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Practical aspects of imputation-driven meta-analysis of genome-wide association studies
Open accessAbstract
Motivated by the overwhelming success of genome-wide association studies, droves of researchers are working vigorously to exchange and to combine genetic data to expediently discover genetic risk factors for common human traits. The primary tools that fuel these new efforts are imputation, allowing researchers who have collected data on a diversity of genotype platforms to share data in a uniformly exchangeable format, and meta-analysis for pooling statistical support for a genotype-phenotype association. As many groups are forming collaborations to engage in these efforts, this review collects a series of guidelines, practical detail and learned experiences from a variety of individuals who have contributed to the subject.
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“This score is commonly applied as a quality filter for imputed genotypes and is equivalent to the RSQR_HAT value by MACH and the information content (INFO) measure by PLINK (44).”
From Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration (2011) · cites this paper as [44]
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PLINK: a tool set for whole-genome association and population-based linkage analyses.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/519795 · Cited by 34,089
Self-citationPrincipal components analysis corrects for stratification in genome-wide association studies
Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006) · Nature Genetics · doi:10.1038/ng1847 · Cited by 10,248
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
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., et al. (2007) · Nature · doi:10.1038/nature05911 · Cited by 9,442
Genetics of Food Intake Self-Regulation in Childhood: Literature Review and Research Opportunities
Faith, M. S., Carnell, S., & Kral, T. V. E. (2013) · Human Heredity · doi:10.1159/000353879 · Cited by 7,633
Lippa, N. C., & Sanderson, S. C. (2013) · Human Heredity · doi:10.1159/000353712 · Cited by 6,095
Population Structure and Eigenanalysis
Patterson, N., Price, A. L., & Reich, D. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020190 · Cited by 5,280
Frayling, T. M., Timpson, N. J., Weedon, M. N., Zeggini, E., Freathy, R. M., Lindgren, C. M., Perry, J. R. B., Elliott, K. S., Lango, H., Rayner, N. W., et al. (2007) · Science · doi:10.1126/science.1141634 · Cited by 4,531
A second generation human haplotype map of over 3.1 million SNPs
The International HapMap Consortium (2007) · Nature · doi:10.1038/nature06258 · Cited by 4,438
Genomic Control for Association Studies
Devlin, B., & Roeder, K. (1999) · Biometrics · doi:10.1111/j.0006-341x.1999.00997.x · Cited by 3,162 · cited 1×
“The genomic inflation factor l is defined as the ratio of the median of the empirically observed distribution of the test statistic to the expected median, thus quantifying the extent of the bulk inflation and the excess false positive rate (32).”
BackgroundGenome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels
Saxena, R., Voight, B. F., Lyssenko, V., Burtt, N. P., de Bakker, P. I. W., Chen, H., Roix, J. J., Kathiresan, S., Hirschhorn, J. N., Daly, M. J., et al. (2007) · Science · doi:10.1126/science.1142358 · Cited by 2,843
Self-citation
Research works printed but not linked: 3
- 2006, American journal of human genetics, 79, 2290
- 2008, Journal of Clinical Investigation, 118, 2620
- 2008, Genetic epidemiology, 32, 2227
