ArticlePloS one2017
Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study.
Abstract read
In one paragraph
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 7 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
23citing papers in PubMed, 7 pooled it
–field-weighted citation impact
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.
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.
Who cites it
23 citing papers in PubMed, 7 syntheses or guidelines pooled it.
- Genome-wide meta-analysis of macronutrient intake of 91,114 European ancestry participants from the cohorts for heart and aging research in genomic epidemiology consortium.Molecular psychiatry · 2019Pooled it
- Genome-wide association meta-analysis of 30,000 samples identifies seven novel loci for quantitative ECG traits.European journal of human genetics : EJHG · 2019Pooled it
- Multiancestry Genome-Wide Association Study of Lipid Levels Incorporating Gene-Alcohol Interactions.American journal of epidemiology · 2019Pooled it
- Genome-Wide Association Transethnic Meta-Analyses Identifies Novel Associations Regulating Coagulation Factor VIII and von Willebrand Factor Plasma Levels.Circulation · 2019Pooled it
- Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders.American journal of human genetics · 2018Pooled it
- Genome-wide association study across European and African American ancestries identifies a SNP in DNMT3B contributing to nicotine dependence.Molecular psychiatry · 2018Pooled it
- Genome-wide association meta-analysis of circulating odd-numbered chain saturated fatty acids: Results from the CHARGE Consortium.PloS one · 2018Pooled it
- Fibrinogen-associated plasma metabolites and implications for coagulation, inflammation, and vascular diseases.Journal of thrombosis and haemostasis : JTH · 2026Article
- Microbiome composition shapes temperature tolerance in a Hawaiian picture-winged Drosophila.The Journal of experimental biology · 2025Article
- Bivariate genome-wide association study of circulating fibrinogen and C-reactive protein levels.Journal of thrombosis and haemostasis : JTH · 2024Article
- Article
- GWAS meta-analyses clarify the genetics of cervical phenotypes and inform risk stratification for cervical cancer.Human molecular genetics · 2023Article
- Processing genome-wide association studies within a repository of heterogeneous genomic datasets.BMC genomic data · 2023Article
- Whole-exome sequencing of 14 389 individuals from the ESP and CHARGE consortia identifies novel rare variation associated with hemostatic factors.Human molecular genetics · 2022Article
- [Nutrigenetics: potentials and applications in cardiovascular diseases and associated risk factors].Revista de la Facultad de Ciencias Medicas (Cordoba, Argentina) · 2022Article
- GIMAP6 regulates autophagy, immune competence, and inflammation in mice and humans.The Journal of experimental medicine · 2022Article
- A Genome-Wide Association Study and Machine-Learning Algorithm Analysis on the Prediction of Facial Phenotypes by Genotypes in Korean Women.Clinical, cosmetic and investigational dermatology · 2022Article
- A spotter's guide to SNPtic exons: The common splice variants underlying some SNP-phenotype correlations.Molecular genetics & genomic medicine · 2022Article
- Mapping gene and gene pathways associated with coronary artery disease: a CARDIoGRAM exome and multi-ancestry UK biobank analysis.Scientific reports · 2021Article
- Interindividual Differences in DNA Adduct Formation and Detoxification of 1,3-Butadiene-Derived Epoxide in Human HapMap Cell Lines.Chemical research in toxicology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
86 authors.
Paul S de VriesDepartment of Epidemiology, Erasmus MC, Rotterdam, the Netherlands.
Maria Sabater-LlealCardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden.
Daniel I ChasmanDivision of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States of America.
Stella TrompetDepartment of Cardiology, Leiden University Medical Center, Leiden, the Netherlands.
Tarunveer S AhluwaliaSteno Diabetes Center Copenhagen, Gentofte, Denmark.ORCID 0000-0002-7464-3354
Alexander TeumerInstitute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.ORCID 0000-0002-8309-094X
Marcus E KleberVth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
Ming-Huei ChenDepartment of Neurology, Boston University School of Medicine, Boston, MA, United States of America.
Jie Jin WangCentre for Vision Research, Department of Ophthalmology, and Westmead Institute for Medical Research, University of Sydney, Sydney, Australia.
