New Results
A reference panel of 64,976 haplotypes for genotype imputation
Shane McCarthy, Sayantan Das, Warren Kretzschmar, Olivier Delaneau, Andrew R. Wood, Hyun Min Kang, Christian Fuchsberger, Petr Danecek, Kevin Sharp, Yang Luo, Carlo Sidore, Alan Kwong, Nicholas Timpson, Seppo Koskinen, Scott Vrieze, Laura 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, Dorret I. Boomsma, Kari Branham, Chad Brummet, Fabio Busonero, Harry Campbell, Andrew Chan, Sai Chen, Emily Chew, Francis S. Collins, George Davey Smith, George Dedoussis, 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, Gerome Breen, Deborah Nickerson, Aarno Palotie, Michele Pato, Nicola Pirastu, Melvin McInnis, 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, 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 Willer, William Iacono, Samuli Ripatti, Nicole Soranzo, Klaudia Walter, Anand Swaroop, Francesco Cucca, Carl Anderson, Michael Boehnke, Mark I. McCarthy, Richard Durbin, Goncalo Abecasis, Jonathan Marchini
doi: https://doi.org/10.1101/035170
Shane McCarthy
1Human Genetics, Human Genetics, Hinxton, UK.
Sayantan Das
2Department of Biostatistics and Center for Statistical Genetics, Department of Biostatistics and Center for Statistical Genetics, Ann Arbor, Michigan, USA.
Warren Kretzschmar
3Wellcome Trust Centre for Human Genetics, Wellcome Trust Centre for Human Genetics, Oxford, UK.
Olivier Delaneau
4Genetics and Development, Genetics and Development, Geneva, Switzerland.
Andrew R. Wood
16Genetics of Complex Traits, Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK.
Hyun Min Kang
2Department of Biostatistics and Center for Statistical Genetics, Department of Biostatistics and Center for Statistical Genetics, Ann Arbor, Michigan, USA.
Christian Fuchsberger
2Department of Biostatistics and Center for Statistical Genetics, Department of Biostatistics and Center for Statistical Genetics, Ann Arbor, Michigan, USA.
Petr Danecek
30Vertebrate Resequencing Informatics, Vertebrate Resequencing Informatics, Oxford, UK.
Kevin Sharp
58Department of Statistics, Department of Statistics, Oxford, UK.
Yang Luo
1Human Genetics, Human Genetics, Hinxton, UK.
Carlo Sidore
5IRGB, IRGB, Sardinia, Italy.
Alan Kwong
2Department of Biostatistics and Center for Statistical Genetics, Department of Biostatistics and Center for Statistical Genetics, Ann Arbor, Michigan, USA.
Nicholas Timpson
6MRC Integrative Epidemiology Unit, MRC Integrative Epidemiology Unit, Oakfield Grove, UK.
Seppo Koskinen
7THL, Finland.
Scott Vrieze
8Institute for Behavioral Genetics, Institute for Behavioral Genetics, Boulder, Colorado, USA.
9Department of Psychology and Neurosurgery, Department of Psychology and Neurosurgery, Boulder, Colorado, USA
Laura Scott
2Department of Biostatistics and Center for Statistical Genetics, Department of Biostatistics and Center for Statistical Genetics, Ann Arbor, Michigan, USA.
He Zhang
10Department of Internal Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
Anubha Mahajan
3Wellcome Trust Centre for Human Genetics, Wellcome Trust Centre for Human Genetics, Oxford, UK.
Jan Veldink
11Department of Neurology and Neurosurgery, Department of Neurology and Neurosurgery, Utrecht, the Netherlands.
Ulrike Peters
12Public Health Sciences Division, Public Health Sciences Division, Seattle, Washington, USA.
13Department of Epidemiology, Department of Epidemiology, Seattle, Washington, USA.
Carlos Pato
14Department of Psychiatry, Department of Psychiatry, Brooklyn, New York, USA.
Cornelia M. van Duijn
15Genetic Epidemiology Unit, Genetic Epidemiology Unit, ErasmusMC, Rotterdam, the Netherlands.
Christopher E. Gillies
17Department of Pediatrics-Nephrology, Department of Pediatrics-Nephrology, Ann Arbor, Michigan, USA.
Ilaria Gandin
18DSM, DSM, Trieste, Italy.
Massimo Mezzavilla
19Genetica Medica, Genetica Medica, Trieste, Italy.
Arthur Gilly
1Human Genetics, Human Genetics, Hinxton, UK.
Massimiliano Cocca
20Genetics and Cell Biology, Genetics and Cell Biology, Milano, Italy.
Michela Traglia
20Genetics and Cell Biology, Genetics and Cell Biology, Milano, Italy.
Andrea Angius
4Genetics and Development, Genetics and Development, Geneva, Switzerland.
Dorret I. Boomsma
21Department of Biological Psychology, Department of Biological Psychology, Neuroscience Campus, Amsterdam, the Netherlands.
Kari Branham
22Department of Ophthalmology and Visual Sciences, Department of Ophthalmology and Visual Sciences, Ann Arbor, Michigan, USA.
Chad Brummet
23Department of Anesthesiology, Department of Anesthesiology, Ann Arbor, Michigan, USA.
Fabio Busonero
5IRGB, IRGB, Sardinia, Italy.
Harry Campbell
24The Usher Institute of Population Health Sciences and Informatics, The Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK.
Andrew Chan
25Division of Gastroenterology, Division of Gastroenterology, Boston, Massachusetts, USA.
26Brigham and Women’s Hospital, Brigham and Women’s Hospital, Boston, Massachusetts, USA.
Sai Chen
2Department of Biostatistics and Center for Statistical Genetics, Department of Biostatistics and Center for Statistical Genetics, Ann Arbor, Michigan, USA.
27Departments of Computational Medicine & Bioinformatics, Departments of Computational Medicine & Bioinformatics, Ann Arbor, Michigan, USA.
Emily Chew
28Division of Epidemiology and Clinical Applications, Division of Epidemiology and Clinical Applications, Bethesda, Maryland, USA.
Francis S. Collins
29Medical Genomics and Metabolic Genetics Branch, Medical Genomics and Metabolic Genetics Branch, National Institutes of Health, Bethesda, Maryland, USA.
George Davey Smith
6MRC Integrative Epidemiology Unit, MRC Integrative Epidemiology Unit, Oakfield Grove, UK.
George Dedoussis
31Department of Nutrition and Dietetics, Department of Nutrition and Dietetics, Harokopio University, Athens, Greece.
Aliki-Eleni Farmaki
31Department of Nutrition and Dietetics, Department of Nutrition and Dietetics, Harokopio University, Athens, Greece.
Luigi Ferrucci
32Longitudinal Studies Section, Longitudinal Studies Section, Gerontology Research Centre, National Institute on Aging, Baltimore, Maryland, USA.
Lukas Forer
33Center for Biomedicine, Center for Biomedicine, Bolzano, Italy.
Ross M. Fraser
24The Usher Institute of Population Health Sciences and Informatics, The Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK.
Stacey Gabriel
34Program in Medical and Population Genetics, Program in Medical and Population Genetics, Cambridge, Massachusetts, USA.
Shawn Levy
35Genomics, Genomics, Huntsville, Alabama, USA.
Leif Groop
36Department of Clinical Sciences, Department of Clinical Sciences, University of Lund, Malmo, Sweden.
37Finnish Institute for Molecular Medicine, Finnish Institute for Molecular Medicine, Helsinki, Finland.
38Research Programs Unit, Research Programs Unit, University of Helsinki, Helsinki, Finland.
Tabitha Harrison
12Public Health Sciences Division, Public Health Sciences Division, Seattle, Washington, USA.
Andrew Hattersley
39Department of Diabetes and Vascular Medicine, Department of Diabetes and Vascular Medicine, Exeter, UK.
Oddgeir L. Holmen
40Hunt Research Centre, Hunt Research Centre, Norwegian University of Science and Technology, Levanger, Norway.
Kristian Hveem
40Hunt Research Centre, Hunt Research Centre, Norwegian University of Science and Technology, Levanger, Norway.
Matthias Kretzler
27Departments of Computational Medicine & Bioinformatics, Departments of Computational Medicine & Bioinformatics, Ann Arbor, Michigan, USA.
41Department of Internal Medicine, Department of Internal Medicine, Ann Arbor, Michigan, USA.
James Lee
42Cambridge Institute for Medical Research, Cambridge Institute for Medical Research, Cambridge, UK.
43Department of Medicine, Department of Medicine, Addenbrooke’s Hospital, Cambridge, UK.
Matt McGue
44Department of Psychology, Department of Psychology, Minneapolis, Minnesota, USA.
Thomas Meitinger
45Institute of Human Genetics, Institute of Human Genetics, German Research Center for Environmental Health, Neuherberg, Germany.
46Institute of Human Genetics, Institute of Human Genetics, Munich, Germany.
David Melzer
47Epidemiology and Public Health, Epidemiology and Public Health, University of Exeter Medical School, Exeter, UK.
Josine Min
6MRC Integrative Epidemiology Unit, MRC Integrative Epidemiology Unit, Oakfield Grove, UK.
Karen L. Mohlke
48Department of Genetics, Department of Genetics, Chapel Hill, Chapel Hill, North Carolina, USA.
John Vincent
49Molecular Neuropsychiatry and Development Laboratory, Molecular Neuropsychiatry and Development Laboratory, Toronto, Canada.
