We evaluated three sets of candidate genes. The first comprised a small number of candidate genes (n = 16) previously reported to be associated specifically with EEG measures (EEG-specific candidate genes). (One of the 14 genes in this set has been reported to be associated with three different EEG parameters. We treated each as independent associations.) One of the candidate genes was APOE. Because the APOE ε4 risk allele is defined by two SNPs, we did not use VEGAS, which aggregates over SNPs within a gene and flanking it, to evaluate its role. Although not on the Illumina array, these two SNPs could be imputed relatively accurately with reference to haplotypes in the 1000 Genomes reference panel, with imputation r2 values of .875 and .911. We created a dummy variable coding for risk, consisting of either the ε3/ε4 or ε4/ε4 haplotypes, and examined its effect on both measures of alpha power in RFGLS analyses using the same covariates as in all other analyses.
