Extended Data Fig. 1: Genetic histories and polygenic prediction in the MXB.
From: Mexican Biobank advances population and medical genomics of diverse ancestries
A) Admixture histories of individuals in different cultural regions using an AdmixtureBayes approach. Here the admixture graph with the highest posterior probability is shown, inferred using genomic regions with ancestries from the Americas. Internal inferred ancestral node populations are colored grey. The tree is rooted using the Han as an outgroup. B) Trait variance explained and p-value threshold of best predictive polygenic score using MXB-GWAS-based or UKB-GWAS-based prediction. Polygenic scores were computed using SNPs significant at five different p-value thresholds (0.1, 0.01, 0.001, 0.00001, 10−8). A linear null model was created for each trait including age, sex and 10 principal components as covariates. A second polygenic score model was created adding the polygenic score to the null model. We computed the R2 of the polygenic score by taking the difference between the R2 of the polygenic score model and the R2 of the null model. The maximum R2 was used to the pick the p-value threshold for the best predictive polygenic score shown in the table.
