Journal ArticleDOI
Genotype imputation for genome-wide association studies
Jonathan Marchini,Bryan Howie +1 more
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TLDR
The details of several different statistical methods for imputing genotypes are described, the factors that influence imputation performance are illustrated and discussed, and methods that can be used to assess imputations performance and test association at imputed SNPs are reviewed.Abstract:
In the past few years genome-wide association (GWA) studies have uncovered a large number of convincingly replicated associations for many complex human diseases. Genotype imputation has been used widely in the analysis of GWA studies to boost power, fine-map associations and facilitate the combination of results across studies using meta-analysis. This Review describes the details of several different statistical methods for imputing genotypes, illustrates and discusses the factors that influence imputation performance, and reviews methods that can be used to assess imputation performance and test association at imputed SNPs.read more
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Journal ArticleDOI
A Map of Human Genome Variation From Population-Scale Sequencing
Gonçalo R. Abecasis,David Altshuler,David Altshuler,Adam Auton,Lisa D Brooks,Richard Durbin,Richard A. Gibbs,Matthew E. Hurles,Gil McVean +8 more
TL;DR: The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype as mentioned in this paper, and the results of the pilot phase of the project, designed to develop and compare different strategies for genomewide sequencing with high-throughput platforms.
Journal ArticleDOI
Next-generation genotype imputation service and methods.
Sayantan Das,Lukas Forer,Sebastian Schönherr,Carlo Sidore,Carlo Sidore,Adam E. Locke,Alan Kwong,Scott I. Vrieze,Emily Y. Chew,Shawn Levy,Matt McGue,David Schlessinger,Dwight Stambolian,Po-Ru Loh,William G. Iacono,Anand Swaroop,Laura J. Scott,Francesco Cucca,Florian Kronenberg,Michael Boehnke,Gonçalo R. Abecasis,Christian Fuchsberger,Christian Fuchsberger,Christian Fuchsberger +23 more
TL;DR: Improvements to imputation machinery are described that reduce computational requirements by more than an order of magnitude with no loss of accuracy in comparison to standard imputation tools.
Journal ArticleDOI
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis
Stephen Sawcer,Garrett Hellenthal,Matti Pirinen,Chris C. A. Spencer,Nikolaos A. Patsopoulos,Nikolaos A. Patsopoulos,Nikolaos A. Patsopoulos,Loukas Moutsianas,Alexander T. Dilthey,Zhan Su,Colin Freeman,Sarah E. Hunt,Sarah Edkins,Emma Gray,David R. Booth,Simon C. Potter,An Goris,Gavin Band,Annette Bang Oturai,A. Strange,Janna Saarela,Céline Bellenguez,Bertrand Fontaine,Matthew W. Gillman,Bernhard Hemmer,Rhian Gwilliam,Frauke Zipp,Alagurevathi Jayakumar,Roland Martin,Stephen Leslie,Stanley Hawkins,Eleni Giannoulatou,Sandra D'Alfonso,Hannah Blackburn,Filippo Martinelli Boneschi,Jennifer Liddle,Hanne F. Harbo,Hanne F. Harbo,M. Perez,Anne Spurkland,Matthew Waller,Marcin P. Mycko,Michelle Ricketts,Manuel Comabella,Naomi Hammond,Ingrid Kockum,O. T. McCann,Maria Ban,Pamela Whittaker,Anu Kemppinen,Paul A. Weston,Clive Hawkins,Sara Widaa,John Zajicek,John Zajicek,Serge Dronov,Neil Robertson,Suzannah Bumpstead,Lisa F. Barcellos,Lisa F. Barcellos,Rathi Ravindrarajah,Roby Abraham,Lars Alfredsson,Kristin G. Ardlie,Cristin Aubin,Amie Baker,K Baker,Sergio E. Baranzini,Laura Bergamaschi,Roberto Bergamaschi,Allan L. Bernstein,Achim Berthele,Mike Boggild,Jonathan P. Bradfield,David Brassat,Simon Broadley,Dorothea Buck,Helmut Butzkueven,Ruggero Capra,William