Evidence map›Paper›PMID 27548312›Full record

ArticleNature genetics2016

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 and 100 more

Abstract readEvaluation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,846 papers, 10 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
1,846citing papers in PubMed, 10 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1,846 citing papers in PubMed, 10 syntheses or guidelines pooled it.

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  11. Trial
  12. Germline Variation and Somatic Alterations in Ewing Sarcoma.Methods in molecular biology (Clifton, N.J.) · 2027
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1,786 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

110 authors.

Shane McCarthyHuman Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.ORCID 0000-0002-2715-4187
Sayantan DasDepartment of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.ORCID 0000-0001-6346-1590
Warren KretzschmarWellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.ORCID 0000-0002-2575-0807
Olivier DelaneauGenetics and Development, University of Geneva, Geneva, Switzerland.
Andrew R WoodGenetics of Complex Traits, Institute of Biomedical Science, University of Exeter Medical School, Exeter, UK.
Alexander TeumerInstitute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.
Hyun Min KangDepartment of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.
Christian FuchsbergerDepartment of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.
Petr DanecekVertebrate Resequencing Informatics, Wellcome Trust Sanger Institute, Hinxton, UK.
Kevin SharpDepartment of Statistics, University of Oxford, Oxford, UK.
Yang LuoHuman Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
Carlo SidoreIRGB, CNR, Sardinia, Italy.
Alan KwongDepartment of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.
Nicholas TimpsonMRC Integrative Epidemiology Unit, University of Bristol, Oakfield Grove, UK.
Seppo KoskinenTHL, Helsinki, Finland.
Scott VriezeInstitute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA.
Laura J ScottDepartment of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.
He ZhangDivision of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
Anubha MahajanWellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Jan VeldinkDepartment of Neurology and Neurosurgery, Brain Center Rudolf Magnus, Utrecht, the Netherlands.
Ulrike PetersPublic Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Carlos PatoDepartment of Psychiatry, SUNY Downstate, Brooklyn, New York, USA.
Cornelia M van DuijnGenetic Epidemiology Unit, Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands.
Christopher E GilliesDepartment of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA.
Ilaria GandinDepartment of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.
Massimo MezzavillaGenetica Medica, IRCCS Burlo Garofolo, Trieste, Italy.
Arthur GillyHuman Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
Massimiliano CoccaDepartment of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.
Michela TragliaGenetics and Cell Biology, San Raffaele Research Institute, Milan, Italy.
Andrea AngiusIRGB, CNR, Sardinia, Italy.
Jeffrey C BarrettHuman Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
Dorrett BoomsmaNetherlands Twin Register, Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
Kari BranhamDepartment of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan, USA.
Gerome BreenMRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.
Chad M BrummettDepartment of Anesthesiology, University of Michigan, Ann Arbor, Michigan, USA.
Fabio BusoneroIRGB, CNR, Sardinia, Italy.
Harry CampbellUsher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.
Andrew ChanUsher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.
Sai ChenDepartment of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.
Emily ChewDivision of Epidemiology and Clinical Applications, National Eye Institute, Bethesda, Maryland, USA.
Francis S CollinsMedical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, US National Institutes of Health, Bethesda, Maryland, USA.
Laura J CorbinMRC Integrative Epidemiology Unit, University of Bristol, Oakfield Grove, UK.
George Davey SmithMRC Integrative Epidemiology Unit, University of Bristol, Oakfield Grove, UK.
George DedoussisDepartment of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece.
Marcus DorrDepartment of Internal Medicine B, University Medicine Greifswald, Greifswald, Germany.
Aliki-Eleni FarmakiDepartment of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece.
Luigi FerrucciLongitudinal Studies Section, Clinical Research Branch, Gerontology Research Center, National Institute on Aging, Baltimore, Maryland, USA.
Lukas ForerDivision of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria.
Ross M FraserDepartment of Anesthesiology, University of Michigan, Ann Arbor, Michigan, USA.
Stacey GabrielProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Shawn LevyHudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
Leif GroopDepartment of Clinical Sciences, Diabetes and Endocrinology, University of Lund, Malmö, Sweden.
