GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region
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Rullo OJ, Tsao BP . Recent insights into the genetic basis of systemic lupus erythematosus. Ann Rheum Dis 2013; 72 (Suppl 2): 56–61.
Armstrong DL, Reiff A, Myones BL, Quismorio FP, Klein-Gitelman M, McCurdy D et al. Identification of new SLE-associated genes with a two-step Bayesian study design. Genes Immun 2009; 10: 446–456.
Raychaudhuri S, Sandor C, Stahl EA, Freudenberg J, Lee HS, Jia X et al. Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Nat Genet 2012; 44: 291–296.
Benjamini Y, Bogomolov M . Selective inference on multiple families of hypothe- ses. J Royal Stat Soc B 2014; 76: 297–318.
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P et al. A method and server for predicting damaging missense mutations. Nat Methods 2010; 7: 248–249.
Kumar P, Henikoff S, Ng PC . Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009; 4: 1073–1081.
Choi Y, Sims GE, Murphy S, Miller JR, Chan AP . Predicting the functional effect of amino acid substitutions and indels. PLoS ONE 2012; 7: 46688.
Jacob CO, Eisenstein M, Dinauer MC, Ming W, Liu Q, John S et al. Lupus-associated causal mutation in neutrophil cytosolic factor 2 (NCF2) brings unique insights to the structure and function of NADPH oxidase. Proc Natl Acad Sci USA 2012; 109: 59–67.
Marchini J, Howie B . Genotype imputation for genome-wide association studies. Nat Rev Genet 2010; 11: 499–511.
Friedman J, Hastie T, Tibshirani R . Regularization paths for generalized linear models via coordinate descent. J Stat Softw 2010; 33: 1–22.
McClain MT, Ramsland PA, Kaufman KM, James JA . Anti-sm autoantibodies in systemic lupus target highly basic surface structures of complexed spliceosomal autoantigens. J Immunol 2002; 168: 2054–2062.
Dilthey A, Leslie S, Moutsianas L, Shen J, Cox C, Nelson MR et al. Multi-population classical HLA type imputation. PLoS Comput Biol 2013; 9: 1002877.
Dilthey AT, Moutsianas L, Leslie S, McVean G . HLA*IMP–an integrated framework for imputing classical HLA alleles from SNP genotypes. Bioinformatics 2011; 27: 968–972.
Leslie S, Donnelly P, McVean G . A statistical method for predicting classical HLA alleles from SNP data. Am J Hum Genet 2008; 82: 48–56.
Tjernström F, Hellmer G, Nived O, Truedsson L, Sturfelt G . Synergetic effect between interleukin-1 receptor antagonist allele (IL1RN*2) and MHC class II (DR17,DQ2) in determining susceptibility to systemic lupus erythematosus. Lupus 1999; 8: 103–108.
Leng RX, Wang W, Cen H, Zhou M, Feng CC, Zhu Y et al. Gene-gene and gene-sex epistatic interactions of MiR146a, IRF5, IKZF1, ETS1 and IL21 in systemic lupus erythematosus. PLoS ONE 2012; 7: 51090.
Lehtonen A, Ahlfors H, Veckman V, Miettinen M, Lahesmaa R, Julkunen I . Gene expression profiling during differentiation of human monocytes to macrophages or dendritic cells. J Leukoc Biol 2007; 82: 710–720.
Gabriel L, Morley BJ, Rogers NJ . The role of iNKT cells in the immunopathology of systemic lupus erythematosus. Ann NY Acad Sci 2009; 1173: 435–441.
Bijlmakers MJ, Kanneganti SK, Barker JN, Trembath RC, Capon F . Functional analysis of the RNF114 psoriasis susceptibility gene implicates innate immune responses to double-stranded RNA in disease pathogenesis. Hum Mol Genet 2011; 20: 3129–3137.
Jacob CO, Reiff A, Armstrong DL, Myones BL, Silverman E, Klein-Gitelman M et al. Identification of novel susceptibility genes in childhood-onset systemic lupus erythematosus using a uniquely designed candidate gene pathway platform. Arthritis Rheum 2007; 56: 4164–4173.
Morris DL, Taylor KE, Fernando MMA, Nititham J, Alarcón-Riquelme ME, Barcellos LF et al. Unraveling multiple MHC gene associations with systemic lupus erythematosus: model choice indicates a role for HLA alleles and non-HLA genes in Europeans. Am J Hum Genet 2012; 91: 778–793.
Hochberg MC . Updating the American College of Rheumatology revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum 1997; 40: 1725.
Tan EM, Cohen AS, Fries JF, Masi AT, McShane DJ, Rothfield NF et al. The 1982 revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum 1982; 25: 1271–1277.
Harley JB, Alarcón-Riquelme ME, Criswell LA, Jacob CO, Kimberly RP, Moser KL et al. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat Genet 2008; 40: 204–210.
Bouaziz M, Ambroise C, Guedj M . Accounting for population stratification in practice: a comparison of the main strategies dedicated to genome-wide association studies. PLoS ONE 2011; 6: 28845.
Deng HW . Population admixture may appear to mask, change or reverse genetic effects of genes underlying complex traits. Genetics 2001; 159: 1319–1323.
Baye TM, Tiwari HK, Allison DB, Go RC . Database mining for selection of SNP markers useful in admixture mapping. BioData Min 2009; 2: 1.
R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing: Vienna, Austria.
Benjamini Y, Hochberg Y . Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 1995; 57: 289–300.
Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR . Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet 2012; 44: 955–959.
Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE et al. An integrated map of genetic variation from 1,092 human genomes. Nature 2012; 491: 56–65.
Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 2007; 449: 851–861.
Taylor KE, Remmers EF, Lee AT, Ortmann WA, Plenge RM, Tian C et al. Specificity of the STAT4 genetic association for severe disease manifestations of systemic lupus erythematosus. PLoS Genet 2008; 4: 1000084.
Sigurdsson S, Nordmark G, Göring HHH, Lindroos K, Wiman AC, Sturfelt G et al. Polymorphisms in the tyrosine kinase 2 and interferon regulatory factor 5 genes are associated with systemic lupus erythematosus. Am J Hum Genet 2005; 76: 528–537.
Lee YH, Bae SC, Choi SJ, Ji JD, Song GG . Genome-wide pathway analysis of genome-wide association studies on systemic lupus erythematosus and rheumatoid arthritis. Mol Biol Rep 2012; 39: 10627–10635.
Bauer T, Zagórska A, Jurkin J, Yasmin N, Köffel R, Richter S et al. Identification of Axl as a downstream effector of TGF-β1 during Langerhans cell differentiation and epidermal homeostasis. J Exp Med 2012; 209: 2033–2047.