Autoimmune diseases: Insights from genome-wide association studies

Human Molecular Genetics

Volumn 17, Issue R2, 2008, Pages

  Lettre, Guillaume ^a,b   Rioux, John D ^c  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b BOSTON CHILDREN S HOSPITAL   (United States)

^c MONTREAL HEART INSTITUTE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOIMMUNE DISEASE; CROHN DISEASE; GENETIC ASSOCIATION; GENETIC PREDISPOSITION; GENETICS; HUMAN; IMMUNOLOGY; INSULIN DEPENDENT DIABETES MELLITUS; MULTIPLE SCLEROSIS; REVIEW; RHEUMATOID ARTHRITIS; RISK FACTOR; SYSTEMIC LUPUS ERYTHEMATOSUS;

ARTHRITIS, RHEUMATOID; AUTOIMMUNE DISEASES; CROHN DISEASE; DIABETES MELLITUS, TYPE 1; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LUPUS ERYTHEMATOSUS, SYSTEMIC; MULTIPLE SCLEROSIS; RISK FACTORS;

EID: 58149333555     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddn246     Document Type: Article

References (48)

1. Fernando, M.M., Stevens, C.R., Walsh, E.C., De Jager, P.L., Goyette, P., Plenge, R.M., Vyse, T.J. and Rioux, J.D. (2008) Defining the role of the MHC in autoimmunity: a review and pooled analysis. PLoS Genet., 4, e1000024.
2. Oksenberg, J.R., Baranzini, S.E., Sawcer, S. and Hauser, S.L. (2008) The genetics of multiple sclerosis: SNPs to pathways to pathogenesis. Nat. Rev. Genet., 9, 516-526.
3. van Heel, D.A., Hunt, K., Greco, L. and Wijmenga, C. (2005) Genetics in coeliac disease. Best Pract. Res. Clin. Gastroenterol., 19, 323-339.
4. Cho, J.H. (2008) The genetics and immunopathogenesis of inflammatory bowel disease. Nat. Rev. Immunol., 8, 458-466.
5. Gregersen, P.K. (2005) Pathways to gene identification in rheumatoid arthritis: PTPN22 and beyond. Immunol. Rev., 204, 74-86.
6. Wakeland, E.K., Liu, K., Graham, R.R. and Behrens, T.W. (2001) Delineating the genetic basis of systemic lupus erythematosus. Immunity, 15, 397-408.
7. Ounissi-Benkalha, H. and Polychronakos, C. (2008) The molecular genetics of type 1 diabetes: new genes and emerging mechanisms. Trends Mol. Med., 14, 268-275.
8. Chanock, S.J., Manolio, T., Boehnke, M., Boerwinkle, E., Hunter, D.J., Thomas, G., Hirschhorn, J.N., Abecasis, G., Altshuler, D., Bailey-Wilson, J.E. et al. (2007) Replicating genotype-phenotype associations. Nature, 447, 655-660.
9. Wellcome Trust Case Control Consortium. (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447, 661-678.
10. Duerr, R.H., Taylor, K.D., Brant, S.R., Rioux, J.D., Silverberg, M.S., Daly, M.J., Steinhart, A.H., Abraham, C., Regueiro, M., Griffiths, A. et al. (2006) A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science, 314, 1461-1463.
11. Hampe, J., Franke, A., Rosenstiel, P., Till, A., Teuber, M., Huse, K., Albrecht, M., Mayr, G., De La Vega, F.M., Briggs, J. et al. (2007) A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat. Genet., 39, 207-211.
12. Libioulle, C., Louis, E., Hansoul, S., Sandor, C., Farnir, F., Franchimont, D., Vermeire, S., Dewit, O., de Vos, M., Dixon, A. et al. (2007) Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4. PLoS Genet., 3, e58.
13. Rioux, J.D., Xavier, R.J., Taylor, K.D., Silverberg, M.S., Goyette, P., Huett, A., Green, T., Kuballa, P., Barmada, M.M., Datta, L.W. et al. (2007) Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat. Genet., 39, 596-604.
14. Parkes, M., Barrett, J.C., Prescott, N.J., Tremelling, M., Anderson, C.A., Fisher, S.A., Roberts, R.G., Nimmo, E.R., Cummings, F.R., Soars, D. et al. (2007) Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat. Genet., 39, 830-832.
15. Hugot, J.P., Chamaillard, M., Zouali, H., Lesage, S., Cezard, J.P., Belaiche, J., Almer, S., Tysk, C., O'Morain, C.A., Gassull, M. et al. (2001) Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease. Nature, 411, 599-603.
16. Ogura, Y., Bonen, D.K., Inohara, N., Nicolae, D.L., Chen, F.F., Ramos, R., Britton, H., Moran, T., Karaliuskas, R., Duerr, R.H. et al. (2001) A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease. Nature, 411, 603-606.
