A genome-wide screen of gene–gene interactions for rheumatoid arthritis susceptibility (original) (raw)

References

• American College of Rheumatology Subcommittee on Rheumatoid Arthritis Guidelines (2002) Guidelines for the management of rheumatoid arthritis: 2002 Update. Arthritis Rheum 46:328–346
  Google Scholar
• Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263–265
  Article PubMed CAS Google Scholar
• Begovich AB, Carlton VE, Honigberg LA, Schrodi SJ, Chokkalingam AP, Alexander HC, Ardlie KG, Huang Q, Smith AM, Spoerke JM, Conn MT, Chang M, Chang SY, Saiki RK, Catanese JJ, Leong DU, Garcia VE, McAllister LB, Jeffery DA, Lee AT, Batliwalla F, Remmers E, Criswell LA, Seldin MF, Kastner DL, Amos CI, Sninsky JJ, Gregersen PK (2004) A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. Am J Hum Genet 75:330–337
  Article PubMed CAS Google Scholar
• Breiman L (2001) Random forests. Mach Learn 45:5–32
  Article Google Scholar
• Briggs FB, Ramsay PP, Madden E, Norris JM, Holers VM, Mikuls TR, Sokka T, Seldin MF, Gregersen PK, Criswell LA, Barcellos LF (2010) Supervised machine learning and logistic regression identifies novel epistatic risk factors with PTPN22 for rheumatoid arthritis. Genes Immun 11:199–208
  Article PubMed CAS Google Scholar
• Cardon LR, Palmer LJ (2003) Population stratification and spurious allelic association. Lancet 361:598–604
  Article PubMed Google Scholar
• Cordell HJ (2009) Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 10:392–404
  Article PubMed CAS Google Scholar
• Corder EH, Saunders AM, Strittmatter WJ, Schmechel DE, Gaskell PC, Small GW, Roses AD, Haines JL, Pericak-Vance MA (1993) Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer’s disease in late onset families. Science 261:921–923
  Article PubMed CAS Google Scholar
• de Bakker PI, Yelensky R, Pe’er I, Gabriel SB, Daly MJ, Altshuler D (2005) Efficiency and power in genetic association studies. Nat Genet 37:1217–1223
  Article PubMed Google Scholar
• de Bakker PI, McVean G, Sabeti PC, Miretti MM, Green T, Marchini J, Ke X, Monsuur AJ, Whittaker P, Delgado M, Morrison J, Richardson A, Walsh EC, Gao X, Galver L, Hart J, Hafler DA, Pericak-Vance M, Todd JA, Daly MJ, Trowsdale J, Wijmenga C, Vyse TJ, Beck S, Murray SS, Carrington M, Gregory S, Deloukas P, Rioux JD (2006) A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat Genet 38:1166–1172
  Article PubMed Google Scholar
• Diaz-Uriarte R, Alvarez de Andres S (2006) Gene selection and classification of microarray data using random forest. BMC Bioinformatics 7:3
  Article PubMed Google Scholar
• Ding B, Padyukov L, Lundstrom E, Seielstad M, Plenge RM, Oksenberg JR, Gregersen PK, Alfredsson L, Klareskog L (2009) 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 60:30–38
  Article PubMed CAS Google Scholar
• Evans DM, Marchini J, Morris AP, Cardon LR (2006) Two-stage two-locus models in genome-wide association. PLoS Genet 2:e157
  Article PubMed Google Scholar
• Furuya T, Hakoda M, Ichikawa N, Higami K, Nanke Y, Yago T, Kobashigawa T, Tokunaga K, Tsuchiya N, Kamatani N, Kotake S (2007) Differential association of HLA-DRB1 alleles in Japanese patients with early rheumatoid arthritis in relationship to autoantibodies to cyclic citrullinated peptide. Clin Exp Rheumatol 25:219–224
  PubMed CAS Google Scholar
• Gauderman WJ (2002a) Sample size requirements for association studies of gene-gene interaction. Am J Epidemiol 155:478–484
  Article PubMed Google Scholar
• Gauderman WJ (2002b) Sample size requirements for matched case-control studies of gene-environment interaction. Stat Med 21:35–50
  Article PubMed Google Scholar