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METAL: fast and efficient meta-analysis of genomewide association scans
Willer, C. J., Li, Y., & Abecasis, G. R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq340 · Cited by 5,205
(2013) · The Lancet · doi:10.1016/s0140-6736(12)62129-1 · Cited by 3,010
Jansen, I. E., Savage, J. E., Watanabe, K., Bryois, J., Williams, D. M., Steinberg, S., Sealock, J., Karlsson, I. K., Hägg, S., Athanasiu, L., et al. (2019) · Nature Genetics · doi:10.1038/s41588-018-0311-9 · Cited by 2,277
International Parkinson's Disease Genomics Consortium (IPDGC), Nalls, M. A., Parkinson's Study Group (PSG) Parkinson's Research: The Organized GENetics Initiative (PROGENI), 23andMe, GenePD, NeuroGenetics Research Consortium (NGRC), Hussman Institute of Human Genomics (HIHG), Investigator, T. A. J. D., (CHARGE), C. F. H. A. A. R. I. G. E., North American Brain Expression Consortium (NABEC), et al. (2014) · Nature Genetics · doi:10.1038/ng.3043 · Cited by 1,895
Browning, B. L., & Browning, S. R. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.01.005 · Cited by 1,640
Genotype imputation for genome-wide association studies
Marchini, J., & Howie, B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2796 · Cited by 1,686
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Multicenter Genetic Studies of Schizophrenia Consortium, Ripke, S., Psychosis Endophenotypes International Consortium, Wellcome Trust Case Control Consortium 2, O'Dushlaine, C., Chambert, K., Moran, J. L., Kähler, A. K., Akterin, S., Bergen, S. E., et al. (2013) · Nature Genetics · doi:10.1038/ng.2742 · Cited by 1,496
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Self-citationPleiotropy in complex traits: challenges and strategies
Solovieff, N., Cotsapas, C., Lee, P. H., Purcell, S. M., & Smoller, J. W. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3461 · Cited by 1,085
Genetic architectures of psychiatric disorders: the emerging picture and its implications
Sullivan, P. F., Daly, M. J., & O'Donovan, M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3240 · Cited by 1,177
A mega-analysis of genome-wide association studies for major depressive disorder
Major Depressive Disorder Working Group of the Psychiatric GWAS Consortium, Ripke, S., Wray, N. R., Lewis, C. M., Hamilton, S. P., Weissman, M. M., Breen, G., Byrne, E. M., Blackwood, D. H. R., Boomsma, D. I., et al. (2013) · Molecular Psychiatry · doi:10.1038/mp.2012.21 · Cited by 1,120
A meta-analysis of genome-wide association studies identifies 17 new Parkinson's disease risk loci
Chang, D., Nalls, M. A., Hallgrímsdóttir, I. B., Hunkapiller, J., van der Brug, M., Cai, F., International Parkinson's Disease Genomics Consortium, 23andMe Research Team, Kerchner, G. A., Ayalon, G., et al. (2017) · Nature Genetics · doi:10.1038/ng.3955 · Cited by 1,112
Wada, K., Tanaka, K., & Nakashima, K. (2011) · PubMed · Cited by 1,132
Genome-wide meta-analyses identify multiple loci associated with smoking behavior
The Tobacco and Genetics Consortium (2010) · Nature Genetics · doi:10.1038/ng.571 · Cited by 1,098
Self-citationHLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin
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Howie, B., Marchini, J., & Stephens, M. (2011) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.111.001198 · Cited by 966
Bentham, J., Morris, D. L., Graham, D. S. C., Pinder, C. L., Tombleson, P., Behrens, T. W., Martin, J. J., Fairfax, B. P., Knight, J. C., Chen, L., et al. (2015) · Nature Genetics · doi:10.1038/ng.3434 · Cited by 1,004
