Table 2

The Kolmogorov-Smirnov (KS) test for AP p value distributions of the interaction analysis with the HLA-DRB1 SE alleles and risk or non-risk SNPs in EIRA and NARAC imputed data

Case–control groupSNP groupNumber of initial input SNPsNumber of SNPs after cut-off * % of SNPs analysedNumber of SNPs with AP p<0.05% of analysed SNPs with AP p<0.05D^+value from KS test (risk vs
Group of SNPs with enrichment of significant interactions
EIRARisk241 759160 35866.3339 51824.640.354Risk
No risk4 515 1102 979 34465.9983 2872.80
NARACRisk787 499209 89026.6531 99215.240.247Risk
No risk8 244 9551 916 70123.2564 0123.44
  • *Interaction was estimated using sex and the 10 first eigenvectors as covariables. A minimum of five individuals in each of the four combinations that formed the basis for the OR calculations was required.

  • †The alternative hypothesis for KS test was that the empirical cumulative distribution function (ECDF) of AP p values for risk SNPs lies above that of non-risk SNPs (figure 2). KS test p<2.2e-16 for both EIRA and NARAC. As mentioned in the Materials and methods section, these KS test p values are lower than the machine precision, meaning that when the precise p value was calculated the result was 0.

  • AP, attributable proportion; EIRA, epidemiological investigation of rheumatoid arthritis; NARAC, North American rheumatoid arthritis consortium; SE, shared epitope; SNP, single nucleotide polymorphism.