Rattray,E. Lee,L. Lennon,K. Douglas,D. Bell,R. Boyle,L. Glass,M. Nauman Akhtar,K. Dent,D. Potoczna,S. Pearson,E. Horsley,S. Spencer,D. Mullan,D. Skinner,J. Gaylard,R. Barber,C. Hewitt,A. Hilldrith,S. Shepardson,M. Wills,K. Jackson-Lawrence,A. Gupta,E. Timlick,C. Gorman,Igor Otahal,A. Gales,S. Coetzee,Christian Sell,M. Raj,M. Peiu,S. Quaid,E. Watson,Katherine S. Elliott,J. Mallinson,B. Chandler,A. Turnbull,C. Finch,C. Holl,J.A. Cooper,Anthony Evans,W. Khaliq,Andrea M. Collins,E. T. Gude,N. Love,L. van Koutrik,John A. Hunt,D. Kaye,Eva Fisher,A. Brayne,V. Tuckey,P. Jackson,J. Parkin,A. Tariq,Henry Houlden,A. Tucci,John Hardy,E. Moncur,J. Highgate,A. Cowley,A. Mitra,R. Stead,T. Behan,C. Burnett,M. Newton,E. Heeney,R. Pollard,J. Hatton,Amita Patel,Vidya Kasipandian,S. Allibone,R. M. Genetu,L. O'Brien,Z. Omar,E. Perkins,Kevin A. Davies,D. Tetla,B. Shelley,V. Irvine,Samantha J. Williams,Patricia Williams,J. Goodsell,R. Tutton,L. Bough,B. Winter-Goodwin,R. Kitson,J. Pinnell,Anthony J. Wilson,T. Nortcliffe,T. Wood,M. Home,K. Holdroyd,Matthew R. Robinson,R. Shaw,J. Greig,M. Brady,A. Haigh,L. Matupe,M. Usher,S. Mellor,S. Dale,L. Gledhill,L. Shaw,G. Turner,Donna Kelly,B. Anwar,Heather L. Riley,H. Sturgeon,A. Ali,L. Thomis,D. Melia,A. Dance,SE Humphreys,I. Frost,V. Gopal,Jo Godden,A. Holden,S. Swann,Tony Smith,M. Clapham,U. Poultney,R. Harper,P. Rice,R. Reece-Anthony,B. Gurung,S. Moultrie,M. Odam,Andreas Mayer,A. Bellini,A. Pickard,J. Bryant,N. Roe,J. Sowter,K. Lang,Jenny C. Taylor,P. Barry,Maria Hobrok,H. Tench,R. Wolf-Roberts,H. McGuinness,R. Loosley,Daniel B Hawcutt,L. Rad,L. O'Malley,P. Saunderson,G. Seddon,Tim J. Anderson,N. Rogers,J. Ruddy,M. Harkins,C. Beith,A. McAlpine,L. Ferguson,Paul Grant,S. MacFadyen,M. McLaughlin,T. Baird,S. Rundell,B. Welsh,R. Hamill,F. Fisher,J. Gregory,Campbell A,S. Smuts,J Kenneth Baillie,J Kenneth Baillie,Gail Carson,Beatrice Alex,B. Bach,Wendy S. Barclay,Debby Bogaert,Meera Chand,Graham S Cooke,Annemarie B Docherty,Jake Dunning,A. da Silva Filipe,Tom Fletcher,Christopher A Green,Ewen M Harrison,Julian A. Hiscox,Ho A. Y. W.,Peter Horby,Samreen Ijaz,S. Khoo,W. S. Lim,Alexander J. Mentzer,Laura Merson,Alison M. Meynert,Mahdad Noursadeghi,Massimo Palmarini,William A. Paxton,Georgios Pollakis,Nicholas Price,Andrew Rambaut,David Robertson,Vanessa Sancho-Shimizu,Janet T Scott,T I de Silva,Louise Sigfrid,Tom Solomon,Shiranee Sriskandan,David I. Stuart,R.S. Tedder,E. Thomson,Alfred A.R. Thompson,Ryan S Thwaites,L Turtle,Maria Zambon,Hayley Hardwick,Chloe Donohue,Ronan A Lyons,Lisa Norman,Riinu Pius,Thomas M Drake,Cameron J Fairfield,Stephen R Knight,Kenneth A. McLean,Derek Murphy,C. A. Shaw,Jo Dalton,Michelle Girvan,Egle Saviciute,Stuart K. Roberts,Janet Harrison,Laura Marsh,Marie Connor,Sophie Halpin,Carrol Gamble,Gary Leeming,Murray Wham,William Greenhalf,V. Shaw,Sarah D. McDonald,Andrea Ganna,Patrick Sulem,D A van Heel,M. Cordioli,Gardar Sveinbjornsson,M. E. K. Niemi,Janie F. Shelton,A. J. Shastri,C. Ye,C. H. Weldon,T. Filshtein-Sonmez,D. Coker,A. Symons,J. Esparza-Gordillo,Stella Aslibekyan,Adam Auton,J. E. Krieger,E. Marques,C. E. Jannes,Francesca Mari,S. Daga,Margherita Baldassarri,Elisa Benetti,Simone Furini,Chiara