A reference panel of 64,976 haplotypes for genotype imputation

Shane McCarthy; Sayantan Das; Warren Kretzschmar; Olivier Delaneau; Andrew R. Wood; Alexander Teumer; Hyun Min Kang; Christian Fuchsberger; Petr Danecek; Kevin Sharp; Yang Luo; Carlo Sidorel; Alan Kwong; Nicholas Timpson; Seppo Koskinen; Scott Vrieze; Laura J. Scott; He Zhang; Anubha Mahajan; Jan Veldink; Ulrike Peters; Carlos Pato; Cornelia M. van Duijn; Christopher E. Gillies; Ilaria Gandin; Massimo Mezzavilla; Arthur Gilly; Massimiliano Cocca; Michela Traglia; Andrea Angius; Jeffrey C. Barrett; Dorrett Boomsma; Kari Branham; Gerome Breen; Chad M. Brummett; Fabio Busonero; Harry Campbell; Andrew Chan; Sai Che; Emily Chew; Francis S. Collins; Laura J. Corbin; George Davey Smith; George Dedoussis; Marcus Dorr; Aliki-Eleni Farmaki; Luigi Ferrucci; Lukas Forer; Ross M. Fraser; Stacey Gabriel; Shawn Levy; Leif Groop; Tabitha Harrison; Andrew Hattersley; Oddgeir L. Holmen; Kristian Hveem; Matthias Kretzler; James C. Lee; Matt McGue; Thomas Meitinger; David Melzer; Josine L. Min; Karen L. Mohlke; John B. Vincent; Matthias Nauck; Deborah Nickerson; Aarno Palotie; Michele Pato; Nicola Pirastu; Melvin McInnis; J. Brent Richards; Cinzia Sala; Veikko Salomaa; David Schlessinger; Sebastian Schoenherr; P. Eline Slagboom; Kerrin Small; Timothy Spector; Dwight Stambolian; Marcus Tuke; Jaakko Tuomilehto; Leonard H. van den Berg; Wouter Van Rheenen; Uwe Volker; Cisca Wijmenga; Daniela Toniolo; Eleftheria Zeggini; Paolo Gasparini; Matthew G. Sampson; James F. Wilson; Timothy Frayling; Paul I. W. de Bakker; Morris A. Swertz; Steven McCarroll; Charles Kooperberg; Annelot Dekker; David Altshuler; Cristen Willer; William Iacono; Samuli Ripatti; Nicole Soranzo; Klaudia Walter; Anand Swaroop; Francesco Cucca; Carl A. Anderson; Richard M. Myers; Michael Boehnke; Mark I. McCarthy; Richard Durbin; Goncalo Abecasis; Jonathan Marchini; Haplotype Reference Consortium

doi:10.1038/ng.3643

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A reference panel of 64,976 haplotypes for genotype imputation

Journal article

Peer reviewed

A reference panel of 64,976 haplotypes for genotype imputation

Shane McCarthy, Sayantan Das, Warren Kretzschmar, Olivier Delaneau, Andrew R. Wood, Alexander Teumer, Hyun Min Kang, Christian Fuchsberger, Petr Danecek, Kevin Sharp, …

Nature genetics, Vol.48(10), pp.1279-1283

01/10/2016

DOI: https://doi.org/10.1038/ng.3643

PMID: 27548312

Abstract

Genetics & Heredity

Life Sciences & Biomedicine

Science & Technology

We describe 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. Using this resource 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, and it can help to discover and refine causal loci. We describe remote server resources that allow researchers to carry out imputation and phasing consistently and efficiently.

