Given this background, we performed a systematic evaluation of polygenic prediction accuracy across 17 quantitative anthropometric and blood panel traits and five disease endpoints in British and Japanese individuals23,57,58 by performing GWAS with the exact same sample sizes in each population. We symmetrically demonstrate that prediction accuracy is consistently higher with GWAS summary statistics from ancestry-matched summary statistics (Figure 4, Supplementary Figures 2–6). Keeping in mind issues of comparability described above, we note that BBJ is a hospital-based disease-ascertained cohort, whereas UKBB is a healthier than average59 population-based cohort; thus, differences in observed heritability among these cohorts (rather than among populations) due to differences in phenotype precision likely explain lower prediction accuracy from the BBJ GWAS summary statistics for anthropometric and blood panel traits, but higher prediction accuracy for five ascertained diseases (Supplementary Table 2). Indeed, other East Asian studies have estimated higher heritability for some quantitative traits than BBJ using the same methods, such as for height (h2 = 0.48±0.04 in Chinese women60). Some statistical fluctuations in the relative differences in prediction accuracy across populations are likely driven by
