AEon: A global genetic ancestry estimation tool

Abstract

BackgroundGenetic ancestry is a major confounding factor in genetic association studies, and it is essential to estimate and account for ancestry in genomic research. 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. ResultsAEon predicts an individuals fractional ancestral population membership, accounting for possible admixture. Unlike previous global ancestry estimation tools, 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. ConclusionsAEons turnkey design significantly reduces the time taken to estimate ancestry from VCFs without compromising accuracy compared to ADMIXTURE analysis, with a 4.8-fold decrease in runtime for a file with 10,000 sites and 100 individuals. AEon is available at github.com/GenomicRisk/aeon.