John R AttiaPublic Health Stream, Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia.
Riccardo E MarioniCentre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom.
Maristella SteriIstituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy.ORCID 0000-0001-5869-3872
Lu-Chen WengDivision of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, United States of America.
Rene PoolDepartment of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, the Netherlands.ORCID 0000-0001-5579-0933
Vera GrossmannCenter for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
Jennifer A BrodyDepartment of Medicine, University of Washington, Seattle WA, United States of America.
Cristina VenturiniDivision of Infection and Immunology, UCL, London, United Kingdom.
Toshiko TanakaTranslational Gerontology Branch, National Institute on Aging, Baltimore, MD, United States of America.
Lynda M RoseDivision of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States of America.
Christopher OldmeadowPublic Health Stream, Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia.
Johanna MazurInstitute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
Saonli BasuDivision of Biostatistics, University of Minnesota, Minneapolis, MN, United States of America.
Mattias FrånbergCardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden.ORCID 0000-0002-0749-9903
Qiong YangFramingham Heart Study, Population Sciences Branch, Division of Intramural Research National Heart Lung and Blood Institute, National Institutes of Health, Framingham, MA, United States of America.
Symen LigthartDepartment of Epidemiology, Erasmus MC, Rotterdam, the Netherlands.
Jouke J HottengaDepartment of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, the Netherlands.
Ann RumleyInstitute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom.
Antonella MulasIstituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy.
Anton J M de CraenDepartment of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands.
Anne GrotevendtInstitute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany.
Kent D TaylorInstitute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor/UCLA Medical Center, Torrance, CA, United States of America.
Graciela E DelgadoVth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
Annette KifleyCentre for Vision Research, Department of Ophthalmology, and Westmead Institute for Medical Research, University of Sydney, Sydney, Australia.
Lorna M LopezCentre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom.
Tina L BerentzenInstitute of Preventive Medicine, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark.
Massimo ManginoDepartment of Twin Research and Genetic Epidemiology, Kings College London, London, United Kingdom.
Stefania BandinelliGeriatric Unit, Azienda Sanitaria Firenze (ASF), Florence, Italy.
Alanna C MorrisonDepartment of Epidemiology, Erasmus MC, Rotterdam, the Netherlands.
Anders HamstenCardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden.
Geoffrey ToflerRoyal North Shore Hospital, Sydney University, Sydney, Australia.
Moniek P M de MaatDepartment of Hematology, Erasmus MC, Rotterdam, the Netherlands.
Harmen H M DraismaDepartment of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, the Netherlands.
Gordon D LoweInstitute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom.
Magdalena ZoledziewskaIstituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy.
Naveed SattarBHF Glasgow Cardiovascular Research Centre, Faculty of Medicine, Glasgow, United Kingdom.
Karl J LacknerInstitute of Clinical Chemistry and Laboratory Medicine, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany.
Uwe VölkerInterfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
Barbara McKnightDepartment of Biostatistics, University of Washington, Seattle, WA, United States of America.
Jie HuangDepartment of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom.
Elizabeth G HollidayPublic Health Stream, Hunter Medical Research Institute, and School of Medicine and Public Health, University of Newcastle, Newcastle, Australia.
Mark A McEvoySchool of Medicine and Public Health, University of Newcastle, Newcastle, Australia.
John M StarrCentre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom.
Pirro G HysiDepartment of Twin Research and Genetic Epidemiology, Kings College London, London, United Kingdom.
Dena G HernandezLaboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, United States of America.
Weihua GuanDivision of Biostatistics, University of Minnesota, Minneapolis, MN, United States of America.
Fernando RivadeneiraDepartment of Epidemiology, Erasmus MC, Rotterdam, the Netherlands.
Wendy L McArdleSchool of Social and Community Medicine, University of Bristol, Bristol, United Kingdom.
P Eline SlagboomDepartment of Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands.
Tanja ZellerDepartment of General and Interventional Cardiology, University Heart Centre, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
Bruce M PsatyDepartment of Medicine, Epidemiology, and Health Services, University of Washington, Seattle WA, United States of America.
André G UitterlindenDepartment of Epidemiology, Erasmus MC, Rotterdam, the Netherlands.
