AEon: A global genetic ancestry estimation tool

Abstract

AbstractGenetic ancestry is a significant confounding factor in genetic association studies. It is therefore essential to estimate and account for ancestry if we hope to translate genomic research into equitable clinical utility for ethnically diverse populations. Despite this importance, accurate ancestry information is difficult to obtain, and existing methods to estimate ancestry are not designed for modern sequencing data. This methodological gap hinders the integration of genetic ancestry information in modern research, and limits progress in finding the genetic determinants of disease in diverse populations. To address this gap we present AEon, a probabilistic model-based global ancestry estimation tool, ready for use on modern genomic data. AEon predicts fractional population membership, accounting for possible admixture. Unlike previous global ancestry estimation tools such as EIGENSTRAT and ADMIXTURE, AEon takes input directly from a VCF/BCF, includes default training data based on the 26 reference populations of the 1000 Genomes Project, and produces visualisation aids and diagnostics to complement data output. AEon’s turnkey design significantly reduces the time taken to estimate ancestry from VCFs, without compromising on accuracy compared to ADMIXTURE analysis. AEon is available atgithub.com/GenomicRisk/aeon.