Chunk #67 — ONLINE METHODS — Enrichment of genes in associated loci in known and novel pathways — Data-Driven Expression-Prioritized Integration for Complex Traits (DEPICT) analysis
identifying the most likely causal gene(s) at a given locus (see Supplementary Note for a more detailed description of DEPICT). In order to run DEPICT, we first clumped the summary statistics from the meta-analysis using 500kb flanking regions, r2>0.1, and excluded SNPs with P≥5×10−8, which resulted in 628 SNPs. We then mapped genes to each of the 628 best-associated SNPs. For a given SNP, this was accomplished by including all genes that resided within LD r2>0.5 boundaries of that SNP, and always including the nearest gene, to its locus gene set. We used a locus definition that was calibrated using the GWAS data for height levels presented in this paper and optimized capture of known monogenic genes for those traits. We merged overlapping loci, and excluded loci that mapped near or within the major histocompatibility complex locus (chromosome 6, location: 20 to 40 Mb), which resulted in a list of 566 non-overlapping loci that were used as input to DEPICT. HapMap Project Phase II CEU genotype data was used for all LD calculations.