Fallerini,Francesca Fava,Floriana Valentino,G. Doddato,Annarita Giliberti,Rossella Tita,Sara Amitrano,Mirella Bruttini,S. Croci,I. Meloni,A. M. Pinto,E. Frullanti,Maria Antonietta Mencarelli,C. L. Rizzo,Francesca Montagnani,L. Di Sarno,A. Tommasi,Marta Palmieri,Arianna Emiliozzi,M. Fabbiani,Barbara Rossetti,Giacomo Zanelli,Elena Bargagli,Laura Bergantini,Miriana d'Alessandro,Paolo Cameli,D. Bennet,Federico Anedda,Simona Marcantonio,Sabino Scolletta,Federico Franchi,Maria Antonietta Mazzei,S. Guerrini,Edoardo Conticini,Luca Cantarini,Bruno Frediani,D. Tacconi,C. Spertilli,M. Feri,Abele Donati,R. Scala,L. Guidelli,G. Spargi,M. Corridi,C. Nencioni,L. Croci,G. P. Caldarelli,M. Spagnesi,P. Piacentini,M. Bandini,E. Desanctis,S. Cappelli,A. Canaccini,A. Verzuri,V. Anemoli,A. Ognibene,M. Vaghi,A d'Arminio Monforte,Esther Merlini,M. U. Mondelli,S. Mantovani,S. Ludovisi,Massimo Girardis,S. Venturelli,M. Sita,Andrea Cossarizza,A. Antinori,Alessandra Vergori,Stefano Rusconi,M. Siano,A. Gabrieli,Agostino Riva,Daniela Francisci,Elisabetta Schiaroli,P. G. Scotton,F. Andretta,S. Panese,R. Scaggiante,F. Gatti,S. G. Parisi,Francesco Castelli,M. E. Quiros-Roldan,P. Magro,Isabella Zanella,M. Della Monica,Carmelo Piscopo,Mario Capasso,Roberta Russo,Immacolata Andolfo,Achille Iolascon,G. Fiorentino,M. Carella,Marco Castori,Giuseppe Merla,Filippo Aucella,P. Raggi,C. Marciano,R. Perna,Matteo Bassetti,A. Di Biagio,M. Sanguinetti,L. Masucci,Serafina Valente,Marco Mandalà,A. Giorli,L. Salerni,P. Zucchi,P. Parravicini,E. Menatti,S. Baratti,T. Trotta,F. Giannattasio,G. Coiro,F. Lena,D. A. Coviello,Cristina Mussini,G. Bosio,E. Martinelli,Sandro Mancarella,L. Tavecchia,L. Crotti,N. Picchiotti,M. Gori,C. Gabbi,M. Sanarico,S. Ceri,P. Pinoli,F. Raimondi,F. Biscarini,A. Stella,Xia Shen,Xia Shen,Chris P. Ponting,Angie Fawkes,Albert Tenesa,Albert Tenesa,Mark J. Caulfield,Richard H Scott,K Rowan,Lee Murphy,Peter J. M. Openshaw,Peter J. M. Openshaw,Malcolm G Semple,Veronique Vitart,James F. Wilson +1449 more
TL;DR: The GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2244 critically ill Covid-19 patients from 208 UK intensive care units is reported, finding evidence in support of a causal link from low expression of IFNAR2, and high expression of TYK2, to life-threatening disease.
Journal ArticleDOI
A meta-analysis of genome-wide association studies identifies 17 new Parkinson's disease risk loci.
Diana Chang,Mike A. Nalls,Ingileif B Hallgrímsdóttir,Julie Hunkapiller,Marcel P. van der Brug,Fang Cai,Geoffrey A. Kerchner,Gai Ayalon,Baris Bingol,Morgan Sheng,David A. Hinds,Timothy W. Behrens,Andrew B. Singleton,Tushar Bhangale,Robert R. Graham +14 more
TL;DR: A key role for autophagy and lysosomal biology in PD risk is indicated, and potential new drug targets for PD are suggested.
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The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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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
TL;DR: 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.
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TL;DR: VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.
