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Cited by 9,442Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and AnimalsGenetic and phenotypic traits in livestock

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Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls

Open access
The Wellcome Trust Case Control Consortium, Management Committee, Burton, Paul R., Clayton, David G., Cardon, Lon R., Craddock, Nick, Deloukas, Panos, Duncanson, Audrey, Kwiatkowski, Dominic P., McCarthy, Mark I., Ouwehand, Willem H., Samani, Nilesh J., Todd, John A., Donnelly, Peter, Data and Analysis Committee, Barrett, Jeffrey C., Burton, Paul R., Davison, Dan, Donnelly, Peter, Easton, Doug, Evans, David, Leung, Hin-Tak, Marchini, Jonathan L., Morris, Andrew P., Spencer, Chris C. A., Tobin, Martin D., Cardon, Lon R., Clayton, David G., UK Blood Services and University of Cambridge Controls, Attwood, Antony P., Boorman, James P., Cant, Barbara, Everson, Ursula, Hussey, Judith M., Jolley, Jennifer D., Knight, Alexandra S., Koch, Kerstin, Meech, Elizabeth, Nutland, Sarah, Prowse, Christopher V., Stevens, Helen E., Taylor, Niall C., Walters, Graham R., Walker, Neil M., Watkins, Nicholas A., Winzer, Thilo, Todd, John A., Ouwehand, Willem H., 1958 Birth Cohort Controls, Jones, Richard W., McArdle, Wendy L., Ring, Susan M., Strachan, David P., Pembrey, Marcus, Bipolar Disorder, Breen, Gerome, St Clair, David, Caesar, Sian, Gordon-Smith, Katherine, Jones, Lisa, Fraser, Christine, Green, Elaine K., Grozeva, Detelina, Hamshere, Marian L., Holmans, Peter A., Jones, Ian R., Kirov, George, Moskvina, Valentina, Nikolov, Ivan, O'Donovan, Michael C., Owen, Michael J., Craddock, Nick, Collier, David A., Elkin, Amanda, Farmer, Anne, Williamson, Richard, McGuffin, Peter, Young, Allan H., Ferrier, I. Nicol, Coronary Artery Disease, Ball, Stephen G., Balmforth, Anthony J., Barrett, Jennifer H., Bishop, D. Timothy, Iles, Mark M., Maqbool, Azhar, Yuldasheva, Nadira, Hall, Alistair S., Braund, Peter S., Burton, Paul R., Dixon, Richard J., Mangino, Massimo, Stevens, Suzanne, Tobin, Martin D., Thompson, John R., Samani, Nilesh J., Crohn’s Disease, Bredin, Francesca, Tremelling, Mark, Parkes, Miles, Drummond, Hazel, Lees, Charles W., Nimmo, Elaine R., Satsangi, Jack, Fisher, Sheila A., Forbes, Alastair, Lewis, Cathryn M., Onnie, Clive M., Prescott, Natalie J., Sanderson, Jeremy, Mathew, Christopher G., Barbour, Jamie, Mohiuddin, M. Khalid, Todhunter, Catherine E., Mansfield, John C., Ahmad, Tariq, Cummings, Fraser R., Jewell, Derek P., Hypertension, Webster, John, Brown, Morris J., Clayton, David G., Lathrop, G. Mark, Connell, John, Dominiczak, Anna, Samani, Nilesh J., Marcano, Carolina A. Braga, Burke, Beverley, Dobson, Richard, Gungadoo, Johannie, Lee, Kate L., Munroe, Patricia B., Newhouse, Stephen J., Onipinla, Abiodun, Wallace, Chris, Xue, Mingzhan, Caulfield, Mark, Farrall, Martin, Rheumatoid Arthritis, Barton, Anne, and Genomics, The Biologics in RA Genetics, Bruce, Ian N., Donovan, Hannah, Eyre, Steve, Gilbert, Paul D., Hider, Samantha L., Hinks, Anne M., John, Sally L., Potter, Catherine, Silman, Alan J., Symmons, Deborah P. M., Thomson, Wendy, Worthington, Jane, Type 1 Diabetes, Clayton, David G., Dunger, David B., Nutland, Sarah, Stevens, Helen E., Walker, Neil M., Widmer, Barry, Todd, John A., Type 2 Diabetes, Frayling, Timothy M., Freathy, Rachel M., Lango, Hana, Perry, John R. B., Shields, Beverley M., Weedon, Michael N., Hattersley, Andrew T., Hitman, Graham A., Walker, Mark, Elliott, Kate S., Groves, Christopher J., Lindgren, Cecilia M., Rayner, Nigel W., Timpson, Nicholas J., Zeggini, Eleftheria, McCarthy, Mark I., Tuberculosis, Newport, Melanie, Sirugo, Giorgio, Lyons, Emily, Vannberg, Fredrik, Hill, Adrian V. S., Ankylosing Spondylitis, Bradbury, Linda A., Farrar, Claire, Pointon, Jennifer J., Wordsworth, Paul, Brown, Matthew