Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
Open accessAbstract
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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Genome-wide association studies have confirmed a number of non-HLA genetic factors that increase the risk of a first appearing b-cell autoantibody or type 1 diabetes, both in first degree relatives of individuals with type 1 diabetes and in the general population.
“Genome-wide association studies have confirmed a number of non-HLA genetic factors that increase the risk of a first appearing b-cell autoantibody or type 1 diabetes, both in first degree relatives of individuals with type 1 diabetes and in the general population (386,387,404,405).”
From Guidelines and Recommendations for Laboratory Analysis in the Diagnosis and Management of Diabetes Mellitus (2023) · cites this paper as [404]
The Type 1 diabetes (T1D) section reports associations between several non-HLA regions and T1D susceptibility, including findings confirmed in independent populations. It does not report risk of a first-appearing beta-cell autoantibody or assess these associations specifically in first-degree relatives of people with T1D. (LLM, conf=0.88)
Experimental — accuracy not yet measuredGWAS confirm that non-HLA factors INS, VNTR, CTLA4, PTPN22, and others raise type 1 diabetes risk in first-degree relatives and the general population.
“Genomewide association studies have confirmed that the following non-HLA genetic factors increase the risk for type 1 diabetes, both in first-degree relatives of type 1 diabetic patients and in the general population: INS, VNTR, CTLA4, PTPN22, and others (263,265,282,283).”
From Guidelines and recommendations for laboratory analysis in the diagnosis and management of diabetes mellitus (2011) · cites this paper as [282]
Only a handful of proteins (e.g., Tnfaip2) show peaked, transient protein expression within the time scale; all have very high basal degradation rates, which typically do not increase further.
“Only a handful of proteins (e.g., Tnfaip2 (26, 35, 36)), show peaked, transient protein expression within our time scale; all have very high basal degradation rates, which typically do not increase further.”
From Dynamic profiling of the protein life cycle in response to pathogens (2015) · cites this paper as [36]
Progress on study size, denser genotyping arrays, imputation strategies, bias attention, and appropriate significance thresholds delivered robust associations across a range of diseases.
“and progress on several fronts–expansion of study size, denser genotyping arrays, novel strategies for imputation, attention to biases and appropriate significance thresholds–delivered robust associations across a range of diseases40.”
From A brief history of human disease genetics (2020) · cites this paper as [40]
The SCZ risk profile was not predictive of case status for any of six non-psychiatric diseases.
“As an important test of specificity, the SCZ risk profile was not predictive of case status for any of six non-psychiatric diseases. 177”
From Genetic architectures of psychiatric disorders: the emerging picture and its implications (2012) · cites this paper as [177]
The LCT gene is a locus well-documented as showing substantial genetic differentiation within Europe.
“The LCT gene is a locus well-documented as showing substantial genetic differentiation within Europe [29], [30].”
From Genome-Wide Association Studies of Quantitatively Measured Skin, Hair, and Eye Pigmentation in Four European Populations (2012) · cites this paper as [29]
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Self-citationGenome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease
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Genomewide Association Analysis of Coronary Artery Disease
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Self-citationRobust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes
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A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
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Copy number variation in human health, disease, and evolution
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Self-citationIn vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target
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Estimating Missing Heritability for Disease from Genome-wide Association Studies
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The genetic architecture of type 2 diabetes
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Self-citationHuman genetic variation and its contribution to complex traits
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Glucolipotoxicity: fuel excess and β-cell dysfunction
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Genotype Imputation with Thousands of Genomes
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Self-citationThe Neuropsychopharmacology of Fronto-Executive Function: Monoaminergic Modulation
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The GABAergic deficit hypothesis of major depressive disorder
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Self-citationGenomics, type 2 diabetes, and obesity
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Self-citationThe genetics and immunopathogenesis of inflammatory bowel disease
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A HapMap harvest of insights into the genetics of common disease
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Autophagy in inflammation, infection, and immunometabolism
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Rare Variants Create Synthetic Genome-Wide Associations
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Genome-wide association analysis identifies 20 loci that influence adult height
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Self-citationMapping complex disease traits with global gene expression
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The Genetics of Alzheimer Disease: Back to the Future
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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
- Jones, Richard W.
- Ring, Susan M.
- Strachan, David P.
- Breen, Gerome
- Jones, Lisa
- Fraser, Christine
- Green, Elaine K.
- Grozeva, Detelina
- Hamshere, Marian L.
- Holmans, Peter A.
- Jones, Ian R.
- Kirov, George
- Owen, Michael J.
- Collier, David A.
- McGuffin, Peter
- Young, Allan H.
- Ferrier, I. Nicol
- Ball, Stephen G.
- Barrett, Jennifer H.
- Bishop, D. Timothy
- Iles, Mark M.
- Maqbool, Azhar
- Yuldasheva, Nadira
- Braund, Peter S.
- Mangino, Massimo
- Satsangi, Jack
- Fisher, Sheila A.
- Forbes, Alastair
- Lewis, Cathryn M.
- Prescott, Natalie J.
- Sanderson, Jeremy
- Mansfield, John C.
- Brown, Morris J.
- Dominiczak, Anna
- Burke, Beverley
- Dobson, Richard
- Lee, Kate L.
- Munroe, Patricia B.
- Newhouse, Stephen J.
- Wallace, Chris
- Xue, Mingzhan
- Barton, Anne
- Bruce, Ian N.
- Hider, Samantha L.
- Hinks, Anne M.
- Silman, Alan J.
- Symmons, Deborah P. M.
- Thomson, Wendy
- Dunger, David B.
- Frayling, Timothy M.
- Freathy, Rachel M.
- Perry, John R. B.
- Shields, Beverley M.
- Weedon, Michael N.
- Hitman, Graham A.
- Groves, Christopher J.
- Lindgren, Cecilia M.
- Rayner, Nigel W.
- Timpson, Nicholas J.
- Zeggini, Eleftheria
- Lyons, Emily
- Vannberg, Fredrik
- Bradbury, Linda A.
- Simmonds, Matthew J.
- Ban, Maria
- Goris, An
- Sawcer, Stephen J.
- Compston, Alastair
- Conway, David
- Jallow, Muminatou
- Downes, Kate
- Hunt, Sarah E.
- Inouye, Michael
- King, Emma
- McGinnis, Ralph
- Potter, Simon
- Ravindrarajah, Rathi
- Withers, David
- Ferreira, Teresa
- Su, Zhan
- Vukcevic, Damjan
- Venue
- Nature
- Published
- 2007-06-07
- Volume
- 447
- Issue
- 7145
- Pages
- 661-678
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- 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
- bronze
- doi.org
- 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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