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Title: A reference panel of 64,976 haplotypes for genotype imputation
Creators - without role: Shane McCarthy - Wellcome Sanger Institute
Sayantan Das - Biostat
Warren Kretzschmar - University of Oxford
Olivier Delaneau - University of Geneva
Andrew R. Wood - University of Exeter
Alexander Teumer - College Station Medical Center
Hyun Min Kang - Biostat
Christian Fuchsberger - Biostat
Petr Danecek - Wellcome Sanger Institute
Kevin Sharp - University of Oxford
Yang Luo - Wellcome Sanger Institute
Carlo Sidorel - CNR, IRGB, Sardinia, Italy
Alan Kwong - Biostat
Nicholas Timpson - University of Bristol
Seppo Koskinen - THL, Helsinki, Finland
Scott Vrieze - Univ Colorado, Inst Behav Genet, Boulder, CO 80309 USA
Laura J. Scott - Biostat
He Zhang - College Station Medical Center
Anubha Mahajan - University of Oxford
Jan Veldink - Brain Ctr Rudolf Magnus, Dept Neurol & Neurosurg, Utrecht, Netherlands
Ulrike Peters - Hutchinson
Carlos Pato - SUNY Downstate, Dept Psychiat, Brooklyn, NY USA
Cornelia M. van Duijn - Erasmus MC
Christopher E. Gillies - Supreme Council Of Health
Ilaria Gandin - University of Trieste
Massimo Mezzavilla - College Station Medical Center
Arthur Gilly - Wellcome Sanger Institute
Massimiliano Cocca - University of Trieste
Michela Traglia - San Raffaele Res Inst, Genet & Cell Biol, Milan, Italy
Andrea Angius - CNR, IRGB, Sardinia, Italy
Jeffrey C. Barrett - Wellcome Sanger Institute
Dorrett Boomsma - University of Amsterdam
Kari Branham - Univ Michigan, Dept Ophthalmol & Visual Sci, Ann Arbor, MI 48109 USA
Gerome Breen - Massachusetts Rehabilitation Commission
Chad M. Brummett - Univ Michigan, Dept Anesthesiol, Ann Arbor, MI 48109 USA
Fabio Busonero - CNR, IRGB, Sardinia, Italy
Harry Campbell - University of Edinburgh
Andrew Chan - Massachusetts Gen Hosp, Div Gastroenterol, Boston, MA 02114 USA
Sai Che - Biostat
Emily Chew - NEI, Div Epidemiol & Clin Applicat, Bethesda, MD 20892 USA
Francis S. Collins - College Station Medical Center
Laura J. Corbin - University of Bristol
George Davey Smith - University of Bristol
George Dedoussis - Harokopio University of Athens
Marcus Dorr - College Station Medical Center
Aliki-Eleni Farmaki - Harokopio University of Athens
Luigi Ferrucci - NIA, Longitudinal Studies Sect, Clin Res Branch, Gerontol Res Ctr, Baltimore, MD 21224 USA
Lukas Forer
Ross M. Fraser - Univ Michigan, Dept Anesthesiol, Ann Arbor, MI 48109 USA
Stacey Gabriel - Broad Institute
Shawn Levy - HudsonAlpha Inst Biotechnol, Huntsville, AL USA
Leif Groop - Lund University
Tabitha Harrison - Hutchinson
Andrew Hattersley - University of Exeter
Oddgeir L. Holmen - Norwegian Univ Sci & Technol, Dept Publ Hlth & Gen Practice, Hunt Res Ctr, Levanger, Norway
Kristian Hveem - Norwegian Univ Sci & Technol, Dept Publ Hlth & Gen Practice, Hunt Res Ctr, Levanger, Norway
Matthias Kretzler - College Station Medical Center
James C. Lee - University of Cambridge
Matt McGue - University of Minnesota
Thomas Meitinger - Helmholtz Zentrum München
David Melzer - University of Exeter
Josine L. Min - University of Bristol
Karen L. Mohlke - Univ N Carolina, Dept Genet, Chapel Hill, NC USA
John B. Vincent - Ctr Addict & Mental Hlth, Mol Neuropsychiat & Dev Lab, Toronto, ON, Canada
