Primary analyses were conducted in GWAF (Genome-Wide Association analyses with Family) on 12,972,748 SNPs, of which 1,519,440 were genotyped directly, using a generalized estimating equation (GEE) framework to control for the relatedness in the family sample (Chen and Yang, 2010). Sex and log-transformed age (at the time of EEG recording) were included as covariates in the model, as each of these variables were associated with fast beta EEG (p<0.0001). The first three principal components (PC1-PC3) computed from SNPRelate (Zheng et al, 2012) were also included as covariates to reduce the risk of false-positive associations owing to population stratification. Established thresholds for genome-wide significance (p<5×10−8) were utilized. In an effort to assess the influence of alcohol use problems on the genetic associations observed for beta EEG, given the association of AUD and beta EEG in this and previous studies, we conducted a secondary analysis in which we repeated the initial GWAS as described above, with the addition of DSM-V AUD severity as a covariate.
