Consider a GWAS performed in an EA study. Association results are available for d variants, with p-values p1e,…,pde and effect size estimates b1e,…,bde. Assume that almost all variants are also available in a GWAS of individuals with admixed ancestry, such as the HCHS/SOL, with corresponding p-values and effect size estimates p1a,…,pda, and b1a,…,bda. Based on the information from both EA and HCHS/SOL GWASs, we can perform fixed-effects meta-analysis (META) to produce meta-analytic p-values and effect sizes p1m,…,pdm, and b1m,…,bdm. We can also perform generalization analysis (Sofer et ah, 2017a), to test the composite null hypothesis that is rejected if an association exists in both the EA population and in the HCHS/SOL study, and get r-values for these variants r1m,…,rdm.