Tabitha HarrisonPublic Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Andrew HattersleyInstitute of Biomedical and Clinical Research, University of Exeter Medical School, Exeter, UK.
Oddgeir L HolmenHunt Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway.
Kristian HveemHunt Research Centre, Department of Public Health and General Practice, Norwegian University of Science and Technology, Levanger, Norway.
Matthias KretzlerDepartment of Computational Medicine, University of Michigan, Ann Arbor, Michigan, USA.
James C LeeCambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
Matt McGueDepartment of Psychology, University of Minnesota, Minneapolis, Minnesota, USA.
Thomas MeitingerInstitute of Human Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.
David MelzerEpidemiology and Public Health, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.
Josine L MinMRC Integrative Epidemiology Unit, University of Bristol, Oakfield Grove, UK.
Karen L MohlkeDepartment of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
John B VincentMolecular Neuropsychiatry and Development Laboratory, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.
Matthias NauckDZHK (German Centre for Cardiovascular Research), Greifswald, Germany.
Deborah NickersonDepartment of Genome Sciences, University of Washington, Seattle, Washington, USA.
Aarno PalotieProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Michele PatoDepartment of Psychiatry, SUNY Downstate, Brooklyn, New York, USA.
Nicola PirastuDepartment of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.
Melvin McInnisDepartment of Psychiatry, University of Michigan, Ann Arbor, Michigan, USA.
J Brent RichardsDepartment of Medicine, McGill University, Montreal, Quebec, Canada.
Cinzia SalaGenetics and Cell Biology, San Raffaele Research Institute, Milan, Italy.
Veikko SalomaaTHL, Helsinki, Finland.
David SchlessingerNational Institute on Aging, US National Institutes of Health, Baltimore, Maryland, USA.
Sebastian SchoenherrDivision of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria.
P Eline SlagboomMolecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands.
Kerrin SmallDepartment of Twin Research and Genetic Epidemiology, King's College London, London, UK.
Timothy SpectorDepartment of Twin Research and Genetic Epidemiology, King's College London, London, UK.
Dwight StambolianDepartment of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Marcus TukeGenetics of Complex Traits, Institute of Biomedical Science, University of Exeter Medical School, Exeter, UK.
Jaakko TuomilehtoChronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki, Finland.
Leonard H Van den BergDepartment of Neurology and Neurosurgery, Brain Center Rudolf Magnus, Utrecht, the Netherlands.
Wouter Van RheenenDepartment of Neurology and Neurosurgery, Brain Center Rudolf Magnus, Utrecht, the Netherlands.
Uwe VolkerInstitute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany.
Cisca WijmengaDepartment of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
Daniela TonioloGenetics and Cell Biology, San Raffaele Research Institute, Milan, Italy.
Eleftheria ZegginiHuman Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
Paolo GaspariniDepartment of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.
Matthew G SampsonDepartment of Pediatrics-Nephrology, University of Michigan School of Medicine, Ann Arbor, Michigan, USA.
James F WilsonUsher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.
Timothy FraylingGenetics of Complex Traits, Institute of Biomedical Science, University of Exeter Medical School, Exeter, UK.
Paul I W de BakkerMedical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands.
Morris A SwertzDepartment of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
Steven McCarrollDepartment of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
Charles KooperbergPublic Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
Annelot DekkerDepartment of Neurology and Neurosurgery, Brain Center Rudolf Magnus, Utrecht, the Netherlands.
David AltshulerProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Cristen WillerDivision of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
William IaconoDepartment of Psychology, University of Minnesota, Minneapolis, Minnesota, USA.
Samuli RipattiDepartment of Public Health, University of Helsinki, Helsinki, Finland.
Nicole SoranzoHuman Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
Klaudia WalterHuman Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
Anand SwaroopNeurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, US National Institutes of Health, Bethesda, Maryland, USA.
Francesco CuccaIRGB, CNR, Sardinia, Italy.
Carl A AndersonHuman Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
Richard M MyersHudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
Michael BoehnkeDepartment of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA.
Mark I McCarthyWellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Richard DurbinHuman Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.ORCID 0000-0002-9130-1006
Haplotype Reference Consortium

