In the logistic regression analysis of a SNP, we performed a one–degree of freedom (1-d.f.) likelihood ratio test to determine whether a 1-d.f. multiplicative allelic effects model or a 2-d.f. full genotype model was more appropriate28. We assumed a multiplicative allelic effects model, as it was not significantly different from the full genotype model, except for rs2666236 (NRP1). In the forward logistic regression analysis, we started by assessing the evidence against the most significant SNP being the sole variant in the region (in other words, whether this SNP alone was sufficient to model the association). For the purposes of this analysis, we did not assume any specific mode of inheritance for the most associated SNP (A>a) or for any additional SNP with significant independent effects on T1D, so genotype risks of A/A and A/a were modeled relative to the a/a genotype. We then used a 1-d.f. test for adding each of the remaining SNPs to the model by assuming multiplicative allelic effects for the additional SNPs.