17. Rioux, J.D., Daly, M.J., Silverberg, M.S., Lindblad, K., Steinhart, H., Cohen, Z., Delmonte, T., Kocher, K., Miller, K., Guschwan, S. et al. (2001) Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease. Nat. Genet., 29, 223-228.
18. Yamazaki, K., McGovern, D., Ragoussis, J., Paolucci, M., Butler, H., Jewell, D., Cardon, L., Takazoe, M., Tanaka, T., Ichimori, T. et al. (2005) Single nucleotide polymorphisms in TNFSF15 confer susceptibility to Crohn's disease. Hum. Mol. Genet., 14, 3499-3506.
19. Barrett, J.C., Hansoul, S., Nicolae, D.L., Cho, J.H., Duerr, R.H., Rioux, J.D., Brant, S.R., Silverberg, M.S., Taylor, K.D., Barmada, M.M. et al. (2008) Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat. Genet., 40, 955-962.
20. Gudbjartsson, D.F., Walters, G.B., Thorleifsson, G., Stefansson, H., Halldorsson, B.V., Zusmanovich, P., Sulem, P., Thorlacius, S., Gylfason, A., Steinberg, S. et al. (2008) Many sequence variants affecting diversity of adult human height. Nat. Genet., 40, 609-615.
21. Lettre, G., Jackson, A.U., Gieger, C., Schumacher, F.R., Berndt, S.I., Sanna, S., Eyheramendy, S., Voight, B.F., Butler, J.L., Guiducci, C. et al. (2008) Identification of ten loci associated with height highlights new biological pathways in human growth. Nat. Genet., 40, 584-591.
22. Weedon, M.N., Lango, H., Lindgren, C.M., Wallace, C., Evans, D.M., Mangino, M., Freathy, R.M., Perry, J.R., Stevens, S., Hall, A.S. et al. (2008) Genome-wide association analysis identifies 20 loci that influence adult height. Nat. Genet., 40, 575-583.
23. Willer, C.J., Sanna, S., Jackson, A.U., Scuteri, A., Bonnycastle, L.L., Clarke, R., Heath, S.C., Timpson, N.J., Najjar, S.S., Stringham, H.M. et al. (2008) Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat. Genet., 40, 161-169.
24. Kathiresan, S., Melander, O., Guiducci, C., Surti, A., Burtt, N.P., Rieder, M.J., Cooper, G.M., Roos, C., Voight, B.F., Havulinna, A.S. et al. (2008) Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans. Nat. Genet., 40, 189-197.
25. Zeggini, E., Scott, L.J., Saxena, R., Voight, B.F., Marchini, J.L., Hu, T., de Bakker, P.I., Abecasis, G.R., Almgren, P., Andersen, G. et al. (2008) Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat. Genet., 40, 638-645.
26. Vella, A., Cooper, J.D., Lowe, C.E., Walker, N., Nutland, S., Widmer, B., Jones, R., Ring, S.M., McArdle, W., Pembrey, M.E. et al. (2005) Localization of a type 1 diabetes locus in the IL2RA/CD25 region by use of tag single-nucleotide polymorphisms. Am. J. Hum. Genet., 76, 773-779.
27. Lowe, C.E., Cooper, J.D., Brusko, T., Walker, N.M., Smyth, D.J., Bailey, R., Bourget, K., Plagnol, V., Field, S., Atkinson, M. et al. (2007) Large-scale genetic fine mapping and genotype-phenotype associations implicate polymorphism in the IL2RA region in type 1 diabetes. Nat. Genet., 39, 1074-1082.
28. van Heel, D.A., Franke, L., Hunt, K.A., Gwilliam, R., Zhernakova, A., Inouye, M., Wapenaar, M.C., Barnardo, M.C., Bethel, G., Holmes, G.K. et al. (2007) A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21. Nat. Genet., 39, 827-829.
29. Hunt, K.A., Zhernakova, A., Turner, G., Heap, G.A., Franke, L., Bruinenberg, M., Romanos, J., Dinesen, L.C., Ryan, A.W., Panesar, D. et al. (2008) Newly identified genetic risk variants for celiac disease related to the immune response. Nat. Genet., 40, 395-402.
30. Barrett, J.C., Hansoul, S., Nicolae, D.L., Cho, J.H., Duerr, R.H., Rioux, J.D., Brant, S.R., Silverberg, M.S., Taylor, K.D., Barmada, M.M. et al. (2008) Genome-wide association defines more than thirty distinct susceptibility loci for Crohn's disease. Nat. Genet., 40, 955-962.
31. Hafler, D.A., Compston, A., Sawcer, S., Lander, E.S., Daly, M.J., De Jager, P.L., de Bakker, P.I., Gabriel, S.B., Mirel, D.B., Ivinson, A.J. et al. (2007) Risk alleles for multiple sclerosis identified by a genomewide study. N. Engl. J. Med., 357, 851-862.
32. Gregory, S.G., Schmidt, S., Seth, P., Oksenberg, J.R., Hart, J., Prokop, A., Caillier, S.J., Ban, M., Goris, A., Barcellos, L.F. et al. (2007) Interleukin 7 receptor alpha chain (IL7R) shows allelic and functional association with multiple sclerosis. Nat. Genet., 39, 1083-1091.
