Analyses of individual SNPs were performed using a method incorporating a rapid feasible generalized least squares (RFGLS) model (Li et al., 2011), which accounts for correlations among family members attributable to both genetic relatedness and shared environmental effects. SNPs were modeled under assumption of additive effect, entered as number of minor alleles (0, 1, 2). For markers on chromosome X, genotypes for male participants who possessed one minor allele were set to two minor alleles for analysis. To account for genetic ancestry, the first 10 principal components from an EIGENSTRAT analysis were included as covariates (Price et al., 2006). Other covariates included in single SNP analyses were sex, age, birth year, generation (an indicator of whether an individual was a parent or child), a generation-by-age interaction, a generation-by-sex interaction, and a generation-by-birth-year interaction. We calculated the effective number of independent tests, accounting for LD patterns between the included markers in our sample, using the SimpleM method (Gao et al., 2008), which yielded an LD-inferred total of 485 effective independent tests, and therefore a Bonferroni-corrected significance threshold of .05/485 = .0001.
