New Results
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 Sidore, 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 Barrett, Dorret I. Boomsma, Kari Branham, Gerome Breen, Chad Brummet, Fabio Busonero, Hariy Campbell, Andrew Chan, Sai Chen, Emily Chew, Francis S. Collins, Laura 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 Lee, Matt McGue, Thomas Meitinger, David Melzer, Josine Min, Karen L. Mohlke, John Vincent, Matthias Nauck, Deborah Nickerson, Aarno Palotie, Michele Pato, Nicola Pirastu, Melvin Mclnnis, Brent Richards, Cinzia Sala, Veikko Salomaa, David Schlessinger, Sebastian Schoenheer, P Eline Slagboom, Kerrin Small, Timothy Spector, Dwight Stambolian, Marcus Tuke, Jaakko Tuomilehto, Leonard 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 de Bakker, Morris A. Swertz, Steven McCarroll, Charles Kooperberg, Annelot Dekker, David Altshuler, Cristen Wilier, William Iacono, Samuli Ripatti, Nicole Soranzo, Klaudia Walter, Anand Swaroop, Francesco Cucca, Carl Anderson, Michael Boehnke, Mark I. McCarthy, Richard Durbin, Gonçalo Abecasis, Jonathan Marchini
doi: https://doi.org/10.1101/035170
Shane McCarthy
1Human Genetics,Wellcome Trust Sanger Institute, Hinxton, UK.
Sayantan Das
2Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Warren Kretzschmar
3Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Olivier Delaneau
4Genetics and Development, University of Geneva, Geneva, Switzerland.
Andrew R. Wood
16Genetics of Complex Traits, Institute of Biomedical Science, University of Exeter Medical School, Exeter, UK.
Alexander Teumer
91DZHK (German Centre for Cardiovascular Research), Greifswald, Germany.
87Institute for Community Medicine, University Medicine Greifswald, Germany.
Hyun Min Kang
2Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Christian Fuchsberger
2Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Petr Danecek
30Vertebrate Resequencing Informatics, Wellcome Trust Sanger Institute, Oxford, UK.
Kevin Sharp
58Department of Statistics, University of Oxford, Oxford, UK.
Yang Luo
1Human Genetics,Wellcome Trust Sanger Institute, Hinxton, UK.
Carlo Sidore
5IRGB, CNR, Sardinia, Italy.
Alan Kwong
2Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Nicholas Timpson
6MRC Integrative Epidemiology Unit, University of Bristol, Oakfield Grove, UK.
Seppo Koskinen
7THL, Finland.
Scott Vrieze
8Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA.
9Department of Psychology and Neurosurgery, University of Colorado, Boulder, Colorado, USA
Laura J. Scott
2Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
He Zhang
10Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, USA.
Anubha Mahajan
3Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Jan Veldink
11Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, Utrecht, the Netherlands.
Ulrike Peters
12Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
13Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA.
Carlos Pato
14Department of Psychiatry, SUNY Downstate, Brooklyn, New York, USA.
Cornelia M. van Duijn
15Genetic Epidemiology Unit, Department of Epidemiology, ErasmusMC, Rotterdam, the Netherlands.
Christopher E. Gillies
17Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA.
Ilaria Gandin
18DSM, University of Trieste, Trieste, Italy.
Massimo Mezzavilla
19Genetica Medica, IRCCS-Burlo Garofolo, Trieste, Italy.
Arthur Gilly
1Human Genetics,Wellcome Trust Sanger Institute, Hinxton, UK.
Massimiliano Cocca
20Genetics and Cell Biology, San Raffaele Research Institute, Milano, Italy.
Michela Traglia
20Genetics and Cell Biology, San Raffaele Research Institute, Milano, Italy.
Andrea Angius
4Genetics and Development, University of Geneva, Geneva, Switzerland.
Jeffrey Barrett
1Human Genetics,Wellcome Trust Sanger Institute, Hinxton, UK.
Dorret I. Boomsma
21Department of Biological Psychology, VU Amsterdam, Neuroscience Campus, Amsterdam, the Netherlands.
Kari Branham
22Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, USA.
Gerome Breen
51MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College, London, UK.
86NIHR Biomedical Research Centre for Mental Health, Institute of Psychiatry, Psychology & Neuroscience, King’s College London and The South London Maudsley Hospital, London, UK.
Chad Brummet
23Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan, USA.
Fabio Busonero
5IRGB, CNR, Sardinia, Italy.
Hariy Campbell
24The Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.
Andrew Chan
25Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.
26Brigham and Women’s Hospital, Channing Division of Network Medicine, Boston, Massachusetts, USA.
