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de Vries PS, Sabater-Lleal M, Chasman DI, Trompet S, Ahluwalia TS, Teumer A, Kleber ME, Chen MH, Wang JJ, Attia JR, Marioni RE, Steri M, Weng LC, Pool R, Grossmann V, Brody JA, Venturini C, Tanaka T, Rose LM, Oldmeadow C, Mazur J, Basu S, Frånberg M, Yang Q, Ligthart S, Hottenga JJ, Rumley A, Mulas A, de Craen AJM, Grotevendt A, Taylor KD, Delgado GE, Kifley A, Lopez LM, Berentzen TL, Mangino M, Bandinelli S, Morrison AC, Hamsten A, Tofler G, de Maat MPM, Draisma HHM, Lowe GD, Zoledziewska M, Sattar N, Lackner KJ, Völker U, McKnight B, Huang J, Holliday EG, McEvoy MA, Starr JM, Hysi PG, Hernandez DG, Guan W, Rivadeneira F, McArdle WL, Slagboom PE, Zeller T, Psaty BM, Uitterlinden AG, de Geus EJC, Stott DJ, Binder H, Hofman A, Franco OH, Rotter JI, Ferrucci L, Spector TD, Deary IJ, März W, Greinacher A, Wild PS, Cucca F, Boomsma DI, Watkins H, Tang W, Ridker PM, Jukema JW, Scott RJ, Mitchell P, Hansen T, O'Donnell CJ, Smith NL, Strachan DP, Dehghan A. Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study. PLoS One 2017; 12:e0167742. [PMID: 28107422 PMCID: PMC5249120 DOI: 10.1371/journal.pone.0167742] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 11/19/2016] [Indexed: 12/21/2022] Open
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.
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Affiliation(s)
- Paul S. de Vries
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
- University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Maria Sabater-Lleal
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Daniel I. Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Tarunveer S. Ahluwalia
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Novo Nordisk Foundation Center For Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Marcus E. Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ming-Huei Chen
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States of America
- Framingham 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
| | - Jie Jin Wang
- Centre for Vision Research, Department of Ophthalmology, and Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - John R. Attia
- Public Health Stream, Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia
- School of Medicine and Public Health, University of Newcastle, Newcastle, Australia
| | - Riccardo E. Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, United Kingdom
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy
| | - Lu-Chen Weng
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, United States of America
| | - Rene Pool
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, the Netherlands
- EMGO+ institute, VU University & VU medical center, Amsterdam, the Netherlands
| | - Vera Grossmann
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jennifer A. Brody
- Department of Medicine, University of Washington, Seattle WA, United States of America
| | - Cristina Venturini
- Division of Infection and Immunology, UCL, London, United Kingdom
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, United Kingdom
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, United States of America
| | - Lynda M. Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
| | - Christopher Oldmeadow
- Public Health Stream, Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia
- School of Medicine and Public Health, University of Newcastle, Newcastle, Australia
| | - Johanna Mazur
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Saonli Basu
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, United States of America
| | - Mattias Frånberg
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden
| | - Qiong Yang
- Framingham 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
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, United States of America
| | - Symen Ligthart
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Jouke J. Hottenga
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, the Netherlands
| | - Ann Rumley
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Antonella Mulas
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy
| | - Anton J. M. de Craen
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Anne Grotevendt
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor/UCLA Medical Center, Torrance, CA, United States of America
- Division of Genomic Outcomes, Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Graciela E. Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Annette Kifley
- Centre for Vision Research, Department of Ophthalmology, and Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Lorna M. Lopez
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Royal College of Surgeons in Ireland, Department of Psychiatry, Education and Research Centre, Beaumont Hospital, Dublin, Ireland
- University College Dublin, UCD Conway Institute, Centre for Proteome Research, UCD, Belfield, Dublin, Ireland
| | - Tina L. Berentzen
- Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, United Kingdom
- NIHR Biomedical Research Centre at Guy’s and St. Thomas’ Foundation Trust, London, United Kingdom
| | | | | | - Anders Hamsten
- Cardiovascular Medicine Unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Geoffrey Tofler
- Royal North Shore Hospital, Sydney University, Sydney, Australia
| | | | - Harmen H. M. Draisma
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, the Netherlands
- Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - Gordon D. Lowe
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Magdalena Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy
| | - Naveed Sattar
- BHF Glasgow Cardiovascular Research Centre, Faculty of Medicine, Glasgow, United Kingdom
| | - Karl J. Lackner
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Barbara McKnight
- Department of Biostatistics, University of Washington, Seattle, WA, United States of America
| | - Jie Huang
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Elizabeth G. Holliday
- Public Health Stream, Hunter Medical Research Institute, and School of Medicine and Public Health, University of Newcastle, Newcastle, Australia
| | - Mark A. McEvoy
- School of Medicine and Public Health, University of Newcastle, Newcastle, Australia
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, United Kingdom
| | - Dena G. Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, United States of America
| | - Weihua Guan
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, United States of America
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Wendy L. McArdle
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - P. Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Tanja Zeller
- Department of General and Interventional Cardiology, University Heart Centre, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Hamburg, Lübeck, Kiel, Hamburg, Germany
| | - Bruce M. Psaty
- Department of Medicine, Epidemiology, and Health Services, University of Washington, Seattle WA, United States of America
- Group Health Research Institute, Group Health Cooperative, Seattle WA, United States of America
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
| | - Eco J. C. de Geus
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, the Netherlands
- EMGO+ institute, VU University & VU medical center, Amsterdam, the Netherlands
| | - David J. Stott
- Institute of Cardiovascular and Medical Sciences, Faculty of Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Harald Binder
- Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MS, United States of America
| | - Oscar H. Franco
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Jerome I. Rotter
- Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Institute for Translational Genomics and Population Sciences, Torrance, CA, United States of America
- Division of Genomic Outcomes, Departments of Pediatrics & Medicine, Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, United States of America
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, United Kingdom
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Andreas Greinacher
- Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Philipp S. Wild
- Preventive Cardiology and Preventive Medicine, Center for Cardiology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site RhineMain, Mainz, Germany
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy
| | - Dorret I. Boomsma
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, the Netherlands
| | - Hugh Watkins
- Cardiovascular Medicine Dept/Radcliffe Dept of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Weihong Tang
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, United States of America
| | - Paul M. Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
| | - Jan W. Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, the Netherlands
- Durrer Center for Cardiogenetic Research, Amsterdam, the Netherlands
- Interuniversity Cardiology Institute of the Netherlands, Utrecht, the Netherlands
| | - Rodney J. Scott
- Information based Medicine Program, Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Paul Mitchell
- Centre for Vision Research, Department of Ophthalmology, and Westmead Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Torben Hansen
- Novo 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'Donnell
- Framingham 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
- Cardiology Division, Massachusetts General Hospital, Boston, MA, United States of America
| | - Nicholas L. Smith
- Group Health Research Institute, Group Health Cooperative, Seattle WA, United States of America
- Department of Epidemiology, University of Washington, Seattle WA, United States of America
- Seattle Epidemiologic Research and Information Center, Department of Veteran Affairs Office of Research and Development, Seattle, WA, United States of America
| | - David P. Strachan
- Population Health Research Institute, St George's, University of London, London, United Kingdom
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
- * E-mail:
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