• Gauderman WJ (2003) Candidate gene association analysis for a quantitative trait, using parent-offspring trios. Genet Epidemiol 25:327–338
  Article PubMed Google Scholar
• Gregersen PK, Moriuchi T, Karr RW, Obata F, Moriuchi J, Maccari J, Goldberg D, Winchester RJ, Silver J (1986a) Polymorphism of HLA-DR beta chains in DR4, -7, and -9 haplotypes: implications for the mechanisms of allelic variation. Proc Natl Acad Sci USA 83:9149–9153
  Article PubMed CAS Google Scholar
• Gregersen PK, Shen M, Song QL, Merryman P, Degar S, Seki T, Maccari J, Goldberg D, Murphy H, Schwenzer J et al (1986b) Molecular diversity of HLA-DR4 haplotypes. Proc Natl Acad Sci USA 83:2642–2646
  Article PubMed CAS Google Scholar
• Gregersen PK, Silver J, Winchester RJ (1987) The shared epitope hypothesis. An approach to understanding the molecular genetics of susceptibility to rheumatoid arthritis. Arthritis Rheum 30:1205–1213
  Article PubMed CAS Google Scholar
• Gregersen PK, Amos CI, Lee AT, Lu Y, Remmers EF, Kastner DL, Seldin MF, Criswell LA, Plenge RM, Holers VM, Mikuls TR, Sokka T, Moreland LW, Bridges SL Jr, Xie G, Begovich AB, Siminovitch KA (2009) REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis. Nat Genet 41:820–823
  Article PubMed CAS Google Scholar
• Hoh J, Wille A, Zee R, Cheng S, Reynolds R, Lindpaintner K, Ott J (2000) Selecting SNPs in two-stage analysis of disease association data: a model-free approach. Ann Hum Genet 64:413–417
  Article PubMed CAS Google Scholar
• Hom G, Graham RR, Modrek B, Taylor KE, Ortmann W, Garnier S, Lee AT, Chung SA, Ferreira RC, Pant PV, Ballinger DG, Kosoy R, Demirci FY, Kamboh MI, Kao AH, Tian C, Gunnarsson I, Bengtsson AA, Rantapaa-Dahlqvist S, Petri M, Manzi S, Seldin MF, Ronnblom L, Syvanen AC, Criswell LA, Gregersen PK, Behrens TW (2008) Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX. N Engl J Med 358:900–909
  Article PubMed CAS Google Scholar
• Huizinga TW, Amos CI, van der Helm-van Mil AH, Chen W, van Gaalen FA, Jawaheer D, Schreuder GM, Wener M, Breedveld FC, Ahmad N, Lum RF, de Vries RR, Gregersen PK, Toes RE, Criswell LA (2005) Refining the complex rheumatoid arthritis phenotype based on specificity of the HLA-DRB1 shared epitope for antibodies to citrullinated proteins. Arthritis Rheum 52:3433–3438
  Article PubMed CAS Google Scholar
• Kallberg H, Padyukov L, Plenge RM, Ronnelid J, Gregersen PK, van der Helm-van Mil AH, Toes RE, Huizinga TW, Klareskog L, Alfredsson L (2007) Gene-gene and gene-environment interactions involving HLA-DRB1, PTPN22, and smoking in two subsets of rheumatoid arthritis. Am J Hum Genet 80:867–875
  Article PubMed Google Scholar
• Kooperberg C, Leblanc M (2008) Increasing the power of identifying gene × gene interactions in genome-wide association studies. Genet Epidemiol 32:255–263
  Article PubMed Google Scholar
• Kurreeman FA, Padyukov L, Marques RB, Schrodi SJ, Seddighzadeh M, Stoeken-Rijsbergen G, van der Helm-van Mil AH, Allaart CF, Verduyn W, Houwing-Duistermaat J, Alfredsson L, Begovich AB, Klareskog L, Huizinga TW, Toes RE (2007) A candidate gene approach identifies the TRAF1/C5 region as a risk factor for rheumatoid arthritis. PLoS Med 4:e278
  Article PubMed Google Scholar
• Lee AT, Li W, Liew A, Bombardier C, Weisman M, Massarotti EM, Kent J, Wolfe F, Begovich AB, Gregersen PK (2005) The PTPN22 R620W polymorphism associates with RF positive rheumatoid arthritis in a dose-dependent manner but not with HLA-SE status. Genes Immun 6:129–133
  Article PubMed CAS Google Scholar
• Lee HS, Remmers EF, Le JM, Kastner DL, Bae SC, Gregersen PK (2007) Association of STAT4 with rheumatoid arthritis in the Korean population. Mol Med 13:455–460