Wightman, D. P., Jansen, I. E., Savage, J. E., Shadrin, A. A., Bahrami, S., Holland, D., Rongve, A., Børte, S., Winsvold, B. S., Drange, O. K., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00921-z · Cited by 1,011
Common genetic variants on 5p14.1 associate with autism spectrum disorders
Wang, K., Zhang, H., Ma, D., Bucan, M., Glessner, J. T., Abrahams, B. S., Salyakina, D., Imielinski, M., Bradfield, J. P., Sleiman, P. M. A., et al. (2009) · Nature · doi:10.1038/nature07999 · Cited by 989
Causal associations between risk factors and common diseases inferred from GWAS summary data
Zhu, Z., Zheng, Z., Zhang, F., Wu, Y., Trzaskowski, M., Maier, R., Robinson, M. R., McGrath, J. J., Visscher, P. M., Wray, N. R., et al. (2018) · Nature Communications · doi:10.1038/s41467-017-02317-2 · Cited by 951
Nalls, M. A. (2011) · The Lancet · doi:10.1016/s0140-6736(10)62345-8 · Cited by 922
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Study, T. P., Schumacher, F. R., (APCB), A. P. C. B., Study, T. I., Canary PASS Investigators, Breast and Prostate Cancer Cohort Consortium (BPC3), The PRACTICAL (Prostate Cancer Association Group to Investigate Cancer-Associated Alterations in the Genome) Consortium, (CAPS), C. O. T. P. I. S., Prostate Cancer Genome-wide Association Study of Uncommon Susceptibility Loci (PEGASUS), The Genetic Associations and Mechanisms in Oncology (GAME-ON)/Elucidating Loci Involved in Prostate Cancer Susceptibility (ELLIPSE) Consortium, et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0142-8 · Cited by 902
GWAS of 126,559 Individuals Identifies Genetic Variants Associated with Educational Attainment
Rietveld, C. A., Medland, S. E., Derringer, J., Yang, J., Esko, T., Martin, N. W., Westra, H.-J., Shakhbazov, K., Abdellaoui, A., Agrawal, A., et al. (2013) · Science · doi:10.1126/science.1235488 · Cited by 827
Rivadeneira, F., Estrada, K., Zillikens, M. C., van Meurs, J. B. J., Pols, H. A. P., Uitterlinden, A. G., Amin, N., Aulchenko, Y. S., Albert Hofman, D., van Duijn, C. M., et al. (2009) · Nature Genetics · doi:10.1038/ng.446 · Cited by 711
International MS Genetics Consortium, De Jager, P. L., Jia, X., Wang, J., de Bakker, P. I. W., Ottoboni, L., Aggarwal, N. T., Piccio, L., Raychaudhuri, S., Tran, D., et al. (2009) · Nature Genetics · doi:10.1038/ng.401 · Cited by 800
Self-citationHunter, D. J., Peltonen, L., Guiducci, C., Crawford, G., Hirschhorn, J. N., Lyon, H. N., & Speliotes, E. K. (2009) · DSpace@MIT (Massachusetts Institute of Technology) · Cited by 687
Han, B., & Eskin, E. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.04.014 · Cited by 680
Genome-wide association identifies multiple ulcerative colitis susceptibility loci
McGovern, D. P. B., Gardet, A., Törkvist, L., Goyette, P., Essers, J. B., Taylor, K. D., Neale, B. M., Ong, R. T., Lagacé, C., Li, C., et al. (2010) · Nature Genetics · doi:10.1038/ng.549 · Cited by 657
Self-citationNew IBD genetics: common pathways with other diseases
Lees, C. W., Barrett, J. C., Parkes, M., & Satsangi, J. (2011) · Gut · doi:10.1136/gut.2009.199679 · Cited by 635
Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application
Cantor, R. M., Lange, K. L., & Sinsheimer, J. S. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2009.11.017 · Cited by 638
Meta-analysis and imputation refines the association of 15q25 with smoking quantity
The Wellcome Trust Case Control Consortium, Liu, J. Z., Tozzi, F., Waterworth, D. M., Pillai, S. G., Muglia, P., Middleton, L., Berrettini, W., Knouff, C. W., Yuan, X., et al. (2010) · Nature Genetics · doi:10.1038/ng.572 · Cited by 614
