. 2016 Oct;48(10):1279-83.

doi: 10.1038/ng.3643. Epub 2016 Aug 22.

A reference panel of 64,976 haplotypes for genotype imputation

Shane McCarthy¹, Sayantan Das^{2

3}, Warren Kretzschmar⁴, Olivier Delaneau⁵, Andrew R Wood⁶, Alexander Teumer^{7

8}, Hyun Min Kang^{2

3}, Christian Fuchsberger^{2

3}, Petr Danecek⁹, Kevin Sharp¹⁰, Yang Luo¹, Carlo Sidore¹¹, Alan Kwong^{2

3}, Nicholas Timpson¹², Seppo Koskinen¹³, Scott Vrieze^{14

15}, Laura J Scott^{2

3}, He Zhang¹⁶, Anubha Mahajan⁴, Jan Veldink¹⁷, Ulrike Peters^{18

19}, Carlos Pato²⁰, Cornelia M van Duijn²¹, Christopher E Gillies²², Ilaria Gandin²³, Massimo Mezzavilla^{24

25}, Arthur Gilly¹, Massimiliano Cocca²³, Michela Traglia²⁶, Andrea Angius¹¹, Jeffrey C Barrett¹, Dorrett Boomsma²⁷, Kari Branham²⁸, Gerome Breen^{29

30}, Chad M Brummett³¹, Fabio Busonero¹¹, Harry Campbell³², Andrew Chan^{32

33}, Sai Chen^{2

3

34

35}, Emily Chew³⁶, Francis S Collins³⁷, Laura J Corbin¹², George Davey Smith¹², George Dedoussis³⁸, Marcus Dorr^{39

40}, Aliki-Eleni Farmaki³⁸, Luigi Ferrucci⁴¹, Lukas Forer⁴², Ross M Fraser³¹, Stacey Gabriel⁴³, Shawn Levy⁴⁴, Leif Groop^{45

46

47}, Tabitha Harrison¹⁸, Andrew Hattersley⁴⁸, Oddgeir L Holmen⁴⁹, Kristian Hveem⁴⁹, Matthias Kretzler^{34

35

50}, James C Lee^{51

52}, Matt McGue⁵³, Thomas Meitinger^{54

55

56}, David Melzer⁵⁷, Josine L Min¹², Karen L Mohlke⁵⁸, John B Vincent^{59

60

61}, Matthias Nauck^{8

40}, Deborah Nickerson⁶², Aarno Palotie^{43

63

64

65

66

67}, Michele Pato²⁰, Nicola Pirastu²³, Melvin McInnis⁶⁸, J Brent Richards^{69

70

71}, Cinzia Sala²⁶, Veikko Salomaa¹³, David Schlessinger⁷², Sebastian Schoenherr⁴², P Eline Slagboom⁷³, Kerrin Small⁷¹, Timothy Spector⁷¹, Dwight Stambolian⁷⁴, Marcus Tuke⁶, Jaakko Tuomilehto^{75

76

77

78}, Leonard H Van den Berg¹⁷, Wouter Van Rheenen¹⁷, Uwe Volker^{40

79}, Cisca Wijmenga⁸⁰, Daniela Toniolo²⁶, Eleftheria Zeggini¹, Paolo Gasparini^{23

25}, Matthew G Sampson²², James F Wilson^{32

81}, Timothy Frayling⁶, Paul I W de Bakker^{82

83}, Morris A Swertz^{80

84}, Steven McCarroll^{85

86}, Charles Kooperberg¹⁸, Annelot Dekker¹⁷, David Altshuler^{43

65

87

88

89

90}, Cristen Willer^{16

34

35}, William Iacono⁵³, Samuli Ripatti⁹¹, Nicole Soranzo^{1

92

93}, Klaudia Walter¹, Anand Swaroop⁹⁴, Francesco Cucca¹¹, Carl A Anderson¹, Richard M Myers⁴⁴, Michael Boehnke^{2

3}, Mark I McCarthy^{4

95

96}, Richard Durbin¹; Haplotype Reference Consortium

Collaborators, Affiliations

Collaborators

Haplotype Reference Consortium:
Gonçalo Abecasis, Jonathan Marchini

Affiliations

¹ Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
² Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.
³ Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
⁴ Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
⁵ Genetics and Development, University of Geneva, Geneva, Switzerland.
⁶ Genetics of Complex Traits, Institute of Biomedical Science, University of Exeter Medical School, Exeter, UK.
⁷ Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.
⁸ DZHK (German Centre for Cardiovascular Research), Greifswald, Germany.
⁹ Vertebrate Resequencing Informatics, Wellcome Trust Sanger Institute, Hinxton, UK.
¹⁰ Department of Statistics, University of Oxford, Oxford, UK.
¹¹ IRGB, CNR, Sardinia, Italy.
¹² MRC Integrative Epidemiology Unit, University of Bristol, Oakfield Grove, UK.
¹³ THL, Helsinki, Finland.
¹⁴ Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA.
¹⁵ Department of Psychology and Neurosurgery, University of Colorado, Boulder, Colorado, USA.
¹⁶ Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
¹⁷ Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, Utrecht, the Netherlands.
¹⁸ Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
¹⁹ Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA.
²⁰ Department of Psychiatry, SUNY Downstate, Brooklyn, New York, USA.
²¹ Genetic Epidemiology Unit, Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands.
²² Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA.
²³ Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.
²⁴ Genetica Medica, IRCCS Burlo Garofolo, Trieste, Italy.
²⁵ Department of Experimental Genetics, Sidra, Doha, Qatar.
²⁶ Genetics and Cell Biology, San Raffaele Research Institute, Milan, Italy.
²⁷ Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
²⁸ Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, USA.
²⁹ MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
³⁰ NIHR Biomedical Research Centre for Mental Health, Institute of Psychiatry, Psychology and Neuroscience, King's College London and the South London Maudsley Hospital, London, UK.
³¹ Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan, USA.
³² Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.
³³ Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.
³⁴ Department of Computational Medicine, University of Michigan, Ann Arbor, Michigan, USA.
³⁵ Department of Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
³⁶ Division of Epidemiology and Clinical Applications, National Eye Institute, Bethesda, Maryland, USA.
³⁷ Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, US National Institutes of Health, Bethesda, Maryland, USA.
³⁸ Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece.
³⁹ Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany.
⁴⁰ Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany.
⁴¹ Longitudinal Studies Section, Clinical Research Branch, Gerontology Research Center, National Institute on Aging, Baltimore, Maryland, USA.
⁴² Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria.
⁴³ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
⁴⁴ HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
⁴⁵ Department of Clinical Sciences, Diabetes and Endocrinology, University of Lund, Malmö, Sweden.
⁴⁶ Finnish Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland.
⁴⁷ Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.
⁴⁸ Institute of Biomedical and Clinical Research, University of Exeter Medical School, Exeter, UK.
⁴⁹ Hunt Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway.
⁵⁰ Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, Michigan, USA.
⁵¹ Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
⁵² Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK.
⁵³ Department of Psychology, University of Minnesota, Minneapolis, Minnesota, USA.
⁵⁴ Institute of Human Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
⁵⁵ Institute of Human Genetics, Technische Universität München, Munich, Germany.
⁵⁶ DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
⁵⁷ Epidemiology and Public Health, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.
⁵⁸ Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
⁵⁹ Molecular Neuropsychiatry and Development Laboratory, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.
⁶⁰ Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.
⁶¹ Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.
⁶² Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
⁶³ Institute for Molecular Medicine, FIMM, Helsinki, Finland.
⁶⁴ Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.
⁶⁵ Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
⁶⁶ Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA.
⁶⁷ Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA.
⁶⁸ Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, USA.
⁶⁹ Department of Medicine, McGill University, Montreal, Quebec, Canada.
⁷⁰ Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
⁷¹ Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
⁷² National Institute on Aging, US National Institutes of Health, Baltimore, Maryland, USA.
⁷³ Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands.
⁷⁴ Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
⁷⁵ Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland.
⁷⁶ Dasman Diabetes Institute, Dasman, Kuwait.
⁷⁷ Center for Vascular Prevention, Danube University Krems, Krems, Austria.
⁷⁸ Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia.
⁷⁹ Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
⁸⁰ Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
⁸¹ MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK.
⁸² Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands.
⁸³ Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands.
⁸⁴ University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands.
⁸⁵ Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
⁸⁶ Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.
⁸⁷ Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.
⁸⁸ Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.
⁸⁹ Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
⁹⁰ Vertex Pharmaceuticals, Boston, Massachusetts, USA.
⁹¹ Department of Public Health, University of Helsinki, Helsinki, Finland.
⁹² Department of Haematology, University of Cambridge, Cambridge, UK.
⁹³ NIHR Blood and Transplant Unit (BTRU) in Donor Health and Genomics, University of Cambridge, Cambridge, UK.
⁹⁴ Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, US National Institutes of Health, Bethesda, Maryland, USA.
⁹⁵ Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
⁹⁶ Oxford NIHR Biomedical Research Centre, Churchill Hospital, Headington, Oxford, UK.

