Motivation Measuring genetic diversity is an important problem because increasing genetic diversity is key to making new genetic discoveries, while also being a major source of confounding to be aware of in genetics studies. Results Using the UK Biobank data, a prospective cohort study with deep genetic and phenotypic data collected on almost 500,000 individuals from across the United Kingdom, we carefully define 21 distinct ancestry groups from all four corners of the world. These ancestry groups can serve as a global reference of worldwide populations, with a handful of applications. Here we develop a method that uses allele frequencies and principal components derived from these ancestry groups to effectively measure ancestry proportions from allele frequencies of any genetic dataset. Availability This method is implemented as function snp_ancestry_summary as part of R package bigsnpr. Contact florian.prive.21@gmail.com
Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics