Presence of multiple independent effects in risk loci of common complex human diseases

American Journal of Human Genetics

Volumn 91, Issue 1, 2012, Pages 185-192

  Ke, Xiayi ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE RECRUITMENT DOMAIN PROTEIN 15; INTERLEUKIN 2; INTERLEUKIN 23 RECEPTOR; PROSTAGLANDIN E RECEPTOR 4;

ALLELE; ARTICLE; CASE CONTROL STUDY; CONTROLLED STUDY; CROHN DISEASE; GENE LOCUS; GENOME; GENOTYPE; HAPLOTYPE MAP; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; LIBRARY SCIENCE; MAJOR CLINICAL STUDY; NON INSULIN DEPENDENT DIABETES MELLITUS; PRIORITY JOURNAL; RHEUMATOID ARTHRITIS; SAMPLE SIZE; SINGLE NUCLEOTIDE POLYMORPHISM; VARIANCE;

ARTHRITIS, RHEUMATOID; CASE-CONTROL STUDIES; CROHN DISEASE; DIABETES MELLITUS, TYPE 1; DIABETES MELLITUS, TYPE 2; GENE FREQUENCY; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; HAPMAP PROJECT; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK;

EID: 84863981380     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2012.05.020     Document Type: Article

References (35)

1. T.A. Manolio, F.S. Collins, N.J. Cox, D.B. Goldstein, L.A. Hindorff, D.J. Hunter, M.I. McCarthy, E.M. Ramos, L.R. Cardon, and A. Chakravarti Finding the missing heritability of complex diseases Nature 461 2009 747 753
2. K. Wang, M. Li, and M. Bucan Pathway-based approaches for analysis of genomewide association studies Am. J. Hum. Genet. 81 2007 1278 1283
3. J. Yang, B. Benyamin, B.P. McEvoy, S. Gordon, A.K. Henders, D.R. Nyholt, P.A. Madden, A.C. Heath, N.G. Martin, and G.W. Montgomery Common SNPs explain a large proportion of the heritability for human height Nat. Genet. 42 2010 565 569
4. J. Yang, T.A. Manolio, L.R. Pasquale, E. Boerwinkle, N. Caporaso, J.M. Cunningham, M. de Andrade, B. Feenstra, E. Feingold, and M.G. Hayes Genome partitioning of genetic variation for complex traits using common SNPs Nat. Genet. 43 2011 519 525
5. H. Lango Allen, K. Estrada, G. Lettre, S.I. Berndt, M.N. Weedon, F. Rivadeneira, C.J. Willer, A.U. Jackson, S. Vedantam, and S. Raychaudhuri Hundreds of variants clustered in genomic loci and biological pathways affect human height Nature 467 2010 832 838
6. S. Nejentsev, J.M. Howson, N.M. Walker, J. Szeszko, S.F. Field, H.E. Stevens, P. Reynolds, M. Hardy, E. King, J. Masters Wellcome Trust Case Control Consortium Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A Nature 450 2007 887 892
7. R.M. Plenge, C. Cotsapas, L. Davies, A.L. Price, P.I. de Bakker, J. Maller, I. Pe'er, N.P. Burtt, B. Blumenstiel, and M. DeFelice Two independent alleles at 6q23 associated with risk of rheumatoid arthritis Nat. Genet. 39 2007 1477 1482
8. G. Orozco, A. Hinks, S. Eyre, X. Ke, L.J. Gibbons, J. Bowes, E. Flynn, P. Martin, A.G. Wilson, D.E. Bax Wellcome Trust Case Control Consortium YEAR consortium Combined effects of three independent SNPs greatly increase the risk estimate for RA at 6q23 Hum. Mol. Genet. 18 2009 2693 2699
9. B. Ding, L. Padyukov, E. Lundström, M. Seielstad, R.M. Plenge, J.R. Oksenberg, P.K. Gregersen, L. Alfredsson, and L. Klareskog Different patterns of associations with anti-citrullinated protein antibody-positive and anti-citrullinated protein antibody-negative rheumatoid arthritis in the extended major histocompatibility complex region Arthritis Rheum. 60 2009 30 38
10. A. Franke, D.P. McGovern, J.C. Barrett, K. Wang, G.L. Radford-Smith, T. Ahmad, C.W. Lees, T. Balschun, J. Lee, and R. Roberts Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci Nat. Genet. 42 2010 1118 1125
11. A.R. Wood, D.G. Hernandez, M.A. Nalls, H. Yaghootkar, J.R. Gibbs, L.W. Harries, S. Chong, M. Moore, M.N. Weedon, and J.M. Guralnik Allelic heterogeneity and more detailed analyses of known loci explain additional phenotypic variation and reveal complex patterns of association Hum. Mol. Genet. 20 2011 4082 4092
12. K.A. Frazer, D.G. Ballinger, D.R. Cox, D.A. Hinds, L.L. Stuve, R.A. Gibbs, J.W. Belmont, A. Boudreau, P. Hardenbol, S.M. Leal International HapMap Consortium A second generation human haplotype map of over 3.1 million SNPs Nature 449 2007 851 861
13. 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing Nature 467 2010 1061 1073
14. Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 447 2007 661 678
15. S. Raychaudhuri, B.P. Thomson, E.F. Remmers, S. Eyre, A. Hinks, C. Guiducci, J.J. Catanese, G. Xie, E.A. Stahl, R. Chen BIRAC Consortium YEAR Consortium Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk Nat. Genet. 41 2009 1313 1318