PMID: 27548312
PMCID: PMC5388176
DOI: 10.1038/ng.3643

A reference panel of 64,976 haplotypes for genotype imputation

Shane McCarthy et al. Nat Genet. 2016 Oct.

. 2016 Oct;48(10):1279-83.

doi: 10.1038/ng.3643. Epub 2016 Aug 22.

Authors

Collaborators

Haplotype Reference Consortium:
Gonçalo Abecasis, Jonathan Marchini

Affiliations

¹ Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
² Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.
³ Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
⁴ Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
⁵ Genetics and Development, University of Geneva, Geneva, Switzerland.
⁶ Genetics of Complex Traits, Institute of Biomedical Science, University of Exeter Medical School, Exeter, UK.
⁷ Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.
⁸ DZHK (German Centre for Cardiovascular Research), Greifswald, Germany.
⁹ Vertebrate Resequencing Informatics, Wellcome Trust Sanger Institute, Hinxton, UK.
¹⁰ Department of Statistics, University of Oxford, Oxford, UK.
¹¹ IRGB, CNR, Sardinia, Italy.
¹² MRC Integrative Epidemiology Unit, University of Bristol, Oakfield Grove, UK.
¹³ THL, Helsinki, Finland.
¹⁴ Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA.
¹⁵ Department of Psychology and Neurosurgery, University of Colorado, Boulder, Colorado, USA.
¹⁶ Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
¹⁷ Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, Utrecht, the Netherlands.
¹⁸ Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
¹⁹ Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, USA.
²⁰ Department of Psychiatry, SUNY Downstate, Brooklyn, New York, USA.
²¹ Genetic Epidemiology Unit, Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands.
²² Department of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA.
²³ Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.
²⁴ Genetica Medica, IRCCS Burlo Garofolo, Trieste, Italy.
²⁵ Department of Experimental Genetics, Sidra, Doha, Qatar.
²⁶ Genetics and Cell Biology, San Raffaele Research Institute, Milan, Italy.
²⁷ Netherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
²⁸ Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, USA.
²⁹ MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
³⁰ NIHR Biomedical Research Centre for Mental Health, Institute of Psychiatry, Psychology and Neuroscience, King's College London and the South London Maudsley Hospital, London, UK.
³¹ Department of Anesthesiology, University of Michigan, Ann Arbor, Michigan, USA.
³² Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.
³³ Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.
³⁴ Department of Computational Medicine, University of Michigan, Ann Arbor, Michigan, USA.
³⁵ Department of Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
³⁶ Division of Epidemiology and Clinical Applications, National Eye Institute, Bethesda, Maryland, USA.
³⁷ Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, US National Institutes of Health, Bethesda, Maryland, USA.
³⁸ Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece.
³⁹ Department of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany.
⁴⁰ Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany.
⁴¹ Longitudinal Studies Section, Clinical Research Branch, Gerontology Research Center, National Institute on Aging, Baltimore, Maryland, USA.
⁴² Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria.
⁴³ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
⁴⁴ HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
⁴⁵ Department of Clinical Sciences, Diabetes and Endocrinology, University of Lund, Malmö, Sweden.
⁴⁶ Finnish Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland.
⁴⁷ Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.
⁴⁸ Institute of Biomedical and Clinical Research, University of Exeter Medical School, Exeter, UK.
⁴⁹ Hunt Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway.
⁵⁰ Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, Michigan, USA.
⁵¹ Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
⁵² Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK.
⁵³ Department of Psychology, University of Minnesota, Minneapolis, Minnesota, USA.
⁵⁴ Institute of Human Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
⁵⁵ Institute of Human Genetics, Technische Universität München, Munich, Germany.
⁵⁶ DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
⁵⁷ Epidemiology and Public Health, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.
⁵⁸ Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
⁵⁹ Molecular Neuropsychiatry and Development Laboratory, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.
⁶⁰ Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.
⁶¹ Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.
⁶² Department of Genome Sciences, University of Washington, Seattle, Washington, USA.
⁶³ Institute for Molecular Medicine, FIMM, Helsinki, Finland.
⁶⁴ Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.
⁶⁵ Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
⁶⁶ Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA.
⁶⁷ Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA.
⁶⁸ Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, USA.
⁶⁹ Department of Medicine, McGill University, Montreal, Quebec, Canada.
⁷⁰ Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
⁷¹ Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
⁷² National Institute on Aging, US National Institutes of Health, Baltimore, Maryland, USA.
⁷³ Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands.
⁷⁴ Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
⁷⁵ Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland.
⁷⁶ Dasman Diabetes Institute, Dasman, Kuwait.
⁷⁷ Center for Vascular Prevention, Danube University Krems, Krems, Austria.
⁷⁸ Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia.
⁷⁹ Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
⁸⁰ Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
⁸¹ MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK.
⁸² Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands.
⁸³ Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands.
⁸⁴ University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands.
⁸⁵ Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
⁸⁶ Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.
⁸⁷ Diabetes Research Center (Diabetes Unit), Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.
⁸⁸ Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.
⁸⁹ Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
⁹⁰ Vertex Pharmaceuticals, Boston, Massachusetts, USA.
⁹¹ Department of Public Health, University of Helsinki, Helsinki, Finland.
⁹² Department of Haematology, University of Cambridge, Cambridge, UK.
⁹³ NIHR Blood and Transplant Unit (BTRU) in Donor Health and Genomics, University of Cambridge, Cambridge, UK.
⁹⁴ Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, US National Institutes of Health, Bethesda, Maryland, USA.
⁹⁵ Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
⁹⁶ Oxford NIHR Biomedical Research Centre, Churchill Hospital, Headington, Oxford, UK.

