T1D risk by HLA and rs2476601 (PTPN22) genotype.

HLA risk is grouped by tertiles of a prediction score using the six MHC SNPs listed in Supplementary Table 1 in Text S1. The first entry in each section shows effects of rs2476601 for each HLA group, expressed as relative risks with the ��GG�� genotype as reference (shown in italic). The second line in each section shows these expressed relative to the low- risk HLA group. The four ratios of relative risks that remain after sweeping out the first row and column are the interaction parameters in the logistic regression model, and the test for interaction is a test of the hypothesis that these do not differ from unity. These ��ratios of ratios�� are difficult to interpret, but are the only parameters identifiable from case-only data. The third entry in each section shows joint effects of HLA and PTPN22 when main effects are included, and the final line expresses these as absolute risks per 1,000 in a population in which the overall cumulative incidence is 1%.