We tested the robustness of our DEPICT results using the bioinformatics tools MAGMA43 and PANTHER44,45. For MAGMA, we used the “multi=snp-wise” option, mapping a SNP to a gene if it resides within the gene boundaries or 5kb of either endpoint. We estimated LD using a reference panel of Europeans in 1000 Genomes phase 3, and we defined a gene as significant if its joint P value falls below the threshold corresponding to FDR < 0.05 (Supplementary Table 29). For PANTHER, we used the binomial overrepresentation test with the DEPICT-prioritized genes as input (Supplementary Table 30).