PMID: 27548312
PMCID: PMC5388176
DOI: 10.1038/ng.3643

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% 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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Figures

**Figure 1. Performance of imputation using different reference panel.**
The x-axis shows the non-reference allele frequency of the SNP being imputed on a log scale. The y-axis shows imputation accuracy measured by aggregate r² when imputing SNP genotypes into 10 CEU samples. These results are based on using genotypes from sites on Illumina OMNI 1M SNP array was used as pseudo-GWAS data.

**Figure 2. Association signal α₁-antitripsin phenotype at the *SERPINA1* locus.**
Association test statistics on the –log10 p-value scale (y-axis) are plotted for each SNP position (x-axis). Three different imputation panels were used : HapMap2 (left), 1000GP3 (middle), HRC release 1 (right). The SNP rs28929474 is shown as a purple and other SNPs are coloured according to the levels of LD (r²) with this SNP (see r² legend in each subplot)

See this image and copyright information in PMC

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References

1. International HapMap Consortium et al. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007;449:851–861. - PMC - PubMed
1. 1000 Genomes Project Consortium et al. A global reference for human genetic variation. Nature. 2015;526:68–74. - PMC - PubMed
1. Genome of the Netherlands Consortium. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat Genet. 2014;46:818–825. - PubMed
1. Huang J, et al. Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel. Nature Communications. 2015;6:8111. - PMC - PubMed
1. Sidore C, et al. Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers. Nat Genet. 2015;47:1272–1281. - PMC - PubMed

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A reference panel of 64,976 haplotypes for genotype imputation

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A reference panel of 64,976 haplotypes for genotype imputation

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