The Partners HealthCare Biobank included individuals from diverse populations. We used the 1KG samples as a population reference panel to infer the ancestry of Partners Biobank participants. Specifically, we computed principal components (PCs) of the genotype data in all the 1KG samples, and trained a random forest model using the top 4 PCs on the super population labels (African [AFR], American [AMR], East Asian [EAS], European [EUR], and South Asian [SAS]), in which EUR (N = 503) included TSI, IBS, GBR, CEU, and FIN subpopulations. The random forest model was then applied to the Partners Biobank participants, and identified 19,136 unrelated subjects (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hat \pi \, < \, 0.2$$\end{document}π^<0.2) with European ancestry.