50Institute of Medical Science, Institute of Medical Science, Toronto, Canada.
Gerome Breen
51MRC Social Genetic and Developmental Psychiatry Centre, MRC Social Genetic and Developmental Psychiatry Centre, Psychology, and Neuroscience, King’s College, London, UK.
Deborah Nickerson
52Genome Sciences, Genome Sciences, Seattle, Washington, USA.
Aarno Palotie
34Program in Medical and Population Genetics, Program in Medical and Population Genetics, Cambridge, Massachusetts, USA.
52Genome Sciences, Genome Sciences, Seattle, Washington, USA.
53Institute for Molecular Medicine, Institute for Molecular Medicine, Helsinki, Finland.
Michele Pato
14Department of Psychiatry, Department of Psychiatry, Brooklyn, New York, USA.
Nicola Pirastu
18DSM, DSM, Trieste, Italy.
Melvin McInnis
54Department of Psychiatry, Department of Psychiatry, Ann Arbor, Michigan, USA.
Brent Richards
55Massachusetts General Hospital, Massachusetts General Hospital, Massachusetts, USA.
Cinzia Sala
20Genetics and Cell Biology, Genetics and Cell Biology, Milano, Italy.
Veikko Salomaa
7THL, Finland.
David Schlessinger
56Departments of Medicine and Human Genetics, Departments of Medicine and Human Genetics, Montreal, Canada.
Sebastian Schoenheer
33Center for Biomedicine, Center for Biomedicine, Bolzano, Italy.
P Eline Slagboom
59Molecular Epidemiology Section, Molecular Epidemiology Section, Leiden University Medical Center, Leiden, the Netherlands.
Kerrin Small
59Molecular Epidemiology Section, Molecular Epidemiology Section, Leiden University Medical Center, Leiden, the Netherlands.
Timothy Spector
60The Department of Twin Research and Genetic Epidemiology, The Department of Twin Research and Genetic Epidemiology, London, UK.
Dwight Stambolian
61Department of Ophthalmology, Department of Ophthalmology, Philadelphia, Pennsylvania, USA.
Marcus Tuke
16Genetics of Complex Traits, Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK.
Jaakko Tuomilehto
63Chronic Disease Prevention Unit, Chronic Disease Prevention Unit, Helsinki, Finland.
64Instituto de Investigacion Sanitaria del Hospital Universario LaPaz, Instituto de Investigacion Sanitaria del Hospital Universario LaPaz, Autonomous University of Madrid, Madrid, Spain.
65Center for Vascular Prevention, Center for Vascular Prevention, Krems, Austria.
65Center for Vascular Prevention, Center for Vascular Prevention, Krems, Austria.
66Diabetes Research Group, Diabetes Research Group, Saudi Arabia.
Leonard Van den Berg
11Department of Neurology and Neurosurgery, Department of Neurology and Neurosurgery, Utrecht, the Netherlands.
Wouter Van Rheenen
11Department of Neurology and Neurosurgery, Department of Neurology and Neurosurgery, Utrecht, the Netherlands.
Cisca Wijmenga
85Department of Genetics, Department of Genetics, Netherlands
Daniela Toniolo
20Genetics and Cell Biology, Genetics and Cell Biology, Milano, Italy.
Eleftheria Zeggini
1Human Genetics, Human Genetics, Hinxton, UK.
Paolo Gasparini
18DSM, DSM, Trieste, Italy.
67Department of Experimental Genetics, Department of Experimental Genetics, Doha, Qatar.
Matthew G. Sampson
17Department of Pediatrics-Nephrology, Department of Pediatrics-Nephrology, Ann Arbor, Michigan, USA.
James F. Wilson
24The Usher Institute of Population Health Sciences and Informatics, The Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK.
68MRC Human Genetics Unit, MRC Human Genetics Unit, University of Edinburgh, Western General Hospital, Edinburgh, UK.
Timothy Frayling
16Genetics of Complex Traits, Genetics of Complex Traits, University of Exeter Medical School, Exeter, UK.
Paul de Bakker
69Medical Genetics, Medical Genetics, Utrecht, the Netherlands.
70Department of Epidemiology, Department of Epidemiology, University Medical Center Utrecht, Utrecht, the Netherlands.
Morris A. Swertz
71Department of Genetics, Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands.
72Genomics Coordination Center, Genomics Coordination Center, University Medical Center Groningen, Groningen, the Netherlands.
Steven McCarroll
73Stanley Center for Psychiatric Research, Stanley Center for Psychiatric Research, Cambridge, Massachusetts, USA.
74Department of Genetics, Department of Genetics, Boston, Massachusetts, USA.
Charles Kooperberg
12Public Health Sciences Division, Public Health Sciences Division, Seattle, Washington, USA.
Annelot Dekker
11Department of Neurology and Neurosurgery, Department of Neurology and Neurosurgery, Utrecht, the Netherlands.
