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Table 4 Genotype-based associations with R620W and RA sub-type (reference is major allele CC 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
RA Phenotype Genotype OR 95% CI p d OR 95% CI p d OR 95% CI p e OR 95% CI p
RF+ vs. Ctrls. CT or TT 1.80 1.29–2.49 <0.001 2.34 1.82–3.00 <0.001 2.13 1.76–2.57 <0.001 2.36 1.76–3.16 <0.001
RF- vs. Ctrls. CT or TT 1.40 0.87–2.27 0.20 1.08 0.71–1.65 0.77 1.20 0.87–1.65 0.31 1.17 0.6–2.31 0.64
RF+ vs. RF- CT or TT 1.07 0.58–2.00 0.79 1.46 0.83–2.56 0.12 1.30 0.86–1.95 0.18    
            Previously publishedf
CCP+ vs. Ctrls. CT or TT 1.69 1.18–2.41 0.001 2.03 1.57–2.62 <0.001 1.90 1.55–2.34 <0.001 1.49 1.23–1.79 <0.001
CCP- vs. Ctrls. CT or TT 1.59 1.04–2.45 0.035 1.41 1.03–1.95 0.029 1.47 1.15–1.88 0.001 1.04 0.83–1.29 0.40
CCP+ vs. CCP- CT or TT 1.05 0.61–1.80 0.93 1.16 0.83–1.60 0.32 1.12 0.84–1.50 0.47    
RF or CCP+ vs. RF-/CCP- CT or TT 1.29 0.65–2.53 0.55 1.43 0.81–2.52 0.06 1.38 0.89–2.13 0.051 1.43 1.16–1.77 <0.001
  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. cBegovich et al. [3] replication sample (NARAC; 463 independent-sib cases, 926 independent controls), CLR analysis.
  4. dEmpirical confidence intervals and chi-square p-values, 1000 simulations; p < 0.05 in bold.
  5. eEmpirical confidence intervals and CMH chi-square general association test, 1000 simulations; p < 0.05 in bold.
  6. fPlenge et al. [6] first clinical collection, Epidemiological Investigation of RA (EIRA) Swedish cohort (2370 cases 1757 controls); allele association.