Funding

Systems BiologyU19AG023122 · NIA · TRANSLATIONAL GENOMICS RESEARCH INST · PI NICHOLAS Joseph SCHORK · 2004 to 2026
$102.6M
Medical Scientist Training ProgramT32GM007753 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI WALENSKY, LOREN DAVID · 1985 to 2021
$50.0M
Validity of Diet and Activity Measures in WomenP01CA055075 · NCI · HARVARD UNIVERSITY (SCH OF PUBLIC HLTH) · PI WILLETT, WALTER C. · 1991 to 2009
$41.8M
Genetic analysis of type II diabetes in Finnish populationZIAHG000024 · NHGRI · NATIONAL HUMAN GENOME RESEARCH INSTITUTE · PI ERDOS, MICHAEL · 2009 to 2025
$38.2M
Mechanisms, modeling and therapies of retinal and macular neurodegenerationZIAEY000546 · NEI · NATIONAL EYE INSTITUTE · PI SWAROOP, ANAND · 2015 to 2025
$36.3M
Tissue and Pathology ResourcesP50CA127003 · NCI · DANA-FARBER CANCER INST · PI EL-BARDEESY, NABEEL, SELLERS, WILLIAM R · 2007 to 2023
$33.2M
THE LUTEIN/ZEAXANTHIN AND OMEGA-3 SUPPLEMENT TRIAL--A MULTI CENTER, RANDOMIZED TN01EY50007 · NEI · THE EMMES COMPANY, LLC · PI CLEMONS, TRACI · 2007 to 2011
$23.3M
Molecular pathological epidemiology of colorectal cancerU01CA137088 · NCI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI PETERS, ULRIKE · 2009 to 2018
$21.8M
Pilot and Feasibility ProgramP30DK020595 · NIDDK · UNIVERSITY OF CHICAGO · PI Matthew J Brady · 2013 to 2026
$20.9M
Training Program in Clinical & Translationa Research in Human Glomerular DiseaseU54DK083912 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI KRETZLER, MATTHIAS · 2009 to 2023
$20.3M
Scientific TransparencyP30EY001583 · NEI · UNIVERSITY OF PENNSYLVANIA · PI Qi N Cui · 1985 to 2026
$19.5M
Low-Pass Sequencing and High-Density SNP Genotyping for Type 2 DiabetesRC2DK088389 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ALTSHULER, DAVID, BOEHNKE, MICHAEL L · 2009 to 2010
$17.9M
Arthritis Research UKBritish Heart Foundation SP/04/002Chief Scientist Office CZB/4/276Chief Scientist Office CZB/4/710CIHR MOP-172013Medical Research Council G0601261Medical Research Council G0601966Medical Research Council G0700931Medical Research Council G0900747Medical Research Council G9815508Medical Research Council MC_PC_15018Medical Research Council MC_UU_12013/3Medical Research Council MR/J00314X/1NCI NIH HHS P01 CA055075NCI NIH HHS P50 CA127003NCI NIH HHS R01 CA059045NCI NIH HHS R01 CA137178NCI NIH HHS R01 CA151993NCI NIH HHS U01 CA137088NCI NIH HHS U01 CA164930NCI NIH HHS UM1 CA167552NEI NIH HHS N01EY50007NEI NIH HHS P30 EY001583NEI NIH HHS ZIA EY000546NHGRI NIH HHS R01 HG000376NHGRI NIH HHS R01 HG007022NHGRI NIH HHS U01 HG005773NHLBI NIH HHS HHSN268201100046CNHLBI NIH HHS HHSN268201300046CNHLBI NIH HHS HHSN268201300047CNHLBI NIH HHS HHSN268201300048CNHLBI NIH HHS HHSN268201300049CNHLBI NIH HHS HHSN268201300050CNHLBI NIH HHS R01 HL102830NHLBI NIH HHS R01 HL109946NHLBI NIH HHS R01 HL117626NHLBI NIH HHS R01 HL127564NHLBI NIH HHS U01 HL117626NIAAA NIH HHS R01 AA009367NIA NIH HHS HHSN271201100004CNIA NIH HHS U19 AG023122NIDA NIH HHS R01 DA005147NIDA NIH HHS R01 DA024417NIDA NIH HHS R01 DA036216NIDA NIH HHS R01 DA037904NIDDK NIH HHS K24 DK080140NIDDK NIH HHS K99 DK092251NIDDK NIH HHS P30 DK020595NIDDK NIH HHS R01 DK072193NIDDK NIH HHS R01 DK073541NIDDK NIH HHS R01 DK093757NIDDK NIH HHS R01 DK098032NIDDK NIH HHS RC2 DK088389NIDDK NIH HHS U01 DK062370NIDDK NIH HHS U01 DK085501NIDDK NIH HHS U01 DK085526NIDDK NIH HHS U01 DK085545NIDDK NIH HHS U54 DK083912NIGMS NIH HHS T32 GM007753NIMH NIH HHS N01 MH080001NIMH NIH HHS R01 MH085548NIMH NIH HHS R01 MH090937NIMH NIH HHS R01 MH094145NIMH NIH HHS R01 MH101820NIMH NIH HHS R01 MH104964NIMH NIH HHS U01 MH105641NIMH NIH HHS U01 MH105653Wellcome Trust 202802/Z/16/ZWellcome Trust WT090851Wellcome Trust WT091310Wellcome Trust WT097307Wellcome Trust WT098051WHI NIH HHS HHSN268201100001CWHI NIH HHS HHSN268201100002CWHI NIH HHS HHSN268201100003CWHI NIH HHS HHSN268201100004C
6 · The paper itself

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.

Indexed as

GenotypeHaplotypesPolymorphism, Single NucleotideAllelesGenetic TechniquesGenome-Wide Association StudyHumansInternetReference Values

Identifiers

PMID27548312
PMCPMC5388176

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