For the second analysis, we a priori selected 48 genes (Table 2) with evidence for association with AD from four previous gene-finding efforts for AD: COGA (Begleiter 1995), the IASPSAD (Prescott et al. 2005), the Connecticut sample (Lappalainen et al. 2002), and the GWAS results from the German sample (Treutlein et al. 2009). We identified SNPs in these genes in the MGS dataset and performed set-based permutations at the gene-wise level to correct for multiple testing of SNPs and at the experiment-wise level to correct for multiple testing of genes.
