Case Study on Rheumatoid Arthritis

Analysis of Complex Disease Association Studies

Volumn , Issue , 2011, Pages 307-323

  Eyre, Stephen ^a   Thomson, Wendy ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84882389061     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-0-12-375142-3.10019-7     Document Type: Chapter

References (65)

1. Stastny P. Association of the B-cell alloantigen DRw4 with rheumatoid arthritis. N. Engl. J. Med. 1978, 298:869-871.
2. Gregersen P.K., Silver J., Winchester R.J. The shared epitope hypothesis. An approach to understanding the molecular genetics of susceptibility to rheumatoid arthritis. Arthritis Rheum. 1987, 30:1205-1213.
3. Bottini N., Musumeci L., Alonso A., Rahmouni S., Nika K., Rostamkhani M., et al. A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes. Nat. Genet. 2004, 36:337-338.
4. Begovich A.B., Carlton V.E., Honigberg L.A., Schrodi S.J., Chokkalingam A.P., Alexander H.C., et al. A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Am. J. Hum. Genet. 2004, 75:330-337.
5. Plenge R.M., Padyukov L., Remmers E.F., Purcell S., Lee A.T., Karlson E.W., et al. Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. Am. J. Hum. Genet. 2005, 77:1044-1060.
6. Hinks A., Barton A., John S., Bruce I., Hawkins C., Griffiths C.E., et al. Association between the PTPN22 gene and rheumatoid arthritis and juvenile idiopathic arthritis in a UK population: further support that PTPN22 is an autoimmunity gene. Arthritis Rheum. 2005, 52:1694-1699.
7. van O.M., Wintle R.F., Liu X., Yazdanpanah M., Gu X., Newman B., et al. Association of the lymphoid tyrosine phosphatase R620W variant with rheumatoid arthritis, but not Crohn's disease, in Canadian populations. Arthritis Rheum. 2005, 52:1993-1998.
8. Seldin M.F., Shigeta R., Laiho K., Li H., Saila H., Savolainen A., et al. Finnish case-control and family studies support PTPN22 R620W polymorphism as a risk factor in rheumatoid arthritis, but suggest only minimal or no effect in juvenile idiopathic arthritis. Genes Immun. 2005, 6(8):720-722.
9. Pierer M., Kaltenhauser S., Arnold S., Wahle M., Baerwald C., Hantzschel H., et al. Association of PTPN22 1858 single-nucleotide polymorphism with rheumatoid arthritis in a German cohort: higher frequency of the risk allele in male compared to female patients. Arthritis Res.Ther. 2006, 8:R75.
10. Orozco G., Sanchez E., Gonzalez-Gay M.A., Lopez-Nevot M.A., Torres B., Caliz R., et al. Association of a functional single-nucleotide polymorphism of PTPN22, encoding lymphoid protein phosphatase, with rheumatoid arthritis and systemic lupus erythematosus. Arthritis Rheum. 2005, 52:219-224.
11. Ikari K., Momohara S., Inoue E., Tomatsu T., Hara M., Yamanaka H., et al. Haplotype analysis revealed no association between the PTPN22 gene and RA in a Japanese population. Rheumatology (Oxford) 2006, 45:1345-1348.
12. Remmers E.F., Plenge R.M., Lee A.T., Graham R.R., Hom G., Behrens T.W., et al. STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N. Engl. J. Med. 2007, 357:977-986.
13. Barton A., Thomson W., Ke X., Eyre S., Hinks A., Bowes J., et al. Re-evaluation of putative rheumatoid arthritis susceptibility genes in the post-genome wide association study era and hypothesis of a key pathway underlying susceptibility. Hum. Mol. Genet. 2008, 17:2274-2279.
14. Orozco G., Alizadeh B.Z., gado-Vega A.M., Gonzalez-Gay M.A., Balsa A., Pascual-Salcedo D., et al. Association of STAT4 with rheumatoid arthritis: a replication study in three European populations. Arthritis Rheum. 2008, 58:1974-1980.
15. Zervou M.I., Sidiropoulos P., Petraki E., Vazgiourakis V., Krasoudaki E., Raptopoulou A., et al. Association of a TRAF1 and a STAT4 gene polymorphism with increased risk for rheumatoid arthritis in a genetically homogeneous population. Hum. Immunol. 2008, 69:567-571.
