Each of the cohorts carried out genotype and expression data pre-processing, PGS calculation and cis-eQTL-, trans-eQTL- and eQTS-mapping following the steps outlined in the online analysis plans, specific for each platform (https://github.com/molgenis/systemsgenetics/wiki/eQTL-mapping-analysis-cookbook; https://github.com/molgenis/systemsgenetics/wiki/eQTL-mapping-analysis-cookbook-for-RNA-seq-data; https://github.com/molgenis/systemsgenetics/wiki/QTL-mapping-analysis-cookbook-for-Affymetrix-expression-arrays), or with slight alterations as described in Supplementary Table 1 and the Supplementary Note. All but one cohort (Framingham Heart Study), included unrelated individuals into the analysis.