GWAMA: software for genome-wide association meta-analysis
Mägi, R., & Morris, A. P. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-288 · Cited by 600
Meta-analysis identifies six new susceptibility loci for atrial fibrillation
Ellinor, P. T., Lunetta, K. L., Albert, C. M., Glazer, N. L., Ritchie, M. D., Smith, A. V., Arking, D. E., Müller-Nurasyid, M., Krijthe, B. P., Lubitz, S. A., et al. (2012) · Nature Genetics · doi:10.1038/ng.2261 · Cited by 601
Self-citationHigh-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis
Syndicate, B. I. R. A. G. A. G. S., Eyre, S., Wellcome Trust Case Control Consortium, Bowes, J., Diogo, D., Lee, A., Barton, A., Martin, P., Zhernakova, A., Stahl, E., et al. (2012) · Nature Genetics · doi:10.1038/ng.2462 · Cited by 653
Self-citationMeta-analysis methods for genome-wide association studies and beyond
Evangelou, E., & Ioannidis, J. P. A. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3472 · Cited by 596
Petersen, G. M., Amundadottir, L. T., Fuchs, C. S., Kraft, P. L., Stolzenberg‐Solomon, R. Z., Jacobs, K. B., Arslan, A. A., Bueno-de-Mesquita, H. B., Gallinger, S., Gross, M. D., et al. (2010) · Nature Genetics · doi:10.1038/ng.522 · Cited by 598
The Autism Spectrum Disorders Working Group of The Psychiatric Genomics Consortium (2017) · Molecular Autism · doi:10.1186/s13229-017-0137-9 · Cited by 587
Genome-wide association studies in diverse populations
Rosenberg, N. A., Huang, L., Jewett, E. M., Szpiech, Z. A., Jankovic, I., & Boehnke, M. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2760 · Cited by 566
Quality control and conduct of genome-wide association meta-analyses
Winkler, T. W., Day, F. R., Croteau‐Chonka, D. C., Wood, A. R., Locke, A. E., Mägi, R., Ferreira, T., Fall, T., Graff, M., Justice, A. E., et al. (2014) · Nature Protocols · doi:10.1038/nprot.2014.071 · Cited by 517
Reilly, M. P., Li, M., He, J., Ferguson, J. F., Stylianou, I. M., Mehta, N. N., Burnett, M. S., Devaney, J. M., Knouff, C. W., Thompson, J. R., et al. (2011) · The Lancet · doi:10.1016/s0140-6736(10)61996-4 · Cited by 547
The International League Against Epilepsy Consortium on Complex Epilepsies, Abou-Khalil, B., Auce, P., Avbersek, A., Bahlo, M., Balding, D. J., Bast, T., Baum, L., Becker, A. J., Becker, F., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07524-z · Cited by 482
Basic statistical analysis in genetic case-control studies
Clarke, G. M., Anderson, C. A., Pettersson, F. H., Cardon, L. R., Morris, A. P., & Zondervan, K. T. (2011) · Nature Protocols · doi:10.1038/nprot.2010.182 · Cited by 531
Abnet, C. C., Freedman, N. D., Hu, N., Wang, Z., Yu, K. F., Shu, X., Yuan, J., Zheng, W., Dawsey, S. M., Dong, L. M., et al. (2010) · Nature Genetics · doi:10.1038/ng.649 · Cited by 490
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Ellinor, P. T., Lunetta, K. L., Glazer, N. L., Pfeufer, A., Alonso, A., Chung, M. K., Sinner, M. F., de Bakker, P. I. W., Mueller, M., Lubitz, S. A., et al. (2010) · Nature Genetics · doi:10.1038/ng.537 · Cited by 485
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Stranger, B. E., Stahl, E. A., & Raj, T. (2011) · Genetics · doi:10.1534/genetics.110.120907 · Cited by 567
Rothman, N., García‐Closas, M., Chatterjee, N., Malats, N., Wu, X., Figueroa, J. D., Real, F. X., Berg, D. V. D., Matullo, G., Baris, D., et al. (2010) · Nature Genetics · doi:10.1038/ng.687 · Cited by 471
Hayes, M. G., Urbanek, M., Ehrmann, D. A., Armstrong, L. L., Lee, J. Y., Sisk, R., Karaderi, T., Barber, T. M., McCarthy, M. I., Franks, S., et al. (2015) · Nature Communications · doi:10.1038/ncomms8502 · Cited by 478