Eco J C de GeusDepartment of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, the Netherlands.
David J StottInstitute of Cardiovascular and Medical Sciences, Faculty of Medicine, University of Glasgow, Glasgow, United Kingdom.
Harald BinderInstitute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
Albert HofmanDepartment of Epidemiology, Erasmus MC, Rotterdam, the Netherlands.
Oscar H FrancoDepartment of Epidemiology, Erasmus MC, Rotterdam, the Netherlands.
Jerome I RotterLos Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Institute for Translational Genomics and Population Sciences, Torrance, CA, United States of America.
Luigi FerrucciTranslational Gerontology Branch, National Institute on Aging, Baltimore, MD, United States of America.
Tim D SpectorDepartment of Twin Research and Genetic Epidemiology, Kings College London, London, United Kingdom.
Ian J DearyCentre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom.
Winfried MärzVth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
Andreas GreinacherInstitute for Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany.
Philipp S WildPreventive Cardiology and Preventive Medicine, Center for Cardiology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.
Francesco CuccaIstituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy.
Dorret I BoomsmaDepartment of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, the Netherlands.
Hugh WatkinsCardiovascular Medicine Dept/Radcliffe Dept of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
Weihong TangDivision of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, United States of America.
Paul M RidkerDivision of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States of America.
Jan W JukemaDepartment of Cardiology, Leiden University Medical Center, Leiden, the Netherlands.
Rodney J ScottInformation based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia.
Paul MitchellCentre for Vision Research, Department of Ophthalmology, and Westmead Institute for Medical Research, University of Sydney, Sydney, Australia.
Torben HansenNovo Nordisk Foundation Centre for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Christopher J O'DonnellFramingham Heart Study, Population Sciences Branch, Division of Intramural Research National Heart Lung and Blood Institute, National Institutes of Health, Framingham, MA, United States of America.
Nicholas L SmithGroup Health Research Institute, Group Health Cooperative, Seattle WA, United States of America.
David P StrachanPopulation Health Research Institute, St George's, University of London, London, United Kingdom.
Abbas DehghanDepartment of Epidemiology, Erasmus MC, Rotterdam, the Netherlands.ORCID 0000-0001-6403-016X
Funding
NIMH Center Repository Supporting Stem Cell ResearchU24MH068457 · NIMH · RUTGERS THE ST UNIV OF NJ NEW BRUNSWICK · PI BRZUSTOWICZ, LINDA M, KNOWLES, JAMES A · 2003 to 2024
$213.8MInstitute for Clinical and Translational Research (UL1)UL1RR025005 · NCRR · JOHNS HOPKINS UNIVERSITY · PI FORD, DANIEL ERNEST · 2007 to 2011
$75.8MType 1 Diabetes Genetics ConsortiumU01DK062418 · NIDDK · WAKE FOREST UNIVERSITY HEALTH SCIENCES · PI RICH, STEPHEN S. · 2002 to 2007
$59.8MUCLA Clinical and Translational Science InstituteUL1TR000124 · NCATS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI DUBINETT, STEVEN M. · 2012 to 2015
$57.0MTransgenic & Knock-out MouseP30DK063491 · NIDDK · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Andrea L Hevener · 2003 to 2026
$40.4MWomen's Health Study: Continued Follow-upR01CA047988 · NCI · BRIGHAM AND WOMEN'S HOSPITAL · PI BURING, JULIE E., LEE, I-MIN · 1991 to 2014