A., Autoimmune Thyroid Disease, Franklyn, Jayne A., Heward, Joanne M., Simmonds, Matthew J., Gough, Stephen C. L., Breast Cancer, Seal, Sheila, Susceptibility Collaboration, Breast Cancer, Stratton, Michael R., Rahman, Nazneen, Multiple Sclerosis, Ban, Maria, Goris, An, Sawcer, Stephen J., Compston, Alastair, Gambian Controls, Conway, David, Jallow, Muminatou, Newport, Melanie, Sirugo, Giorgio, Rockett, Kirk A., Kwiatkowski, Dominic P., DNA, Genotyping, Data QC and Informatics, Bumpstead, Suzannah J., Chaney, Amy, Downes, Kate, Ghori, Mohammed J. R., Gwilliam, Rhian, Hunt, Sarah E., Inouye, Michael, Keniry, Andrew, King, Emma, McGinnis, Ralph, Potter, Simon, Ravindrarajah, Rathi, Whittaker, Pamela, Widden, Claire, Withers, David, Deloukas, Panos, Leung, Hin-Tak, Nutland, Sarah, Stevens, Helen E., Walker, Neil M., Todd, John A., Statistics, Easton, Doug, Clayton, David G., Burton, Paul R., Tobin, Martin D., Barrett, Jeffrey C., Evans, David, Morris, Andrew P., Cardon, Lon R., Cardin, Niall J., Davison, Dan, Ferreira, Teresa, Pereira-Gale, Joanne, Hallgrimsdóttir, Ingileif B., Howie, Bryan N., Marchini, Jonathan L., Spencer, Chris C. A., Su, Zhan, Teo, Yik Ying, Vukcevic, Damjan, Donnelly, Peter, Primary Investigators, Bentley, David, Brown, Matthew A., Cardon, Lon R., Caulfield, Mark, Clayton, David G., Compston, Alistair, Craddock, Nick, Deloukas, Panos, Donnelly, Peter, Farrall, Martin, Gough, Stephen C. L., Hall, Alistair S., Hattersley, Andrew T., Hill, Adrian V. S., Kwiatkowski, Dominic P., Mathew, Christopher G., McCarthy, Mark I., Ouwehand, Willem H., Parkes, Miles, Pembrey, Marcus, Rahman, Nazneen, Samani, Nilesh J., Stratton, Michael R., Todd, John A., Worthington, Jane·2007·Nature
DOI 10.1038/nature05911PMC PMC2719288
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Abstract

There is increasing evidence that genome-wide association (GWA) studies represent a powerful approach to the identification of genes involved in common human diseases. We describe a joint GWA study (using the Affymetrix GeneChip 500K Mapping Array Set) undertaken in the British population, which has examined approximately 2,000 individuals for each of 7 major diseases and a shared set of approximately 3,000 controls. Case-control comparisons identified 24 independent association signals at P < 5 x 10(-7): 1 in bipolar disorder, 1 in coronary artery disease, 9 in Crohn's disease, 3 in rheumatoid arthritis, 7 in type 1 diabetes and 3 in type 2 diabetes. On the basis of prior findings and replication studies thus-far completed, almost all of these signals reflect genuine susceptibility effects. We observed association at many previously identified loci, and found compelling evidence that some loci confer risk for more than one of the diseases studied. Across all diseases, we identified a large number of further signals (including 58 loci with single-point P values between 10(-5) and 5 x 10(-7)) likely to yield additional susceptibility loci. The importance of appropriately large samples was confirmed by the modest effect sizes observed at most loci identified. This study thus represents a thorough validation of the GWA approach. It has also demonstrated that careful use of a shared control group represents a safe and effective approach to GWA analyses of multiple disease phenotypes; has generated a genome-wide genotype database for future studies of common diseases in the British population; and shown that, provided individuals with non-European ancestry are excluded, the extent of population stratification in the British population is generally modest. Our findings offer new avenues for exploring the pathophysiology of these important disorders. We anticipate that our data, results and software, which will be widely available to other investigators, will provide a powerful resource for human genetics research.