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PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
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Resch,Jonathan Barker,Laura Clarke,Laurent Gil,Sarah E. Hunt,Gavin Kelman,Eugene Kulesha,Rasko Leinonen,William M. McLaren,Rajesh Radhakrishnan,Asier Roa,Dmitriy Smirnov,Richard Smith,Ian Streeter,Anja Thormann,Iliana Toneva,Brendan Vaughan,Xiangqun Zheng-Bradley,Russell J. Grocock,Sean Humphray,Terena James,Zoya Kingsbury,Ralf Sudbrak,M. Albrecht,Vyacheslav Amstislavskiy,Tatiana A. Borodina,Matthias Lienhard,Florian Mertes,Marc Sultan,Bernd Timmermann,Marie-Laure Yaspo,Lucinda Fulton,Victor Ananiev,Zinaida Belaia,Dimitriy Beloslyudtsev,Nathan Bouk,Chao Chen,Deanna M. Church,Robert M. Cohen,Charles Cook,John Garner,Timothy Hefferon,Mikhail Kimelman,Chunlei Liu,John Lopez,Peter Meric,Chris O’Sullivan,Yuri Ostapchuk,Lon Phan,Sergiy Ponomarov,Valerie A. Schneider,Eugene Shekhtman,Karl Sirotkin,Douglas J. Slotta,Hua Zhang,Senduran Balasubramaniam,John Burton,Petr Danecek,Thomas M. Keane,Anja Kolb-Kokocinski,Shane A. McCarthy,James Stalker,Michael A. 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Grant,Carla Gallo,Giovanni Poletti,Danish Saleheen,Asif Rasheed,Lisa D. Brooks,Adam Felsenfeld,Jean E. McEwen,Yekaterina Vaydylevich,Audrey Duncanson,Michael Dunn,Jeffery A. Schloss +517 more
A reference panel of 64,976 haplotypes for genotype imputation
Shane A. McCarthy,Sayantan Das,Warren W. Kretzschmar,Olivier Delaneau,Andrew R. Wood,Alexander Teumer,Hyun Min Kang,Christian Fuchsberger,Petr Danecek,Kevin Sharp,Yang Luo,C Sidore,Alan Kwong,Nicholas J. Timpson,Seppo Koskinen,Scott I. Vrieze,Laura J. Scott,He Zhang,Anubha Mahajan,Jan H. Veldink,Ulrike Peters,Ulrike Peters,Carlos N. Pato,Cornelia M. van Duijn,Christopher E. Gillies,Ilaria Gandin,Massimo Mezzavilla,Arthur Gilly,Massimiliano Cocca,Michela Traglia,Andrea Angius,Jeffrey C. Barrett,D.I. Boomsma,Kari Branham,Gerome Breen,Gerome Breen,Chad M. Brummett,Fabio Busonero,Harry Campbell,Andrew T. Chan,Sai Chen,Emily Y. Chew,Francis S. Collins,Laura J Corbin,George Davey Smith,George Dedoussis,Marcus Dörr,Aliki-Eleni Farmaki,Luigi Ferrucci,Lukas Forer,Ross M. Fraser,Stacey Gabriel,Shawn Levy,Leif Groop,Leif Groop,Tabitha A. Harrison,Andrew T. Hattersley,Oddgeir L. Holmen,Kristian Hveem,Matthias Kretzler,James Lee,Matt McGue,Thomas Meitinger,David Melzer,Josine L. Min,Karen L. Mohlke,John B. Vincent,Matthias Nauck,Deborah A. Nickerson,Aarno Palotie,Aarno Palotie,Michele T. Pato,Nicola Pirastu,Melvin G. McInnis,J. Brent Richards,J. Brent Richards,Cinzia Sala,Veikko Salomaa,David Schlessinger,Sebastian Schoenherr,P. Eline Slagboom,Kerrin S. Small,Tim D. Spector,Dwight Stambolian,Marcus A. Tuke,Jaakko Tuomilehto,Leonard H. van den Berg,Wouter van Rheenen,Uwe Völker,Cisca Wijmenga,Daniela Toniolo,Eleftheria Zeggini,Paolo Gasparini,Matthew G. Sampson,James F. Wilson,Timothy M. Frayling,Paul I.W. de Bakker,Morris A. Swertz,Steven A. McCarroll,Charles Kooperberg,Annelot M. Dekker,David Altshuler,Cristen J. Willer,William G. Iacono,Samuli Ripatti,Nicole Soranzo,Nicole Soranzo,Klaudia Walter,Anand Swaroop,Francesco Cucca,Carl A. Anderson,Richard M. Myers,Michael Boehnke,Mark I. McCarthy,Mark I. McCarthy,Richard Durbin,Gonçalo R. Abecasis,Jonathan Marchini +117 more