Brain related SNP weights (multivariate GReX) for TWAS were derived from GTEx v7 and PsychENCODE, whilst whole blood weights were also obtained from GTEx v7 (Gandal et al., 2018; Gusev et al., 2016). The GTEx v7 SNP weights comprise data from twelve different brain regions – with the sample sizes of the cohorts utilised for GReX estimation as follows: amygdala (N = 88), anterior cingulate cortex (N = 109), caudate (N = 144), cerebellar hemisphere (N = 125), cerebellum (N = 154), cortex (N = 136), frontal cortex (N = 136), hippocampus (N = 111), hypothalamus (N = 108), nucleus accumbens (N = 130), putamen (N = 80) and substantia nigra (N = 80). HapMap3 SNPs from the 1000 genomes phase 3 European reference panel were used as a linkage disequilibrium (LD) estimate, to correspond with how the weights were calculated with those same HapMap3 SNPs. The TWAS using whole blood weights utilised the same LD reference strategy, with 369 GTEx v7 participants in these models. Frontal or cerebral cortex tissue from the larger PsychENCODE cohort was also utilised in
