Partitioned heritability analysis by stratified LDSC

To independently validate the gene-set specific PRS analysis and account for potential confounding factors (e.g., numbers of SNPs) in PRS analysis, we performed a sLDSC analysis (Bulik-Sullivan et al., 2015; Finucane et al., 2015) for different gene sets using PGC SCZ wave_3 GWAS summary statistics. For calculating partitioned LD scores, a 20 kb window size (similar to what was used in Figures 2A and 2B) was applied to all genes within the ten gene sets. For partitioned heritability (h²), we used baseline model LD scores from the 1,000 Genomes project European cohort (1000G_EUR_Phase3_baseline v2.2). Finally, we used the cell-type group analysis algorithm as described in the LDSC documentation (Bulik-Sullivan et al., 2015; Finucane et al., 2015) to estimate the proportion of heritability and identify the enrichment of h² in each gene set.