David Altshuler
75Program in Medical and Population Genetics, Program in Medical and Population Genetics, Cambridge, Massachusetts, USA.
76Department of Molecular Biology, Department of Molecular Biology, Boston, Massachusetts, USA.
77Diabetes Research Center (Diabetes Unit), Diabetes Research Center (Diabetes Unit), Massachusetts General Hospital, Boston, Massachusetts, USA.
78Department of Medicine, Department of Medicine, Boston, Massachusetts, USA.
79Department of Genetics, Department of Genetics, Boston, Massachusetts, USA.
80Department of Biology, Department of Biology, Cambridge, Massachusetts, USA.
Cristen Willer
10Department of Internal Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
27Departments of Computational Medicine & Bioinformatics, Departments of Computational Medicine & Bioinformatics, Ann Arbor, Michigan, USA.
William Iacono
44Department of Psychology, Department of Psychology, Minneapolis, Minnesota, USA.
Samuli Ripatti
83Department of Public Health, Department of Public Health, Helsinki, Finland.
Nicole Soranzo
1Human Genetics, Human Genetics, Hinxton, UK.
Klaudia Walter
1Human Genetics, Human Genetics, Hinxton, UK.
Anand Swaroop
84Neurobiology-Neurodegeneration and Repair Laboratory, Neurobiology-Neurodegeneration and Repair Laboratory, National Institutes of Health, Bethesda, Maryland, USA.
Francesco Cucca
5IRGB, IRGB, Sardinia, Italy.
Carl Anderson
1Human Genetics, Human Genetics, Hinxton, UK.
Michael Boehnke
2Department of Biostatistics and Center for Statistical Genetics, Department of Biostatistics and Center for Statistical Genetics, Ann Arbor, Michigan, USA.
Mark I. McCarthy
3Wellcome Trust Centre for Human Genetics, Wellcome Trust Centre for Human Genetics, Oxford, UK.
81Oxford Centre for Diabetes, Oxford Centre for Diabetes, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
82Oxford NIHR Biomedical Research Centre, Oxford NIHR Biomedical Research Centre, Headington, Oxford, UK.
Richard Durbin
1Human Genetics, Human Genetics, Hinxton, UK.
Goncalo Abecasis
2Department of Biostatistics and Center for Statistical Genetics, Department of Biostatistics and Center for Statistical Genetics, Ann Arbor, Michigan, USA.
Jonathan Marchini
58Department of Statistics, Department of Statistics, Oxford, UK.
3Wellcome Trust Centre for Human Genetics, Wellcome Trust Centre for Human Genetics, Oxford, UK.
Abstract
We describe a reference panel of 64,976 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 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 December 23, 2015.
A reference panel of 64,976 haplotypes for genotype imputation
Shane McCarthy, Sayantan Das, Warren Kretzschmar, Olivier Delaneau, Andrew R. Wood, Hyun Min Kang, Christian Fuchsberger, Petr Danecek, Kevin Sharp, Yang Luo, Carlo Sidore, Alan Kwong, Nicholas Timpson, Seppo Koskinen, Scott Vrieze, Laura 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, Dorret I. Boomsma, Kari Branham, Chad Brummet, Fabio Busonero, Harry Campbell, Andrew Chan, Sai Chen, Emily Chew, Francis S. Collins, George Davey Smith, George Dedoussis, 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, Gerome Breen, Deborah Nickerson, Aarno Palotie, Michele Pato, Nicola Pirastu, Melvin McInnis, 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, 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 Willer, William Iacono, Samuli Ripatti, Nicole Soranzo, Klaudia Walter, Anand Swaroop, Francesco Cucca, Carl Anderson, Michael Boehnke, Mark I. McCarthy, Richard Durbin, Goncalo 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, Hyun Min Kang, Christian Fuchsberger, Petr Danecek, Kevin Sharp, Yang Luo, Carlo Sidore, Alan Kwong, Nicholas Timpson, Seppo Koskinen, Scott Vrieze, Laura 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, Dorret I. Boomsma, Kari Branham, Chad Brummet, Fabio Busonero, Harry Campbell, Andrew Chan, Sai Chen, Emily Chew, Francis S. Collins, George Davey Smith, George Dedoussis, 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, Gerome Breen, Deborah Nickerson, Aarno Palotie, Michele Pato, Nicola Pirastu, Melvin McInnis, 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, 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 Willer, William Iacono, Samuli Ripatti, Nicole Soranzo, Klaudia Walter, Anand Swaroop, Francesco Cucca, Carl Anderson, Michael Boehnke, Mark I. McCarthy, Richard Durbin, Goncalo Abecasis, Jonathan Marchini
bioRxiv 035170; doi: https://doi.org/10.1101/035170
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