Guided by rigorous method comparisons conducted by PGC members 51,75, p-values quantifying the degree of association of genes and gene sets with BD were generated using MAGMA (v1.06) 51. We used ENSEMBL gene coordinates for 18,172 genes giving a Bonferroni corrected P-value threshold of 2.8×10−6. Joint multi-SNP LD-adjusted gene-level p-values were calculated using SNPs 35 kb upstream to 10 kb downstream, adjusting for LD using 1,000 Genomes Project (Phase 3 v5a, MAF ≥ 0.01, European-ancestry subjects) 76. Gene sets were compiled from multiple sources. Competitive gene set tests were conducted correcting for gene size, variant density, and LD within and between genes. The pathway map (Supplementary Figure 5) was constructed using the kernel generative topographic mapping algorithm (k-GTM) as described by 77.
