Chunk #57 — Methods — Statistical methods. — GWAS in BBJ.

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Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements.

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As described in the previous section, we held out 5,000 randomly selected individuals for the PRS analysis and performed GWAS on the remaining individuals (sample sizes in Supplementary Tables 16 and 17). GWAS was conducted with PLINK2 using the same imputed dosages as used in the PRS analysis. For quantitative traits, normalized residuals were analyzed by linear regression. For diseases, affection status was analyzed by logistic regression using age, sex and the top 10 genotype PCs as covariates.