Matthias Nauck - DZHK German Ctr Cardiovasc Res, Greifswald, Germany
Deborah Nickerson - University of Washington
Aarno Palotie - Broad Institute
Michele Pato - SUNY Downstate, Dept Psychiat, Brooklyn, NY USA
Nicola Pirastu - University of Trieste
Melvin McInnis - Univ Michigan, Dept Psychiat, Ann Arbor, MI 48109 USA
J. Brent Richards - McGill University
Cinzia Sala - San Raffaele Res Inst, Genet & Cell Biol, Milan, Italy
Veikko Salomaa - THL, Helsinki, Finland
David Schlessinger - Institute of Aging
Sebastian Schoenherr
P. Eline Slagboom - Leiden University
Kerrin Small - Kings Coll London, Dept Twin Res & Genet Epidemiol, London, England
Timothy Spector - Kings Coll London, Dept Twin Res & Genet Epidemiol, London, England
Dwight Stambolian - Univ Penn, Dept Ophthalmol, Philadelphia, PA 19104 USA
Marcus Tuke - University of Exeter
Jaakko Tuomilehto - Natl Inst Hlth & Welf, Chron Dis Prevent Unit, Helsinki, Finland
Leonard H. van den Berg - Brain Ctr Rudolf Magnus, Dept Neurol & Neurosurg, Utrecht, Netherlands
Wouter Van Rheenen - Brain Ctr Rudolf Magnus, Dept Neurol & Neurosurg, Utrecht, Netherlands
Uwe Volker - College Station Medical Center
Cisca Wijmenga - University of Groningen
Daniela Toniolo - San Raffaele Res Inst, Genet & Cell Biol, Milan, Italy
Eleftheria Zeggini - Wellcome Sanger Institute
Paolo Gasparini - University of Trieste
Matthew G. Sampson - Supreme Council Of Health
James F. Wilson - University of Edinburgh
Timothy Frayling - University of Exeter
Paul I. W. de Bakker - College Station Medical Center
Morris A. Swertz - University of Groningen
Steven McCarroll - Supreme Council Of Health
Charles Kooperberg - Hutchinson
Annelot Dekker - Brain Ctr Rudolf Magnus, Dept Neurol & Neurosurg, Utrecht, Netherlands
David Altshuler - Broad Institute
Cristen Willer - College Station Medical Center
William Iacono - University of Minnesota
Samuli Ripatti - University of Helsinki
Nicole Soranzo - Wellcome Sanger Institute
Klaudia Walter - Wellcome Sanger Institute
Anand Swaroop - US Natl Inst Hlth, Neurobiol Neurodegenerat & Repair Lab, NEI, Bethesda, MD USA
Francesco Cucca - CNR, IRGB, Sardinia, Italy
Carl A. Anderson - Wellcome Sanger Institute
Richard M. Myers - HudsonAlpha Inst Biotechnol, Huntsville, AL USA
Michael Boehnke - Biostat
Mark I. McCarthy - University of Oxford
Richard Durbin - Wellcome Sanger Institute
Goncalo Abecasis - Biostat
Jonathan Marchini - University of Oxford
Haplotype Reference Consortium
Publication Details: Nature genetics, Vol.48(10), pp.1279-1283
Publisher: NATURE PORTFOLIO
Number of pages: 5
Grant note: MR/J00314X/1; G9815508; MC_UU_12013/3; MC_PC_15018; G0601261 / Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) 617306 / ERC; European Research Council (ERC); European Commission NF-SI-0611-10219; NF-SI-0611-10099 / National Institute for Health Research; National Institute for Health Research (NIHR) WT097307; WT090851 / Wellcome Trust G0601261; G0601966; MR/J00314X/1; G0700931; G0900747; MC_UU_12013/3 / MRC; UK Research & Innovation (UKRI); Medical Research Council UK (MRC)
Identifiers: 9934779308331
Academic Unit: King Abdulaziz University
Language: English
Resource Type: Journal article