PRS-CS138 was used to apply continuous shrinkage priors to the effect sizes from depression GWAS summary statistics. A European LD reference panel provided by the developers of PRS-CS was utilized (https://github.com/getian107/PRScs), which draws from the 1000 Genomes Project data. The following PRS-CS default settings were used: parameter a in the γ-γ prior=1, parameter b in the γ-γ prior=0.5, MCMC iterations=1,000, number of bum-in iterations=500, and thinning of the Markov chain factor=5. The global shrinkage parameter phi was set using a fully Bayesian determination method. Individual-level DEP-PRS were calculated using Plink v2.0139. The associations between scaled (mean=0, SD=1) DEP-PRS and 15 scaled (mean=0, SD=1) neurocognitive phenotypes in the PNC were assessed using linear regression of phenotypes on DEP-PRS.
