As shown in Fig. 2, polygenic score performance was worst among African ancestry samples. The median effect size of polygenic scores in African ancestry samples was only 42% that of matched European ancestry samples (t = −5.97, df = 24, p = 3.7 × 10−6). Relative to matched European ancestry samples, performance was also lower in South (60%) and East Asian (95%) samples, but not significantly so (see top right portion of Fig. 2). In sum, an expectation of poorer polygenic score performance in non-European ancestry populations seems reasonable given these data. Attenuation of predictive performances is likely to be most extreme in samples of African ancestry, consistent with, on average, greater genetic distance between European and African ancestry populations, than between European and other ancestry populations28,43.
