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Table 3 Genotype-based associations with RA (case-control comparison, reference is major allele homozygote)

From: Meta-genetic association of rheumatoid arthritis and PTPN22using PedGenie 2.1

  PedGenie 2.1    
  NARAC Study 1a NARAC Study 2b Meta-analysis Previously publishedc
PTPN22 Genotyped OR 95% CI p-trende OR 95% CI p-trende OR 95% CI p-trendf OR 95% CI p-trend
rs3789604 AC 0.94 0.69–1.26   1.16 0.93–1.46   1.07 0.91–1.26   1.15 0.93–1.42  
  CC 1.68 0.83–3.38 0.39 1.25 0.70–2.21 0.18 1.43 0.93–2.18 0.12 1.78 1.13–2.79 0.014
rs1217413 TC 1.44 1.11–1.87   1.34 1.08–1.66   1.38 1.17–1.63     
  CC 1.71 1.06–2.75 0.003 1.52 1.00–2.31 0.002 1.59 1.14–2.22 <0.001    
rs1217388 TC 1.49 1.14–1.93   1.30 1.05–1.61   1.37 1.15–1.63     
  CC 1.30 0.78–2.17 0.017 1.27 0.86–1.87 0.026 1.28 0.94–1.74 0.003    
ss38346943 TC 0.32 0.15–0.69   0.88 0.48–1.61   0.61 0.39–0.95     
  CC -- -- -- -- -- -- -- -- --    
rs1310182 CT 1.55 1.13–2.13   1.39 1.11–1.73   1.45 1.20–1.75   1.22 0.98–1.77  
  TT 1.57 1.07–2.30 0.011 1.62 1.18–2.22 <0.01 1.60 1.25–2.03 <0.001 1.32 0.97–1.54 0.052
rs2476601 CT 1.92 1.41–2.60   2.36 1.84–3.04   2.18 1.80–2.65   2.19 1.73–2.78  
(R620W) TT 1.96 0.74–5.21 <0.001 2.91 1.26–6.74 <0.001 2.53 1.32–4.84 <0.001 2.90 1.37–6.18 <0.001
rs12730735 AG 1.00 0.75–1.31   1.10 0.89–1.36   1.06 0.89–1.25     
  GG 0.48 0.29–0.80 0.08 0.56 0.37–0.83 0.14 0.53 0.39–0.72 0.024    
rs12760457 AG 1.01 0.75–1.36   1.09 0.87–1.37   1.06 0.89–1.26     
  GG 0.48 0.28–0.82 0.09 0.55 0.37–0.82 0.14 0.52 0.38–0.72 0.023    
rs2488458 GA 1.51 1.15–1.97   1.33 1.07–1.66   1.40 1.18–1.67     
  AA 1.27 0.79–2.05 0.014 1.20 0.81–1.78 0.037 1.23 0.91–1.67 0.003    
rs1217414 CT 1.02 0.77–1.35   0.85 0.69–1.04   0.91 0.78–1.06     
  TT 0.60 0.34–1.03 0.20 0.70 0.46–1.06 0.053 0.65 0.46–0.92 0.018    
  1. aProblem 2 data, 446 family cases and 103 family controls in 202 affected NARAC pedigrees, 664 independent NYC controls; excludes Plenge et al. [6] samples.
  2. bProblem 2 data, samples in Plenge et al. [6] candidate gene file, 839 family cases in 463 pedigrees and 854 independent NYC controls.
  3. cCarlton et al. [5] sample set 2, 661 random independent cases from NARAC pedigrees and 1322 NYC controls; adjusted for R620W or rs3789604 (R620W).
  4. dMinor allele heterozygote and homozygote genotypes according to Carlton et al. [5] Table 1.
  5. eEmpirical confidence intervals and chi-square p-values, 1000 simulations; p < 0.05 in bold.
  6. fEmpirical confidence intervals and CMH chi-square trend test p-values, 1000 simulations; p < 0.05 in bold.