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Neale, B. M., Medland, S. E., Ripke, S., Asherson, P., Franke, B., Lesch, K.-P., Faraone, S. V., Nguyen, T. T., Schäfer, H., Holmans, P., et al. (2010) · Journal of the American Academy of Child & Adolescent Psychiatry · doi:10.1016/j.jaac.2010.06.008 · Cited by 450
Self-citationGenetic Structure of Europeans: A View from the North–East
Nelis, M., Esko, T., Mägi, R., Zimprich, F., Zimprich, A. A., Toncheva, D. I., Karachanak-Yankova, S., Piskackova, T., Balaščák, I., Peltonen, L., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005472 · Cited by 432
Common variants at ten loci influence QT interval duration in the QTGEN Study
Newton‐Cheh, C., Eijgelsheim, M., Rice, K. M., de Bakker, P. I. W., Yin, X., Estrada, K., Bis, J. C., Marciante, K. D., Rivadeneira, F., Noseworthy, P. A., et al. (2009) · Nature Genetics · doi:10.1038/ng.364 · Cited by 414
van Es, M. A., Veldink, J. H., Saris, C. G. J., Blauw, H. M., van Vught, P. W. J., Birve, A., Lemmens, R., Schelhaas, H. J., Groen, E. J. N., Huisman, M. H. B., et al. (2009) · Nature Genetics · doi:10.1038/ng.442 · Cited by 408
Genetics and epigenetics of rheumatoid arthritis
Viatte, S., Plant, D., & Raychaudhuri, S. (2013) · Nature Reviews Rheumatology · doi:10.1038/nrrheum.2012.237 · Cited by 406
Self-citationMeta-analysis identifies common variants associated with body mass index in east Asians
Wen, W., Cho, Y.-S., Zheng, W., Dorajoo, R., Kato, N., Qi, L., Chen, C.-H., Delahanty, R., Okada, Y., Tabara, Y., et al. (2012) · Nature Genetics · doi:10.1038/ng.1087 · Cited by 399
Validating, augmenting and refining genome-wide association signals
Ioannidis, J. P. A., Thomas, G. D., & Daly, M. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2544 · Cited by 382
Zhernakova, A., Stahl, E. A., Trynka, G., Raychaudhuri, S., Festen, E. A. M., Franke, L., Westra, H.-J., Fehrmann, R. S. N., Kurreeman, F. A. S., Thomson, B. P., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002004 · Cited by 362
Self-citationCommon variants in 22 loci are associated with QRS duration and cardiac ventricular conduction
Sotoodehnia, N., Isaacs, A. J., de Bakker, P. I. W., Dörr, M., Newton‐Cheh, C., Nolte, I. M., van der Harst, P., Müller‐Nurasyid, M., Eijgelsheim, M., Alonso, Á., et al. (2010) · Nature Genetics · doi:10.1038/ng.716 · Cited by 352
Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk
Raychaudhuri, S., Thomson, B. P., Remmers, E. F., Eyre, S., Hinks, A., Guiducci, C., Catanese, J. J., ., G. X., Stahl, E. A., Chen, R., et al. (2009) · Nature Genetics · doi:10.1038/ng.479 · Cited by 352
Self-citationEllinghaus, D., Ellinghaus, E., Nair, R. P., Stuart, P. E., Esko, T., Metspalu, A., Debrus, S., Raelson, J., Tejasvi, T., Belouchi, M., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.02.020 · Cited by 356
Cho, M. H., McDonald, M., Zhou, X., Mattheisen, M., Castaldi, P. J., Hersh, C. P., DeMeo, D. L., Sylvia, J. S., Ziniti, J. P., Laird, N. M., et al. (2014) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(14)70002-5 · Cited by 345
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Mühleisen, T. W., Leber, M., Schulze, T. G., Strohmaier, J., Degenhardt, F., Treutlein, J., Mattheisen, M., Forstner, A. J., Schumacher, J., Breuer, R., et al. (2014) · Nature Communications · doi:10.1038/ncomms4339 · Cited by 346
Lan, Q., Hsiung, C. A., Matsuo, K., Hong, Y., Seow, A., Wang, Z., Hosgood, H. D., Chen, K., Wang, J.-C., Chatterjee, N., et al. (2012) · Nature Genetics · doi:10.1038/ng.2456 · Cited by 339
Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer
Wolpin, B. M., Rizzato, C., Kraft, P. L., Kooperberg, C. L., Petersen, G. M., Wang, Z., Arslan, A. A., Freeman, L. E. B., Bracci, P. M., Buring, J. E., et al. (2014) · Nature Genetics · doi:10.1038/ng.3052 · Cited by 335
Okada, Y., Terao, C., Ikari, K., Kochi, Y., Ohmura, K., Suzuki, A., Kawaguchi, T., Stahl, E. A., Kurreeman, F. A. S., Nishida, N., et al. (2012) · Nature Genetics · doi:10.1038/ng.2231 · Cited by 335
Genome-wide association analysis identifies three psoriasis susceptibility loci
Stuart, P. E., Nair, R. P., Ellinghaus, E., Ding, J., Tejasvi, T., Gudjonsson, J. E., Li, Y., Weidinger, S., Eberlein, B., Gieger, C., et al. (2010) · Nature Genetics · doi:10.1038/ng.693 · Cited by 339
Genome‐wide meta‐analysis identifies novel multiple sclerosis susceptibility loci
Patsopoulos, N. A., the Bayer Pharma MS Genetics Working Group, T. S. C. O. S. E. I. A. A. C., & de Bakker, P. I. W. (2011) · Annals of Neurology · doi:10.1002/ana.22609 · Cited by 353
Lee, C. H., Cook, S., Lee, J. S., & Han, B. (2016) · Genomics & Informatics · doi:10.5808/gi.2016.14.4.173 · Cited by 308
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Study, A. C. (., Song, H., The Australian Ovarian Cancer Study Group, Ramus, S. J., Tyrer, J. P., Bolton, K. L., Gentry‐Maharaj, A., Wozniak, E., Anton‐Culver, H., Chang-Claude, J. C., et al. (2009) · Nature Genetics · doi:10.1038/ng.424 · Cited by 308
Okada, Y., Sim, X., Go, M. J., Wu, J., Gu, D., Takeuchi, F., Takahashi, A., Maeda, S., Tsunoda, T., Chen, P., et al. (2012) · Nature Genetics · doi:10.1038/ng.2352 · Cited by 310
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Yasuno, K., Bilgüvar, K., Bijlenga, P., Low, S., Krischek, B., Auburger, G. W. J., Simon, M., Krex, D., Arlıer, Z., Nayak, N. R., et al. (2010) · Nature Genetics · doi:10.1038/ng.563 · Cited by 307
Holmes, A. J., Lee, P. H., Hollinshead, M. O., Bakst, L., Roffman, J. L., Smoller, J. W., & Buckner, R. L. (2012) · The Journal of Neuroscience · doi:10.1523/jneurosci.2531-12.2012 · Cited by 293
“Imputation increases genomic coverage providing additional support for genotyped-allele-based analysis (de Bakker et al., 2008).”
BackgroundReplication in Genome-Wide Association Studies
Kraft, P. L., Zeggini, E., & Ioannidis, J. P. A. (2009) · Statistical Science · doi:10.1214/09-sts290 · Cited by 301
The Psychiatric GWAS Consortium: Big Science Comes to Psychiatry
Sullivan, P. F. (2010) · Neuron · doi:10.1016/j.neuron.2010.10.003 · Cited by 285
Cichon, S., Mühleisen, T. W., Degenhardt, F. A., Mattheisen, M., Miró, X., Strohmaier, J., Steffens, M., Meesters, C., Herms, S., Weingarten, M., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.01.017 · Cited by 286
Richards, J. B., Kavvoura, F. K., Rivadeneira, F., Styrkársdóttir, U., Estrada, K., Halldórsson, B. V., Hsu, Y., Zillikens, M. C., Wilson, S. G., Mullin, B. H., et al. (2009) · Annals of Internal Medicine · doi:10.7326/0003-4819-151-8-200910200-00006 · Cited by 281
Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer
Klein, A. P., Wolpin, B. M., Risch, H. A., Stolzenberg-Solomon, R. Z., Mocci, E., Zhang, M., Canzian, F., Childs, E. J., Hoskins, J. W., Jermusyk, A., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-02942-5 · Cited by 268
Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases
Li, Y. R., Li, J., Zhao, S. D., Bradfield, J. P., Mentch, F. D., Maggadottir, S. M., Hou, C., Abrams, D. J., Chang, D., Gao, F., et al. (2015) · Nature Medicine · doi:10.1038/nm.3933 · Cited by 266