16. Lee H.S., Remmers E.F., Le J.M., Kastner D.L., Bae S.C., Gregersen P.K. Association of STAT4 with rheumatoid arthritis in the Korean population. Mol. Med. 2007, 13:455-460.
17. Lee Y.H., Woo J.H., Choi S.J., Ji J.D., Song G.G. Association between the rs7574865 polymorphism of STAT4 and rheumatoid arthritis: a meta-analysis. Rheumatol. Int. 2009, 30(5):661-666.
18. Suzuki A., Yamada R., Chang X., Tokuhiro S., Sawada T., Suzuki M., et al. Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis. Nat. Genet. 2003, 34:395-402.
19. Barton A., Bowes J., Eyre S., Spreckley K., Hinks A., John S., et al. A functional haplotype of the PADI4 gene associated with rheumatoid arthritis in a Japanese population is not associated in a United Kingdom population. Arthritis Rheum. 2004, 50:1117-1121.
20. Ikari K., Kuwahara M., Nakamura T., Momohara S., Hara M., Yamanaka H., et al. Association between PADI4 and rheumatoid arthritis: a replication study. Arthritis Rheum. 2005, 52:3054-3057.
21. Kang C.P., Lee H.S., Ju H., Cho H., Kang C., Bae S.C. A functional haplotype of the PADI4 gene associated with increased rheumatoid arthritis susceptibility in Koreans. Arthritis Rheum. 2006, 54:90-96.
22. Burr M.L., Naseem H., Hinks A., Eyre S., Gibbons L., Bowes J., et al. PADI4 genotype is not associated with rheumatoid arthritis in a large UK Caucasian population. Ann. Rheum. Dis. 2009, 69:666-670.
23. Tokuhiro S., Yamada R., Chang X., Suzuki A., Kochi Y., Sawada T., et al. An intronic SNP in a RUNX1 binding site of SLC22A4, encoding an organic cation transporter, is associated with rheumatoid arthritis. Nat. Genet. 2003, 35:341-348.
24. Barton A., Eyre S., Bowes J., Ho P., John S., Worthington J. Investigation of the SLC22A4 gene (associated with rheumatoid arthritis in a Japanese population) in a United Kingdom population of rheumatoid arthritis patients. Arthritis Rheum. 2005, 52:752-758.
25. Kuwahara M., Ikari K., Momohara S., Nakamura T., Hara M., Yamanaka H., et al. Failure to confirm association between SLC22A4 polymorphism and rheumatoid arthritis in a Japanese population. Arthritis Rheum. 2005, 52:2947-2948.
26. Orozco G., Sanchez E., Gonzalez-Gay M.A., Lopez-Nevot M.A., Torres B., Pascual-Salcedo D., et al. SLC22A4, RUNX1, and SUMO4 polymorphisms are not associated with rheumatoid arthritis: a case-control study in a Spanish population. J. Rheumatol. 2006, 33:1235-1239.
27. Kochi Y., Yamada R., Suzuki A., Harley J.B., Shirasawa S., Sawada T., et al. A functional variant in FCRL3, encoding Fc receptor-like 3, is associated with rheumatoid arthritis and several autoimmunities. Nat. Genet. 2005, 37:478-485.
28. Eyre S., Bowes J., Potter C., Worthington J., Barton A. Association of the FCRL3 gene with rheumatoid arthritis: a further example of population specificity?. Arthritis Res. Ther. 2006, 8:R117.
29. Choi C.B., Kang C.P., Seong S.S., Bae S.C., Kang C. The -169C/T polymorphism in FCRL3 is not associated with susceptibility to rheumatoid arthritis or systemic lupus erythematosus in a case-control study of Koreans. Arthritis Rheum. 2006, 54:3838-3841.
30. Newman W.G., Zhang Q., Liu X., Walker E., Ternan H., Owen J., et al. Rheumatoid arthritis association with the FCRL3-169C polymorphism is restricted to PTPN22 1858T-homozygous individuals in a Canadian population. Arthritis Rheum. 2006, 54:3820-3827.
31. Hu X., Chang M., Saiki R.K., Cargill M.A., Begovich A.B., Ardlie K.G., et al. The functional -169T?C single-nucleotide polymorphism in FCRL3 is not associated with rheumatoid arthritis in white North Americans. Arthritis Rheum. 2006, 54:1022-1025.