33. Lundmark, F., Duvefelt, K., Iacobaeus, E., Kockum, I., Wallstrom, E., Khademi, M., Oturai, A., Ryder, L.P., Saarela, J., Harbo, H.F. et al. (2007) Variation in interleukin 7 receptor alpha chain (IL7R) influences risk of multiple sclerosis. Nat. Genet., 39, 1108-1113.
34. Plenge, R.M., Cotsapas, C., Davies, L., Price, A.L., de Bakker, P.I., Maller, J., Pe'er, I., Burtt, N.P., Blumenstiel, B., DeFelice, M. et al. (2007) Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nat. Genet., 39, 1477-1482.
35. Plenge, R.M., Seielstad, M., Padyukov, L., Lee, A.T., Remmers, E.F., Ding, B., Liew, A., Khalili, H., Chandrasekaran, A., Davies, L.R. et al. (2007) TRAF1-C5 as a risk locus for rheumatoid arthritis-a genomewide study. N. Engl. J. Med., 357, 1199-1209.
36. Hom, G., Graham, R.R., Modrek, B., Taylor, K.E., Ortmann, W., Garnier, S., Lee, A.T., Chung, S.A., Ferreira, R.C., Pant, P.V. et al. (2008) Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. N. Engl. J. Med., 358, 900-909.
37. Kozyrev, S.V., Abelson, A.K., Wojcik, J., Zaghlool, A., Linga Reddy, M.V., Sanchez, E., Gunnarsson, I., Svenungsson, E., Sturfelt, G., Jonsen, A. et al. (2008) Functional variants in the B-cell gene BANK1 are associated with systemic lupus erythematosus. Nat. Genet., 40, 211-216.
38. Levine, B. and Deretic, V. (2007) Unveiling the roles of autophagy in innate and adaptive immunity. Nat. Rev. Immunol., 7, 767-777.
39. Smyth, D.J., Cooper, J.D., Bailey, R., Field, S., Burren, O., Smink, L.J., Guja, C., Ionescu-Tirgoviste, C., Widmer, B., Dunger, D.B. et al. (2006) A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nat. Genet., 38, 617-619.
40. Knip, M., Veijola, R., Virtanen, S.M., Hyoty, H., Vaarala, O. and Akerblom, H.K. (2005) Environmental triggers and determinants of type 1 diabetes. Diabetes, 54 (Suppl. 2), S125-S136.
41. Vang, T., Congia, M., Macis, M.D., Musumeci, L., Orru, V., Zavattari, P., Nika, K., Tautz, L., Tasken, K., Cucca, F. et al. (2005) Autoimmune-associated lymphoid tyrosine phosphatase is a gain-of-function variant. Nat. Genet., 37, 1317-1319.
42. McCarroll, S.A., Huett, A.S., Kuballa, P., Chilewski, S.D., Landry, A., Goyette, P., Zody, M.C., Hall, J.L., Brant, S.R., Cho, J.H. et al. (2008) Deletion polymorphism upstream of IRGM is associated with altered IRGM expression and Crohn's disease. Nat. Genet., 40, 1107-1112.
43. McCarroll, S.A., Kuruvilla, F.G., Korn, J.M., Cawley, S., Nemesh, J., Wysoker, A., Shapero, M.H., de Bakker, P.I.W., Maller, J.B., Kirby, A. et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet., published online 6 September 2008, doi:10.1038/ng.238.
44. Goyette, P., Lefebvre, C.N.G.A., Brant, S.R., Cho, J.H., Duerr, R.H., Silverberg, M.S., Taylor, K.D., Latiano, A., Aumais, G. et al. (2008) Gene-centric association mapping of chromosome 3p implicates MST1 in IBD pathogenesis. Mucosal. Immunol., 1, 131-138.
45. Harley, J.B., Alarcon-Riquelme, M.E., Criswell, L.A., Jacob, C.O., Kimberly, R.P., Moser, K.L., Tsao, B.P., Vyse, T.J., Langefeld, C.D., Nath, S.K. et al. (2008) Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat. Genet., 40, 204-210.
46. Todd, J.A., Walker, N.M., Cooper, J.D., Smyth, D.J., Downes, K., Plagnol, V., Bailey, R., Nejentsev, S., Field, S.F., Payne, F. et al. (2007) Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Nat. Genet., 39, 857-864.
47. Hakonarson, H., Grant, S.F., Bradfield, J.P., Marchand, L., Kim, C.E., Glessner, J.T., Grabs, R., Casalunovo, T., Taback, S.P., Frackelton, E.C. et al. (2007) A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene. Nature, 448, 591-594.
48. Hakonarson, H., Qu, H.Q., Bradfield, J.P., Marchand, L., Kim, C.E., Glessner, J.T., Grabs, R., Casalunovo, T., Taback, S.P., Frackelton, E.C. et al. (2008) A novel susceptibility locus for type 1 diabetes on Chr12q13 identified by a genome-wide association study. Diabetes, 57, 1143-1146