In order to properly assess significance of the AD risk contributions of selected SNPs, therefore, we generated a null distribution by repeating the whole procedure, including SNP selection, 1,000 times with randomized phenotype data (for the LR inclusion criterion) or 10,000 times (for the faster p-value threshold criterion); for each permutation we recorded the total deviance. We then compared the total deviance increase for the SNPs chosen using the true outcomes to the distribution of total deviance increases for SNPs chosen using the identical procedure for randomized outcomes; the p-value associated with each gene set was the proportion of permutation fits whose total explained deviance exceeded that of the true fit. We found that the sets of SNPs chosen and the significance of gene sets differ only modestly depending on which criterion for SNP inclusion is employed or on which log likelihood threshold is used for the likelihood criterion. We report results for the likelihood criterion, since this is more traditional; the results based on the other inclusion criterion were slightly more significant (not shown).
