Subsequent to this genome-wide scan, we examined associations with two targeted sets of candidate SNPs: those implicated in previous genetic studies of EEG (18 EEG-specific candidate SNPs) and those implicated in recent meta-analyses of disorders and traits that are themselves associated with the endophenotypes examined in this special issue (1,180 endophenotype-general candidate SNPs). The papers we consulted for SNPs were identified through MEDLINE and are listed in the Supplementary Material. SNPs not on the Illumina array were imputed using minimac (Howie, Fuchsberger, Stephens, Marchini, & Abecasis, 2012) with reference CEU haplotypes from 1000 Genomes (2/2012) after having been prephased with BEAGLE (Browning & Browning, 2009). Imputation produces an allele dosage for each SNP, which is a weighted sum of the minor allele frequency (0, 1, or 2) and the posterior probability that the imputed SNP belongs to each of these frequency categories. The sum of minor allele dosages constituted the independent variable in these analyses.