$28.2MPRECURSORS OF STROKE INCIDENCE AND PROGNOSISR01NS017950 · NINDS · UNIVERSITY OF TEXAS HLTH SCIENCE CENTER · PI Hugo Javier Aparicio, Jose Rafael Romero · 1985 to 2026
$22.9MGenome-Wide Association Analysis in Essential Hypertension (FEHGAS study)R01HL086694 · NHLBI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI ARAVINDA CHAKRAVARTI · 2007 to 2026
$21.2MEpidemiology of Venous Thrombosis & Pulmonary EmbolismR01HL059367 · NHLBI · UNIVERSITY OF MINNESOTA TWIN CITIES · PI TANG, WEIHONG · 1998 to 2024
$11.8MExceptional Survival: Trajectories to Functional Aging (CHS All Stars)R01AG023629 · NIA · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI NEWMAN, ANNE B. · 2004 to 2016
$9.5MCHARGE Consortium: Omics Discovery for CVD and Aging PhenotypesR01HL105756 · NHLBI · UNIVERSITY OF WASHINGTON · PI Bruce M Psaty, NICHOLAS L SMITH · 2011 to 2026
$9.5MRare variants and NHLBI traits in deeply phenotyped cohortsR01HL120393 · NHLBI · UNIVERSITY OF WASHINGTON · PI PSATY, BRUCE M, RICE, KENNETH M. · 2014 to 2016
$8.9MBiotechnology and Biological Sciences Research Council BB/F019394/1Medical Research Council MR/K026992/1NCATS NIH HHS UL1 TR000124NCI NIH HHS R01 CA047988NCI NIH HHS UM1 CA182913NCRR NIH HHS UL1 RR025005NHGRI NIH HHS U01 HG004402NHLBI NIH HHS HHSN268200800007CNHLBI NIH HHS HHSN268201100005CNHLBI NIH HHS HHSN268201100005GNHLBI NIH HHS HHSN268201100005INHLBI NIH HHS HHSN268201100006CNHLBI NIH HHS HHSN268201100007CNHLBI NIH HHS HHSN268201100007INHLBI NIH HHS HHSN268201100008CNHLBI NIH HHS HHSN268201100008INHLBI NIH HHS HHSN268201100009CNHLBI NIH HHS HHSN268201100009INHLBI NIH HHS HHSN268201100010CNHLBI NIH HHS HHSN268201100011CNHLBI NIH HHS HHSN268201100011INHLBI NIH HHS HHSN268201100012CNHLBI NIH HHS HHSN268201200036CNHLBI NIH HHS N01 HC025195NHLBI NIH HHS N01 HC055222NHLBI NIH HHS N01 HC085079NHLBI NIH HHS N01 HC085080NHLBI NIH HHS N01 HC085081NHLBI NIH HHS N01 HC085082NHLBI NIH HHS N01 HC085083NHLBI NIH HHS N01 HC085086NHLBI NIH HHS R01 HL043851NHLBI NIH HHS R01 HL059367NHLBI NIH HHS R01 HL080467NHLBI NIH HHS R01 HL086694NHLBI NIH HHS R01 HL087641NHLBI NIH HHS R01 HL087652NHLBI NIH HHS R01 HL103612NHLBI NIH HHS R01 HL105756NHLBI NIH HHS R01 HL120393NHLBI NIH HHS U01 HL080295NIAMS NIH HHS F32 AR059469NIA NIH HHS R01 AG023629NIA NIH HHS R01 AG033193NIDDK NIH HHS K24 DK080140NIDDK NIH HHS P30 DK063491NIDDK NIH HHS U01 DK062418NIMHD NIH HHS R01 MD009164NIMH NIH HHS R01 MH081802NIMH NIH HHS RC2 MH089951NIMH NIH HHS U24 MH068457NINDS NIH HHS R01 NS017950Wellcome Trust
Abstract
An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G imputation, while 29 loci were associated using both HapMap and 1000G imputation. One locus identified using HapMap imputation was not significant using 1000G imputation. The genome-wide significance threshold of 5×10-8 is based on the number of independent statistical tests using HapMap imputation, and 1000G imputation may lead to further independent tests that should be corrected for. When using a stricter Bonferroni correction for the 1000G GWA study (P-value < 2.5×10-8), the number of loci significant only using HapMap imputation increased to 4 while the number of loci significant only using 1000G decreased to 5. In conclusion, 1000G imputation enabled the identification of 20% more loci than HapMap imputation, although the advantage of 1000G imputation became less clear when a stricter Bonferroni correction was used. More generally, our results provide insights that are applicable to the implementation of other dense reference panels that are under development.
Indexed as
Genome-Wide Association StudyHapMap ProjectHumans
Identifiers
What OpenQuestion holds
Textmetadata
LicenceCC0
Read underepoch 390
Registered trials
None linked
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.