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Authors
The Wellcome Trust Case Control Consortium, Management Committee, Burton, P. R., Clayton, D. G., Cardon, L. R., Craddock, N., Deloukas, P., Duncanson, A., Kwiatkowski, D. P., McCarthy, M. I., Ouwehand, W. H., Samani, N. J., Todd, J. A., Donnelly, P., Data and Analysis Committee, Barrett, J. C., Burton, P. R., Davison, D., Donnelly, P., Easton, D., Evans, D., Leung, H.-T., Marchini, J. L., Morris, A. P., Spencer, C. C. A., Tobin, M. D., Cardon, L. R., Clayton, D. G., UK Blood Services and University of Cambridge Controls, Attwood, A. P., Boorman, J. P., Cant, B., Everson, U., Hussey, J. M., Jolley, J. D., Knight, A. S., Koch, K., Meech, E., Nutland, S., Prowse, C. V., Stevens, H. E., Taylor, N. C., Walters, G. R., Walker, N. M., Watkins, N. A., Winzer, T., Todd, J. A., Ouwehand, W. H., Controls, 1. B. C., Jones, R. W., McArdle, W. L., Ring, S. M., Strachan, D. P., Pembrey, M., Disorder, B., Breen, G., St Clair, D., Caesar, S., Gordon-Smith, K., Jones, L., Fraser, C., Green, E. K., Grozeva, D., Hamshere, M. L., Holmans, P. A., Jones, I. R., Kirov, G., Moskvina, V., Nikolov, I., O'Donovan, M. C., Owen, M. J., Craddock, N., Collier, D. A., Elkin, A., Farmer, A., Williamson, R., McGuffin, P., Young, A. H., Ferrier, I. N., Disease, C. A., Ball, S. G., Balmforth, A. J., Barrett, J. H., Bishop, D. T., Iles, M. M., Maqbool, A., Yuldasheva, N., Hall, A. S., Braund, P. S., Burton, P. R., Dixon, R. J., Mangino, M., Stevens, S., Tobin, M. D., Thompson, J. R., Samani, N. J., Disease, C., Bredin, F., Tremelling, M., Parkes, M., Drummond, H., Lees, C. W., Nimmo, E. R., Satsangi, J., Fisher, S. A., Forbes, A., Lewis, C. M., Onnie, C. M., Prescott, N. J., Sanderson, J., Mathew, C. G., Barbour, J., Mohiuddin, M. K., Todhunter, C. E., Mansfield, J. C., Ahmad, T., Cummings, F. R., Jewell, D. P., Hypertension, Webster, J., Brown, M. J., Clayton, D. G., Lathrop, G. M., Connell, J., Dominiczak, A., Samani, N. J., Marcano, C. A. B., Burke, B., Dobson, R., Gungadoo, J., Lee, K. L., Munroe, P. B., Newhouse, S. J., Onipinla, A., Wallace, C., Xue, M., Caulfield, M., Farrall, M., Arthritis, R., Barton, A., and Genomics, T. B. I. R. G., Bruce, I. N., Donovan, H., Eyre, S., Gilbert, P. D., Hider, S. L., Hinks, A. M., John, S. L., Potter, C., Silman, A. J., Symmons, D. P. M., Thomson, W., Worthington, J., Diabetes, T. 1., Clayton, D. G., Dunger, D. B., Nutland, S., Stevens, H. E., Walker, N. M., Widmer, B., Todd, J. A., Diabetes, T. 2., Frayling, T. M., Freathy, R. M., Lango, H., Perry, J. R. B., Shields, B. M., Weedon, M. N., Hattersley, A. T., Hitman, G. A., Walker, M., Elliott, K. S., Groves, C. J., Lindgren, C. M., Rayner, N. W., Timpson, N. J., Zeggini, E., McCarthy, M. I., Tuberculosis, Newport, M., Sirugo, G., Lyons, E., Vannberg, F., Hill, A. V. S., Spondylitis, A., Bradbury, L. A., Farrar, C., Pointon, J. J., Wordsworth, P., Brown, M. A., Disease, A. T., Franklyn, J. A., Heward, J. M., Simmonds, M. J., Gough, S. C. L., Cancer, B., Seal, S., Susceptibility Collaboration, B. C., Stratton, M. R., Rahman, N., Sclerosis, M., Ban, M., Goris, A., Sawcer, S. J., Compston, A., Controls, G., Conway, D., Jallow, M., Newport, M., Sirugo, G., Rockett, K. A., Kwiatkowski, D. P., DNA, G., Bumpstead, S. J., Chaney, A., Downes, K., Ghori, M. J. R., Gwilliam, R., Hunt, S. E., Inouye, M., Keniry, A., King, E., McGinnis, R., Potter, S., Ravindrarajah, R., Whittaker, P., Widden, C., Withers, D., Deloukas, P., Leung, H.-T., Nutland, S., Stevens, H. E., Walker, N. M., Todd, J. A., Statistics, Easton, D., Clayton, D. G., Burton, P. R., Tobin, M. D., Barrett, J. C., Evans, D., Morris, A. P., Cardon, L. R., Cardin, N. J., Davison, D., Ferreira, T., Pereira-Gale, J., Hallgrimsdóttir, I. B., Howie, B. N., Marchini, J. L., Spencer, C. C. A., Su, Z., Teo, Y. Y., Vukcevic, D., Donnelly, P., Primary Investigators, Bentley, D., Brown, M. A., Cardon, L. R., Caulfield, M., Clayton, D. G., Compston, A., Craddock, N., Deloukas, P., Donnelly, P., Farrall, M., Gough, S. C. L., Hall, A. S., Hattersley, A. T., Hill, A. V. S., Kwiatkowski, D. P., Mathew, C. G., McCarthy, M. I., Ouwehand, W. H., Parkes, M., Pembrey, M., Rahman, N., Samani, N. J., Stratton, M. R., Todd, J. A., & Worthington, J.