M. Carroll,Paola Cavalla,Elisabeth Gulowsen Celius,Sabine Cepok,Rosetta M. Chiavacci,Françoise Clerget-Darpoux,Katleen Clysters,Giancarlo Comi,Mark D. Cossburn,Isabelle Cournu-Rebeix,M. B. Cox,Wendy Cozen,Bruce A.C. Cree,Anne H. Cross,Daniele Cusi,Mark J. Daly,Mark J. Daly,Emma J. Davis,Paul I.W. de Bakker,Paul I.W. de Bakker,Paul I.W. de Bakker,Marc Debouverie,Marie B. D'hooghe,K Dixon,Rita Dobosi,Bénédicte Dubois,David Ellinghaus,Irina Elovaara,Federica Esposito,Claire Fontenille,Simon J. Foote,Andre Franke,Daniela Galimberti,Angelo Ghezzi,Joseph T. Glessner,Refujia Gomez,Olivier Gout,Colin A. Graham,Struan F.A. Grant,Struan F.A. Grant,Franca Rosa Guerini,Hakon Hakonarson,Hakon Hakonarson,Per Hall,Anders Hamsten,Hans-Peter Hartung,Robert Heard,Simon Heath,Jeremy Hobart,Jeremy Hobart,Muna Hoshi,Carmen Infante-Duarte,Gillian Ingram,Wendy Ingram,Wendy Ingram,Talat Islam,Maja Jagodic,Michael Kabesch,Allan G. Kermode,Trevor J. Kilpatrick,Cecilia Kim,Norman Klopp,Keijo Koivisto,Malin Larsson,Mark Lathrop,Jeannette Lechner-Scott,Maurizio Leone,Virpi M. Leppä,Ulrika Liljedahl,Izaura Lima Bomfim,Robin R. Lincoln,Jenny Link,Jianjun Liu,Åslaug R. Lorentzen,Åslaug R. Lorentzen,Sara Lupoli,Fabio Macciardi,Fabio Macciardi,Thomas M. Mack,Mark Marriott,Vittorio Martinelli,Deborah F. Mason,Jacob L. McCauley,Frank D. Mentch,Inger-Lise Mero,Tania Mihalova,Xavier Montalban,John Mottershead,Kjell-Morten Myhr,Paola Naldi,William E R Ollier,Alison Page,Aarno Palotie,Jean Pelletier,Laura Piccio,Trevor Pickersgill,Fredrik Piehl,Susan Pobywajlo,Hong L. Quach,Patricia P. Ramsay,Mauri Reunanen,Richard Reynolds,John D. Rioux,John D. Rioux,Mariaemma Rodegher,Sabine Roesner,Justin P. Rubio,Ina-Maria Rueckert,Marco Salvetti,Erika Salvi,Adam Santaniello,Catherine Schaefer,Stefan Schreiber,Christian Schulze,Rodney J. Scott,Finn Sellebjerg,Krzysztof Selmaj,David Sexton,Ling Shen,Brigid Simms-Acuna,Sheila Skidmore,Patrick M. A. Sleiman,C. Smestad,Per Soelberg Sørensen,Helle Bach Søndergaard,Jim Stankovich,Richard C. Strange,Anna-Maija Sulonen,Emilie Sundqvist,Ann-Christine Syvaenen,Francesca Taddeo,Bruce V. Taylor,Jenefer M. Blackwell,Jenefer M. Blackwell,Jenefer M. Blackwell,Pentti J. Tienari,Elvira Bramon,Ayman Tourbah,Matthew A. Brown,Ewa Tronczynska,Juan P. Casas,Niall Tubridy,Aiden Corvin,Jane Vickery,Jane Vickery,Janusz Jankowski,Pablo Villoslada,Hugh S. Markus,Kai Wang,Christopher G. Mathew,James Wason,Colin N. A. Palmer,H-Erich Wichmann,H-Erich Wichmann,Robert Plomin,Ernest Willoughby,Anna Rautanen,Juliane Winkelmann,Michael Wittig,Richard C. Trembath,J. Yaouanq,Ananth C. Viswanathan,Ananth C. Viswanathan,Haitao Zhang,Nicholas W. Wood,Rebecca L. Zuvich,Panos Deloukas,Cordelia Langford,Audrey Duncanson,Jorge R. Oksenberg,Margaret A. Pericak-Vance,Jonathan L. Haines,Tomas Olsson,Jan Hillert,Adrian J. Ivinson,Philip L. De Jager,Philip L. De Jager,Philip L. De Jager,Leena Peltonen,Graeme J. Stewart,David A. Hafler,David A. Hafler,Stephen L. Hauser,Gil McVean,Peter Donnelly,Peter Donnelly,Alastair Compston +265 more
TL;DR: In this article, a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, they have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci.
Journal ArticleDOI
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
TL;DR: A reference panel of 64,976 human haplotypes at 39,235,157 SNPs constructed using whole-genome sequence data from 20 studies of predominantly European ancestry leads to accurate genotype imputation at minor allele frequencies as low as 0.1% and a large increase in the number of SNPs tested in association studies.
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