Yu, Y., Bhangale, T. R., Fagerness, J., Ripke, S., Thorleifsson, G., Tan, P. L., Souied, E. H., Richardson, A. J., Merriam, J. E., Buitendijk, G. H. S., et al. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr270 · Cited by 254
Self-citationVariants in ADCY5 and near CCNL1 are associated with fetal growth and birth weight
Freathy, R. M., Mook‐Kanamori, D. O., Sovio, U., Prokopenko, I., Timpson, N. J., Berry, D. J., Warrington, N. M., Widén, E., Hottenga, J., Kaakinen, M., et al. (2010) · Nature Genetics · doi:10.1038/ng.567 · Cited by 252
Loci associated with ischaemic stroke and its subtypes (SiGN): a genome-wide association study
Pulit, S. L., McArdle, P. F., Wong, Q., Malik, R., Gwinn, K. A., Achterberg, S., Algra, A., Amouyel, P., Anderson, C. D., Arnett, D. K., et al. (2015) · The Lancet Neurology · doi:10.1016/s1474-4422(15)00338-5 · Cited by 255
Large-Scale Gene-Centric Meta-analysis across 32 Studies Identifies Multiple Lipid Loci
Asselbergs, F. W., Guo, Y., van Iperen, E. P. A., Sivapalaratnam, S., Tragante, V., Lanktree, M. B., Lange, L. A., Almoguera, B., Appelman, Y., Barnard, J., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.08.032 · Cited by 253
A re‐evaluation of fixed effect(s) meta‐analysis
Rice, K., Higgins, J. P. T., & Lumley, T. (2018) · Journal of the Royal Statistical Society Series A: Statistics in Society · doi:10.1111/rssa.12275 · Cited by 287
Agha, G., Mendelson, M., Ward-Caviness, C. K., Joehanes, R., Huan, T., Gondalia, R., Salfati, E., Brody, J. A., Fiorito, G., Bressler, J., et al. (2019) · Circulation · doi:10.1161/circulationaha.118.039357 · Cited by 244
A genome-wide association study of COPD identifies a susceptibility locus on chromosome 19q13
Cho, M. H., Castaldi, P. J., Wan, E. S., Siedliński, M., Hersh, C. P., DeMeo, D. L., Himes, B. E., Sylvia, J. S., Klanderman, B. J., Ziniti, J. P., et al. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr524 · Cited by 253
Zhu, Z., Lee, P. H., Chaffin, M. D., Chung, W., Loh, P., Lu, Q., Christiani, D. C., & Liang, L. (2018) · Nature Genetics · doi:10.1038/s41588-018-0121-0 · Cited by 239
Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma
Law, M. H., Bishop, D. T., Lee, J. E., Brossard, M., Martin, N. G., Moses, E. K., Song, F., Barrett, J. H., Kumar, R., Easton, D. F., et al. (2015) · Nature Genetics · doi:10.1038/ng.3373 · Cited by 240
Lesseur, C., Diergaarde, B. B., Olshan, A. F., Wünsch‐Filho, V., Ness, A., Liu, G., Lacko, M., Eluf‐Neto, J., Franceschi, S., Λάγιου, Π., et al. (2016) · Nature Genetics · doi:10.1038/ng.3685 · Cited by 245
Purdue, M. P., Johansson, M., Zélénika, D., Toro, J. R., Scélo, G., Moore, L. E., Prokhortchouk, E., Wu, X., Kiemeney, L. A. L. M., Gaborieau, V., et al. (2010) · Nature Genetics · doi:10.1038/ng.723 · Cited by 238
The meta-analysis of genome-wide association studies
Thompson, J. R., Attia, J., & Minelli, C. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr020 · Cited by 251
Lindström, S., Wang, L., Smith, E. N., Gordon, W., van Hylckama Vlieg, A., de Andrade, M., Brody, J. A., Pattee, J. W., Haessler, J., Brumpton, B. M., et al. (2019) · Blood · doi:10.1182/blood.2019000435 · Cited by 223
Stevelink, R., Campbell, C., Chen, S., Abou-Khalil, B. W., Adesoji, O. M., Afawi, Z., Amadori, E., Anderson, A., Anderson, J., Andrade, D. M., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01485-w · Cited by 242
Li, Y. R., & Keating, B. J. (2014) · Genome Medicine · doi:10.1186/s13073-014-0091-5 · Cited by 214
The 5p15.33 Locus Is Associated with Risk of Lung Adenocarcinoma in Never-Smoking Females in Asia