32. Ikari K., Momohara S., Nakamura T., Hara M., Yamanaka H., Tomatsu T., et al. Supportive evidence for a genetic association of the FCRL3 promoter polymorphism with rheumatoid arthritis. Ann. Rheum. Dis. 2006, 65:671-673.
33. Swanberg M., Lidman O., Padyukov L., Eriksson P., Akesson E., Jagodic M., et al. MHC2TA is associated with differential MHC molecule expression and susceptibility to rheumatoid arthritis, multiple sclerosis and myocardial infarction. Nat. Genet. 2005, 37:486-494.
34. Eyre S., Bowes J., Spreckley K., Potter C., Ring S., Strachan D., et al. Investigation of the MHC2TA gene, associated with rheumatoid arthritis in a Swedish population, in a UK rheumatoid arthritis cohort. Arthritis Rheum. 2006, 54:3417-3422.
35. Orozco G., Robledo G., Linga Reddy M.V., Garcia A., Pascual-Salcedo D., Balsa A., et al. Study of the role of a functional polymorphism of MHC2TA in rheumatoid arthritis in three ethnically different populations. Rheumatology (Oxford) 2006, 45:1442-1444.
36. Yazdani-Biuki B., Brickmann K., Wohlfahrt K., Mueller T., Marz W., Renner W., et al. The MHC2TA -168A>G gene polymorphism is not associated with rheumatoid arthritis in Austrian patients. Arthritis Res. Ther. 2006, 8:R97.
37. Harrison P., Pointon J.J., Farrar C., Harin A., Wordsworth B.P. MHC2TA promoter polymorphism (-168?G/A, rs3087456) is not associated with susceptibility to rheumatoid arthritis in British Caucasian rheumatoid arthritis patients. Rheumatology (Oxford) 2007, 46:409-411.
38. Anonymous Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007, 447:661-678.
39. Plenge R.M., Seielstad M., Padyukov L., Lee A.T., Remmers E.F., Ding B., et al. TRAF1-C5 as a risk locus for rheumatoid arthritis - a genomewide study. N. Engl. J. Med. 2007, 357:1199-1209.
40. Kurreeman F.A., Padyukov L., Marques R.B., Schrodi S.J., Seddighzadeh M., Stoeken-Rijsbergen G., et al. A candidate gene approach identifies the TRAF1/C5 region as a risk factor for rheumatoid arthritis. PLoS. Med. 2007, 4:e278.
41. Kurreeman F.A., Rocha D., Houwing-Duistermaat J., Vrijmoet S., Teixeira V.H., Migliorini P., et al. Replication of the tumor necrosis factor receptor-associated factor 1/complement component 5 region as a susceptibility locus for rheumatoid arthritis in a European family-based study. Arthritis Rheum. 2008, 58:2670-2674.
42. Thomson W., Barton A., Ke X., Eyre S., Hinks A., Bowes J., et al. Rheumatoid arthritis association at 6q23. Nat. Genet. 2007, 39:1431-1433.
43. Plenge R.M., Cotsapas C., Davies L., Price A.L., de Bakker P.I., Maller J., et al. Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nat. Genet. 2007, 39:1477-1482.
44. Barton A., Thomson W., Ke X., Eyre S., Hinks A., Bowes J., et al. Rheumatoid arthritis susceptibility loci at chromosomes 10p15, 12q13 and 22q13. Nat. Genet. 2008, 40:1156-1159.
45. Barton A., Eyre S., Ke X., Hinks A., Bowes J., Flynn E., et al. Identification of AF4/FMR2 family, member 3 (AFF3) as a novel rheumatoid arthritis susceptibility locus and confirmation of two further pan-autoimmune susceptibility genes. Hum. Mol. Genet. 2009, 18:2518-2522.
46. Raychaudhuri S., Remmers E.F., Lee A.T., Hackett R., Guiducci C., Burtt N.P., et al. Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nat. Genet. 2008, 40:1216-1223.
47. Gregersen P.K., Amos C.I., Lee A.T., Lu Y., Remmers E.F., Kastner D.L., et al. REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis. Nat. Genet. 2009, 41:820-823.
48. Raychaudhuri S., Plenge R.M., Rossin E.J., Ng A.C., Purcell S.M., Sklar P., et al. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. PLoS Genet. 2009, 5:e1000534.