16. P.K. Gregersen, C.I. Amos, A.T. Lee, Y. Lu, E.F. Remmers, D.L. Kastner, M.F. Seldin, L.A. Criswell, R.M. Plenge, and V.M. Holers REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis Nat. Genet. 41 2009 820 823
17. E.A. Stahl, S. Raychaudhuri, E.F. Remmers, G. Xie, S. Eyre, B.P. Thomson, Y. Li, F.A. Kurreeman, A. Zhernakova, A. Hinks BIRAC Consortium YEAR Consortium Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci Nat. Genet. 42 2010 508 514
18. J.C. Barrett, S. Hansoul, D.L. Nicolae, J.H. Cho, R.H. Duerr, J.D. Rioux, S.R. Brant, M.S. Silverberg, K.D. Taylor, M.M. Barmada NIDDK IBD Genetics Consortium Belgian-French IBD Consortium Wellcome Trust Case Control Consortium Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease Nat. Genet. 40 2008 955 962
19. D.P. McGovern, M.R. Jones, K.D. Taylor, K. Marciante, X. Yan, M. Dubinsky, A. Ippoliti, E. Vasiliauskas, D. Berel, C. Derkowski International IBD Genetics Consortium Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease Hum. Mol. Genet. 19 2010 3468 3476
20. J.A. Todd, N.M. Walker, J.D. Cooper, D.J. Smyth, K. Downes, V. Plagnol, R. Bailey, S. Nejentsev, S.F. Field, F. Payne Genetics of Type 1 Diabetes in Finland Wellcome Trust Case Control Consortium Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes Nat. Genet. 39 2007 857 864
21. J.D. Cooper, D.J. Smyth, A.M. Smiles, V. Plagnol, N.M. Walker, J.E. Allen, K. Downes, J.C. Barrett, B.C. Healy, and J.C. Mychaleckyj Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci Nat. Genet. 40 2008 1399 1401
22. J.C. Barrett, D.G. Clayton, P. Concannon, B. Akolkar, J.D. Cooper, H.A. Erlich, C. Julier, G. Morahan, J. Nerup, C. Nierras Type 1 Diabetes Genetics Consortium Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes Nat. Genet. 41 2009 703 707
23. L.J. Scott, K.L. Mohlke, L.L. Bonnycastle, C.J. Willer, Y. Li, W.L. Duren, M.R. Erdos, H.M. Stringham, P.S. Chines, and A.U. Jackson A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants Science 316 2007 1341 1345
24. E. Zeggini, L.J. Scott, R. Saxena, B.F. Voight, J.L. Marchini, T. Hu, P.I. de Bakker, G.R. Abecasis, P. Almgren, G. Andersen Wellcome Trust Case Control Consortium Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes Nat. Genet. 40 2008 638 645
25. L. Qi, M.C. Cornelis, P. Kraft, K.J. Stanya, W.H. Linda Kao, J.S. Pankow, J. Dupuis, J.C. Florez, C.S. Fox, G. Paré Meta-Analysis of Glucose and Insulin-related traits Consortium (MAGIC) Diabetes Genetics Replication and Meta-analysis (DIAGRAM) Consortium Genetic variants at 2q24 are associated with susceptibility to type 2 diabetes Hum. Mol. Genet. 19 2010 2706 2715
26. B.F. Voight, L.J. Scott, V. Steinthorsdottir, A.P. Morris, C. Dina, R.P. Welch, E. Zeggini, C. Huth, Y.S. Aulchenko, G. Thorleifsson MAGIC investigators GIANT Consortium Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis Nat. Genet. 42 2010 579 589
27. B.N. Howie, P. Donnelly, and J. Marchini A flexible and accurate genotype imputation method for the next generation of genome-wide association studies PLoS Genet. 5 2009 e1000529
28. J.J. Goeman L1 penalized estimation in the Cox proportional hazards model Biom. J. 52 2010 70 84
29. R. Tibshirani Regression shrinkage and selection via the lasso J Royal Stat Soc Series B Stat Methodol. 58 1996 267 288
30. A.E. Hoerl, and R.W. Kennard Ridge regression: Biased estimation for nonorthogonal problems Technometrics 12 1970 55 67
31. H. Zou, and T. Hastie Regularization and variable selection via the elastic net J. R. Stat. Soc. Series B Stat. Methodol. 67 2005 301 320
32. J.B. Veyrieras, S. Kudaravalli, S.Y. Kim, E.T. Dermitzakis, Y. Gilad, M. Stephens, and J.K. Pritchard High-resolution mapping of expression-QTLs yields insight into human gene regulation PLoS Genet. 4 2008 e1000214
33. S. Nejentsev, N. Walker, D. Riches, M. Egholm, and J.A. Todd Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes Science 324 2009 387 389
34. H.C. So, A.H.S. Gui, S.S. Cherny, and P.C. Sham Evaluating the heritability explained by known susceptibility variants: A survey of ten complex diseases Genet. Epidemiol. 35 2011 310 317
35. S.H. Lee, N.R. Wray, M.E. Goddard, and P.M. Visscher Estimating missing heritability for disease from genome-wide association studies Am. J. Hum. Genet. 88 2011 294 305