Hsiung, C. A., Lan, Q., Hong, Y., Chen, C., Hosgood, H. D., Chang, I., Chatterjee, N., Brennan, P., Wu, C. H., Zheng, W., et al. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001051 · Cited by 211
Chen, D. T., Jiang, X., Akula, N., Shugart, Y. Y., Wendland, J. R., Steele, C. J. M., Kassem, L., Park, J.-H., Chatterjee, N., Jamain, S., et al. (2011) · Molecular Psychiatry · doi:10.1038/mp.2011.157 · Cited by 220
Hou, L., Bergen, S. E., Akula, N., Song, J., Hultman, C. M., Landén, M., Adli, M., Alda, M., Ardau, R., Arias, B., et al. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw181 · Cited by 211
Immunochip Analysis Identifies Multiple Susceptibility Loci for Systemic Sclerosis
Mayes, M. D., Bossini‐Castillo, L., Gorlova, O. Y., Martín, J., Zhou, X., Chen, W. V., Assassi, S., Ying, J., Tan, F. K., Arnett, F. C., et al. (2014) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.12.002 · Cited by 215
Lenz, T. L., Deutsch, A. J., Han, B., Hu, X., Okada, Y., Eyre, S., Knapp, M., Zhernakova, A., Huizinga, T. W. J., Abecasis, G. R., et al. (2015) · Nature Genetics · doi:10.1038/ng.3379 · Cited by 195
Self-citationGenome-wide significant predictors of metabolites in the one-carbon metabolism pathway
Hazra, A., Kraft, P. L., Lazarus, R. M., Chen, C., Chanock, S. J., Jacques, P. F., Selhub, J., & Hunter, D. J. (2009) · Human Molecular Genetics · doi:10.1093/hmg/ddp428 · Cited by 198
Nuclear genetic control of mtDNA copy number and heteroplasmy in humans
Gupta, R., Kanai, M., Durham, T., Tsuo, K., McCoy, J. G., Kotrys, A. V., Zhou, W., Chinnery, P. F., Karczewski, K. J., Calvo, S. E., et al. (2023) · Nature · doi:10.1038/s41586-023-06426-5 · Cited by 200
Self-citationEvaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia
Bryois, J., Garrett, M. E., Song, L., Safi, A., Giusti-Rodriguez, P., Johnson, G. D., Shieh, A. W., Buil, A., Fullard, J. F., Roussos, P., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05379-y · Cited by 167
Meta-analysis of untargeted metabolomic data from multiple profiling experiments
Patti, G. J., Tautenhahn, R., & Siuzdak, G. E. (2012) · Nature Protocols · doi:10.1038/nprot.2011.454 · Cited by 190
Metadata
- Authors
- de Bakker, P. I. W., Ferreira, M. A. R., Jia, X., Neale, B. M., Raychaudhuri, S., & Voight, B. F.
- Affiliations
- Broad Institute (US)
- Harvard–MIT Division of Health Sciences and Technology (US)
- Venue
- Human Molecular Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-10-15
- Volume
- 17
- Issue
- R2
- Pages
- R122-R128
- ISSN
- 0964-6906 (ISSN-L)
- 1460-2083
- PMC
- PMC2782358
- OpenAlex
- W2119067354
- Cited by
- 531
- References
- 44
- Citations by year
- 2026: 7 · 2025: 7 · 2024: 10 · 2023: 16 · 2022: 14 · 2021: 28 · 2020: 6 · 2019: 19 · 2018: 27 · 2017: 26 · 2016: 32 · 2015: 39 · 2014: 42 · 2013: 50 · 2012: 52
- FWCI
- 4.84
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Human Molecular Genetics (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- Funders
- National Institutes of Health
- U.S. Public Health Service (K08-KAR055688A)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (K08AR055688, T32AR007530)
- 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
- imputation, genome-wide association study, meta-analysis, genotype-phenotype correlation, data exchange, genetic risk factors
- MeSH terms
- Data Interpretation, Statistical, Humans, Phenotype, Meta-Analysis as Topic, Genome, Human, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Genome-Wide Association Study
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