49. Raychaudhuri S., Thomson B.P., Remmers E.F., Eyre S., Hinks A., Guiducci C., et al. Genetic variants at CD28, PRDM1, and CD2/CD58 are associated with rheumatoid arthritis risk. Nat. Genet. 2009, 41:1313-1318.
50. Plant D., Cornelis F., Rantapää-Dahlqvist S., Goulielmos G., Hetland M.L., Klareskog L., et al. Investigation of potential non-HLA RA susceptibility loci in a European cohort increases the evidence for 10 markers. Arthritis Rheum. 2009, 60:S278.
51. Smyth D.J., Cooper J.D., Howson J.M., Walker N.M., Plagnol V., Stevens H., et al. PTPN22 Trp620 explains the association of chromosome 1p13 with type 1 diabetes and shows a statistical interaction with HLA class II genotypes. Diabetes 2008, 57:1730-1737.
52. Orozco G., Hinks A., Eyre S., Ke X., Gibbons L.J., Bowes J., et al. Combined effects of three independent SNPs greatly increase the risk estimate for RA at 6q23. Hum. Mol. Genet. 2009, 18:2693-2699.
53. Fung E.Y., Smyth D.J., Howson J.M., Cooper J.D., Walker N.M., Stevens H., et al. Analysis of 17 autoimmune disease-associated variants in type 1 diabetes identifies 6q23/TNFAIP3 as a susceptibility locus. Genes Immun. 2009, 10:188-191.
54. Nair R.P., Duffin K.C., Helms C., Ding J., Stuart P.E., Goldgar D., et al. Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways. Nat. Genet. 2009, 41:199-204.
55. Graham R.R., Cotsapas C., Davies L., Hackett R., Lessard C.J., Leon J.M., et al. Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus. Nat. Genet. 2008, 40:1059-1061.
56. Musone S.L., Taylor K.E., Lu T.T., Nititham J., Ferreira R.C., Ortmann W., et al. Multiple polymorphisms in the TNFAIP3 region are independently associated with systemic lupus erythematosus. Nat. Genet. 2008, 40:1062-1064.
57. Trynka G., Zhernakova A., Romanos J., Franke L., Hunt K.A., Turner G., et al. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. Gut 2009, 58:1078-1083.
58. Maier L.M., Lowe C.E., Cooper J., Downes K., Anderson D.E., Severson C., et al. IL2RA genetic heterogeneity in multiple sclerosis and type 1 diabetes susceptibility and soluble interleukin-2 receptor production. PLoS Genet. 2009, 5:e1000322.
59. McClure A., Lunt M., Eyre S., Ke X., Thomson W., Hinks A., et al. Investigating the viability of genetic screening/testing for RA susceptibility using combinations of five confirmed risk loci. Rheumatology 2009, 48:1369-1374.
60. Kallberg H., Padyukov L., Plenge R.M., Ronnelid J., Gregersen P.K., van der Helm-van Mil A.H., et al. Gene-gene and gene-environment interactions involving HLA-DRB1, PTPN22, and smoking in two subsets of rheumatoid arthritis. Am. J. Hum. Genet. 2007, 80:867-875.
61. Aitman T.J., Dong R., Vyse T.J., Norsworthy P.J., Johnson M.D., Smith J., et al. Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 2006, 439:851-855.
62. Fanciulli M., Norsworthy P.J., Petretto E., Dong R., Harper L., Kamesh L., et al. FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. Nat. Genet. 2007, 39:721-723.
63. McKinney C., Merriman M.E., Chapman P.T., Gow P.J., Harrison A.A., Highton J., et al. Evidence for an influence of chemokine ligand 3-like 1 (CCL3L1) gene copy number on susceptibility to rheumatoid arthritis. Ann. Rheum. Dis. 2008, 67:409-413.
64. Fellermann K., Stange D.E., Schaeffeler E., Schmalzl H., Wehkamp J., Bevins C.L., et al. A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon. Am. J. Hum. Genet. 2006, 79:439-448.
65. Hollox E.J., Huffmeier U., Zeeuwen P.L.J.M., Palla R., Lascorz J., Rodijk-Olthuis D., et al. Psoriasis is associated with increased [beta]-defensin genomic copy number. Nat. Genet. 2008, 40:23-25.