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Chunk #48 — STAR★METHODS — QUANTIFICATION AND STATISTICAL ANALYSIS — SNP-based heritability and Genetic Correlation estimation

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Trans-ancestry genome-wide study of depression identifies 697 associations implicating cell types and pharmacotherapies.
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SNP-based heritability was estimated using SBayesS14 assuming lifetime risk of 15% for comparison with previous work. SBayesS was also used to provide estimates of polygenicity and selection. We estimated genetic correlations with other traits using LDSC. First, we searched for COJO-selected SNPs in the OpenGWAS catalogue70 at the standard lookup threshold (p < 1 × 10−5) and fetched full summary statistics for phenotypes returned by the query. We then estimated LD Score genetic correlations between each phenotype and MD,44 using false discovery rate (FDR) with q < 0.05 to correct for multiple testing. We then compared our results with previous MD GWAS analyses.