  PubMed CAS Google Scholar
• Lee HS, Lee AT, Criswell LA, Seldin MF, Amos CI, Carulli JP, Navarrete C, Remmers EF, Kastner DL, Plenge RM, Li W, Gregersen PK (2008) Several regions in the major histocompatibility complex confer risk for anti-CCP-antibody positive rheumatoid arthritis, independent of the DRB1 locus. Mol Med 14:293–300
  Article PubMed Google Scholar
• Leslie S, Donnelly P, McVean G (2008) A statistical method for predicting classical HLA alleles from SNP data. Am J Hum Genet 82:48–56
  Article PubMed CAS Google Scholar
• Li Y, Abecasis G (2006) Mach 1.0: rapid haplotype reconstruction and missing genotype inference. Am J Hum Genet S792290
• Liaw A, Wiener M (2002) Classification and regression by random forest. R News 2:18–22
  Google Scholar
• Lunetta KL, Hayward LB, Segal J, Van Eerdewegh P (2004) Screening large-scale association study data: exploiting interactions using random forests. BMC Genet 5:32
  Article PubMed Google Scholar
• MacGregor AJ, Snieder H, Rigby AS, Koskenvuo M, Kaprio J, Aho K, Silman AJ (2000) Characterizing the quantitative genetic contribution to rheumatoid arthritis using data from twins. Arthritis Rheum 43:30–37
  Article PubMed CAS Google Scholar
• Majithia V, Geraci SA (2007) Rheumatoid arthritis: diagnosis and management. Am J Med 120:936–939
  Article PubMed Google Scholar
• Manning AK, Ngwa JS, Hendricks AE, Liu CT, Johnson AD, Dupuis J, Cupples LA (2009) Incorporating biological knowledge in the search for gene × gene interaction in genome-wide association studies. BMC Proc 3(Suppl 7):S81
  Google Scholar
• Marchini J, Donnelly P, Cardon LR (2005) Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 37:413–417
  Article PubMed CAS Google Scholar
• Moore JH (2003) The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered 56:73–82
  Article PubMed Google Scholar
• Ohmura K, Terao C, Maruya E, Katayama M, Matoba K, Shimada K, Murasawa A, Honjo S, Takasugi K, Tohma S, Matsuo K, Tajima K, Yukawa N, Kawabata D, Nojima T, Fujii T, Yamada R, Saji H, Matsuda F, Mimori T (2010) Anti-citrullinated peptide antibody-negative RA is a genetically distinct subset: a definitive study using only bone-erosive ACPA-negative rheumatoid arthritis. Rheumatology 49:2298–2304
  Google Scholar
• Pearson TA, Manolio TA (2008) How to interpret a genome-wide association study. JAMA 299:1335–1344
  Article PubMed CAS Google Scholar
• Plenge RM, Padyukov L, Remmers EF, Purcell S, Lee AT, Karlson EW, Wolfe F, Kastner DL, Alfredsson L, Altshuler D, Gregersen PK, Klareskog L, Rioux JD (2005) 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 77:1044–1060
  Article PubMed CAS Google Scholar
• Plenge RM, Seielstad M, Padyukov L, Lee AT, Remmers EF, Ding B, Liew A, Khalili H, Chandrasekaran A, Davies LR, Li W, Tan AK, Bonnard C, Ong RT, Thalamuthu A, Pettersson S, Liu C, Tian C, Chen WV, Carulli JP, Beckman EM, Altshuler D, Alfredsson L, Criswell LA, Amos CI, Seldin MF, Kastner DL, Klareskog L, Gregersen PK (2007) TRAF1-C5 as a risk locus for rheumatoid arthritis—a genomewide study. N Engl J Med 357:1199–1209
  Article PubMed CAS Google Scholar
• Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904–909
  Article PubMed CAS Google Scholar
• Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559–575
  Article PubMed CAS Google Scholar
• Raychaudhuri S (2010) Recent advances in the genetics of rheumatoid arthritis. Curr Opin Rheumatol 22:109–118
  Article PubMed CAS Google Scholar