Sai Chen
2Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
27Departments of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
Emily Chew
28Division of Epidemiology and Clinical Applications, National Eye Institute, Bethesda, Maryland, USA.
Francis S. Collins
29Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
Laura Corbin
6MRC Integrative Epidemiology Unit, University of Bristol, Oakfield Grove, UK.
George Davey Smith
6MRC Integrative Epidemiology Unit, University of Bristol, Oakfield Grove, UK.
George Dedoussis
31Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece.
Marcus Dorr
89Department of Internal Medicine B, University Medicine Greifswald, Germany.
91DZHK (German Centre for Cardiovascular Research), Greifswald, Germany.
Aliki-Eleni Farmaki
31Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece.
Luigi Ferrucci
32Longitudinal Studies Section, Clinical Research Branch, Gerontology Research Centre, National Institute on Aging, Baltimore, Maryland, USA.
Lukas Forer
33Center for Biomedicine, University of Innsbruck, Bolzano, Italy.
Ross M. Fraser
24The Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.
Stacey Gabriel
34Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Shawn Levy
35HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
Leif Groop
36Department of Clinical Sciences, Diabetes and Endocrinology, University of Lund, Malmo, Sweden.
37Finnish Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland.
38Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.
Tabitha Harrison
12Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Andrew Hattersley
39Department of Diabetes and Vascular Medicine, University of Exeter Medical School, Exeter, UK.
Oddgeir L. Holmen
40Hunt Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway.
Kristian Hveem
40Hunt Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway.
Matthias Kretzler
27Departments of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
41Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, Michigan, USA.
James Lee
42Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
43Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke’s Hospital, Cambridge, UK.
Matt McGue
44Department of Psychology, University of Minnesota, Minneapolis, Minnesota, USA.
Thomas Meitinger
45Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
46Institute of Human Genetics, Technische Universität München, Munich, Germany.
David Melzer
47Epidemiology and Public Health, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.
Josine Min
6MRC Integrative Epidemiology Unit, University of Bristol, Oakfield Grove, UK.
Karen L. Mohlke
48Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, USA.
John Vincent
49Molecular Neuropsychiatry and Development Laboratory, Centre for Addiction and Mental Health, Toronto, Canada.
50Institute of Medical Science, University of Toronto and Department of Psychiatry, Toronto, Canada.
Matthias Nauck
90Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Germany.
91DZHK (German Centre for Cardiovascular Research), Greifswald, Germany.
Deborah Nickerson
52Genome Sciences, University of Washington, Seattle, Washington, USA.
Aarno Palotie
34Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
52Genome Sciences, University of Washington, Seattle, Washington, USA.
53Institute for Molecular Medicine, FIMM, Helsinki, Finland.
Michele Pato
14Department of Psychiatry, SUNY Downstate, Brooklyn, New York, USA.
Nicola Pirastu
18DSM, University of Trieste, Trieste, Italy.
Melvin Mclnnis
54Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, USA.
Brent Richards
55Massachusetts General Hospital, Boston, Massachusetts, USA.
Cinzia Sala
20Genetics and Cell Biology, San Raffaele Research Institute, Milano, Italy.
Veikko Salomaa
7THL, Finland.
David Schlessinger
56Departments of Medicine and Human Genetics, McGill University, Montreal, Canada.
Sebastian Schoenheer
33Center for Biomedicine, University of Innsbruck, Bolzano, Italy.
P Eline Slagboom
59Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands.
Kerrin Small
59Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands.
Timothy Spector
60The Department of Twin Research and Genetic Epidemiology, King’s College, London, UK.
Dwight Stambolian
61Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Marcus Tuke
16Genetics of Complex Traits, Institute of Biomedical Science, University of Exeter Medical School, Exeter, UK.
Jaakko Tuomilehto
63Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland.
64Instituto de Investigación Sanitaria del Hospital Universario LaPaz, University Hospital LaPaz, Autonomous University of Madrid, Madrid, Spain.
65Center for Vascular Prevention, Danube University Krems, Krems, Austria.
66Diabetes Research Group, King Abdulaziz University, Saudi Arabia.
Leonard Van den Berg
11Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, Utrecht, the Netherlands.
Wouter Van Rheenen
11Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, Utrecht, the Netherlands.
Uwe Volker
88Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany.
91DZHK (German Centre for Cardiovascular Research), Greifswald, Germany.
Cisca Wijmenga
85Department of Genetics, University Medical Center Groningen, Netherlands.
Daniela Toniolo
20Genetics and Cell Biology, San Raffaele Research Institute, Milano, Italy.
Eleftheria Zeggini
1Human Genetics,Wellcome Trust Sanger Institute, Hinxton, UK.