Affiliations
  • Wellcome Trust (GB)
  • University of Cambridge (GB)
  • National Health Service (GB)
  • Welsh Blood Service (GB)
  • Scottish National Blood Transfusion Service (GB)
  • University of Bristol (GB)
  • St George's, University of London (GB)
  • Wellcome Sanger Institute (GB)
  • University of Aberdeen (GB)
  • Cardiff University (GB)
  • King's College London (GB)
  • University of Leicester (GB)
  • University of Leeds (GB)
  • Western General Hospital (GB)
  • Guy's Hospital (GB)
  • University College London Hospitals NHS Foundation Trust (GB)
  • Guy's and St Thomas' NHS Foundation Trust (GB)
  • Royal Victoria Infirmary (GB)
  • University of Glasgow (GB)
  • University of Manchester (GB)
  • Queen Mary University of London (GB)
  • Centre for Human Genetics (GB)
  • University of Exeter (GB)
  • The University of Queensland (AU)
  • Institute of Cancer Research (GB)
  • University of Birmingham (GB)
  • Cancer Research UK (GB)
  • University of Oxford (GB)
  • Churchill Hospital (GB)
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2007-06-07
Volume
447
Issue
7145
Pages
661-678
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/nature05911
PMC
PMC2719288
OpenAlex
W2134783591
Cited by
9,442
References
148
Citations by year
2026: 88 · 2025: 157 · 2024: 220 · 2023: 211 · 2022: 247 · 2021: 292 · 2020: 285 · 2019: 306 · 2018: 357 · 2017: 386 · 2016: 412 · 2015: 484 · 2014: 532 · 2013: 608 · 2012: 728
FWCI
586.53
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • Research Explorer (The University of Manchester) (publishedVersion)
  • Bristol Research (University of Bristol) (publishedVersion)
  • Lincoln Repository (University of Lincoln) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • LSHTM Research Online (London School of Hygiene and Tropical Medicine) (acceptedVersion)
  • ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (submittedVersion)
  • QUT ePrints (Queensland University of Technology) (submittedVersion)
  • ePrints Soton (University of Southampton) (submittedVersion)
  • UCL Discovery (University College London) (submittedVersion)
  • Figshare (submittedVersion)
  • Figshare (submittedVersion, cc-by)
  • ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
  • Research Portal (King's College London) (submittedVersion)
  • Lirias (submittedVersion)
  • Leicester Research Archive (University of Leicester) (submittedVersion)
  • University of Birmingham Research Portal (University of Birmingham) (submittedVersion)
  • Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
  • ResearchSpace (University of Auckland) (submittedVersion)
  • UEA Digital Repository (University of East Anglia) (submittedVersion)
Funders
  • National Science Foundation
  • Wellcome Trust (077011, 090532, 076113)
  • Cancer Research UK
  • British Heart Foundation
  • Leverhulme Trust
  • Diabetes UK
  • National Institutes of Health
  • Medical Research Council
  • Engineering and Physical Sciences Research Council
  • Fundação para a Ciência e a Tecnologia
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
Keywords
genome-wide association study, disease susceptibility loci, bipolar disorder, coronary artery disease, Crohn's disease, rheumatoid arthritis, type 1 diabetes, type 2 diabetes, population stratification, British population, genotype database, genetic risk factors, Wellcome Trust Case Control Consortium, effect size, replication study, novel loci
MeSH terms
Arthritis, Rheumatoid, Bipolar Disorder, Chromosomes, Human, Coronary Artery Disease, Crohn Disease, Diabetes Mellitus, Gene Frequency, Genetic Markers, Genetics, Population, Geography, United Kingdom, Humans, Hypertension, Genome, Human, Case-Control Studies, Genetic Predisposition to Disease

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