• Raychaudhuri S, Remmers EF, Lee AT, Hackett R, Guiducci C, Burtt NP, Gianniny L, Korman BD, Padyukov L, Kurreeman FA, Chang M, Catanese JJ, Ding B, Wong S, van der Helm-van Mil AH, Neale BM, Coblyn J, Cui J, Tak PP, Wolbink GJ, Crusius JB, van der Horst-Bruinsma IE, Criswell LA, Amos CI, Seldin MF, Kastner DL, Ardlie KG, Alfredsson L, Costenbader KH, Altshuler D, Huizinga TW, Shadick NA, Weinblatt ME, de Vries N, Worthington J, Seielstad M, Toes RE, Karlson EW, Begovich AB, Klareskog L, Gregersen PK, Daly MJ, Plenge RM (2008) Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nat Genet 40:1216–1223
  Article PubMed CAS Google Scholar
• Remmers EF, Plenge RM, Lee AT, Graham RR, Hom G, Behrens TW, de Bakker PI, Le JM, Lee HS, Batliwalla F, Li W, Masters SL, Booty MG, Carulli JP, Padyukov L, Alfredsson L, Klareskog L, Chen WV, Amos CI, Criswell LA, Seldin MF, Kastner DL, Gregersen PK (2007) STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N Engl J Med 357:977–986
  Article PubMed CAS Google Scholar
• Seldin MF, Amos CI, Ward R, Gregersen PK (1999) The genetics revolution and the assault on rheumatoid arthritis. Arthritis Rheum 42:1071–1079
  Article PubMed CAS Google Scholar
• Skol AD, Scott LJ, Abecasis GR, Boehnke M (2007) Optimal designs for two-stage genome-wide association studies. Genet Epidemiol 31:776–788
  Article PubMed Google Scholar
• Stahl EA, Raychaudhuri S, Remmers EF, Xie G, Eyre S, Thomson BP, Li Y, Kurreeman FA, Zhernakova A, Hinks A, Guiducci C, Chen R, Alfredsson L, Amos CI, Ardlie KG, Barton A, Bowes J, Brouwer E, Burtt NP, Catanese JJ, Coblyn J, Coenen MJ, Costenbader KH, Criswell LA, Crusius JB, Cui J, de Bakker PI, De Jager PL, Ding B, Emery P, Flynn E, Harrison P, Hocking LJ, Huizinga TW, Kastner DL, Ke X, Lee AT, Liu X, Martin P, Morgan AW, Padyukov L, Posthumus MD, Radstake TR, Reid DM, Seielstad M, Seldin MF, Shadick NA, Steer S, Tak PP, Thomson W, van der Helm-van Mil AH, van der Horst-Bruinsma IE, van der Schoot CE, van Riel PL, Weinblatt ME, Wilson AG, Wolbink GJ, Wordsworth BP, Wijmenga C, Karlson EW, Toes RE, de Vries N, Begovich AB, Worthington J, Siminovitch KA, Gregersen PK, Klareskog L, Plenge RM (2010) Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat Genet 42:508–514
  Article PubMed CAS Google Scholar
• Suzuki A, Yamada R, Chang X, Tokuhiro S, Sawada T, Suzuki M, Nagasaki M, Nakayama-Hamada M, Kawaida R, Ono M, Ohtsuki M, Furukawa H, Yoshino S, Yukioka M, Tohma S, Matsubara T, Wakitani S, Teshima R, Nishioka Y, Sekine A, Iida A, Takahashi A, Tsunoda T, Nakamura Y, Yamamoto K (2003) Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis. Nat Genet 34:395–402
  Article PubMed CAS Google Scholar
• van der Helm-van Mil AH, Verpoort KN, Breedveld FC, Toes RE, Huizinga TW (2005) Antibodies to citrullinated proteins and differences in clinical progression of rheumatoid arthritis. Arthritis Res Ther 7:R949–R958
  Article PubMed CAS Google Scholar
• van der Linden MP, Feitsma AL, le Cessie S, Kern M, Olsson LM, Raychaudhuri S, Begovich AB, Chang M, Catanese JJ, Kurreeman FA, van Nies J, van der Heijde DM, Gregersen PK, Huizinga TW, Toes RE, van der Helm-van Mil AH (2009) Association of a single-nucleotide polymorphism in CD40 with the rate of joint destruction in rheumatoid arthritis. Arthritis Rheum 60:2242–2247
  Article PubMed Google Scholar
• Walker EJ, Hirschfield GM, Xu C, Lu Y, Liu X, Coltescu C, Wang K, Newman WG, Bykerk V, Keystone EC, Mosher D, Amos CI, Heathcote EJ, Siminovitch KA (2009) CTLA4/ICOS gene variants and haplotypes are associated with rheumatoid arthritis and primary biliary cirrhosis in the Canadian population. Arthritis Rheum 60:931–937
  Article PubMed CAS Google Scholar
• Wordsworth P, Bell J (1991) Polygenic susceptibility in rheumatoid arthritis. Ann Rheum Dis 50:343–346
  Article PubMed CAS Google Scholar

Download references