Paolo Gasparini
18DSM, University of Trieste, Trieste, Italy.
67Department of Experimental Genetics, Sidra, Doha, Qatar.
Matthew G. Sampson
17Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA.
James F. Wilson
24The Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.
68MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK.
Timothy Frayling
16Genetics of Complex Traits, Institute of Biomedical Science, University of Exeter Medical School, Exeter, UK.
Paul de Bakker
69Medical Genetics, University Medical Center, Utrecht, the Netherlands.
70Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands.
Morris A. Swertz
71Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
72Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
Steven McCarroll
73Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
74Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
Charles Kooperberg
12Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Annelot Dekker
11Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, Utrecht, the Netherlands.
David Altshuler
75Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.
76Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.
77Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.
78Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.
79Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
80Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Cristen Wilier
10Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, Michigan, USA.
27Departments of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
William Iacono
44Department of Psychology, University of Minnesota, Minneapolis, Minnesota, USA.
Samuli Ripatti
83Department of Public Health, University of Helsinki, Helsinki, Finland.
Nicole Soranzo
1Human Genetics,Wellcome Trust Sanger Institute, Hinxton, UK.
Klaudia Walter
1Human Genetics,Wellcome Trust Sanger Institute, Hinxton, UK.
Anand Swaroop
84Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA.
Francesco Cucca
5IRGB, CNR, Sardinia, Italy.
Carl Anderson
1Human Genetics,Wellcome Trust Sanger Institute, Hinxton, UK.
Michael Boehnke
2Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Mark I. McCarthy
3Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
81Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
82Oxford NIHR Biomedical Research Centre, Churchill Hospital, Headington, Oxford, UK.
Richard Durbin
1Human Genetics,Wellcome Trust Sanger Institute, Hinxton, UK.
Gonçalo Abecasis
2Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Jonathan Marchini
58Department of Statistics, University of Oxford, Oxford, UK.
3Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Abstract
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%, a large increase in the number of SNPs tested in association studies and 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.
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Posted April 05, 2016.
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 Sidore, 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 Barrett, Dorret I. Boomsma, Kari Branham, Gerome Breen, Chad Brummet, Fabio Busonero, Hariy Campbell, Andrew Chan, Sai Chen, Emily Chew, Francis S. Collins, Laura 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 Lee, Matt McGue, Thomas Meitinger, David Melzer, Josine Min, Karen L. Mohlke, John Vincent, Matthias Nauck, Deborah Nickerson, Aarno Palotie, Michele Pato, Nicola Pirastu, Melvin Mclnnis, Brent Richards, Cinzia Sala, Veikko Salomaa, David Schlessinger, Sebastian Schoenheer, P Eline Slagboom, Kerrin Small, Timothy Spector, Dwight Stambolian, Marcus Tuke, Jaakko Tuomilehto, Leonard 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 de Bakker, Morris A. Swertz, Steven McCarroll, Charles Kooperberg, Annelot Dekker, David Altshuler, Cristen Wilier, William Iacono, Samuli Ripatti, Nicole Soranzo, Klaudia Walter, Anand Swaroop, Francesco Cucca, Carl Anderson, Michael Boehnke, Mark I. McCarthy, Richard Durbin, Gonçalo Abecasis, Jonathan Marchini
bioRxiv 035170; doi: https://doi.org/10.1101/035170
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 Sidore, 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 Barrett, Dorret I. Boomsma, Kari Branham, Gerome Breen, Chad Brummet, Fabio Busonero, Hariy Campbell, Andrew Chan, Sai Chen, Emily Chew, Francis S. Collins, Laura 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 Lee, Matt McGue, Thomas Meitinger, David Melzer, Josine Min, Karen L. Mohlke, John Vincent, Matthias Nauck, Deborah Nickerson, Aarno Palotie, Michele Pato, Nicola Pirastu, Melvin Mclnnis, Brent Richards, Cinzia Sala, Veikko Salomaa, David Schlessinger, Sebastian Schoenheer, P Eline Slagboom, Kerrin Small, Timothy Spector, Dwight Stambolian, Marcus Tuke, Jaakko Tuomilehto, Leonard 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 de Bakker, Morris A. Swertz, Steven McCarroll, Charles Kooperberg, Annelot Dekker, David Altshuler, Cristen Wilier, William Iacono, Samuli Ripatti, Nicole Soranzo, Klaudia Walter, Anand Swaroop, Francesco Cucca, Carl Anderson, Michael Boehnke, Mark I. McCarthy, Richard Durbin, Gonçalo Abecasis, Jonathan Marchini
bioRxiv 035170; doi: https://doi.org/10.1101/035170
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