Before commencing QTL analyses, genotypes at the polymorphic SNP probes on the HumanMethylation 450K array were compared to calls from the HumanOmniExpress genotyping array to confirm sample identity. All genome-wide SNP-methylation probe pairs were tested using the R package MatrixEQTL46. This package enables fast computation of QTLs by only saving those more significant than a pre-defined threshold (set to P = 0.0001 for these analyses). An additive linear model was fitted to test if the number of alleles (coded 0,1,2) predicted DNA methylation (beta value 0–100) at each site, including covariates for age, sex and the first two principal components from the genotype data to control for ethnicity differences. In addition, a brain bank covariate was also included for the adult datasets.
