Enhanced Methods for Local Ancestry Assignment in Sequenced Admixed Individuals

Inferring the ancestry at each locus in the genome of recently admixed individuals (e.g., Latino Americans) plays a major role in medical and population genetic inferences, ranging from finding disease-risk loci, to inferring recombination rates, to mapping missing contigs in the human genome. Although many methods for local ancestry inference have been proposed, most are designed for use with genotyping arrays and fail to make use of the full spectrum of data available from sequencing. In addition, current haplotype-based approaches are very computationally demanding, requiring large computational time for moderately large sample sizes. Here we present new methods for local ancestry inference that leverage continent-specific variants (CSVs) to attain increased performance over existing approaches in sequenced admixed genomes. A key feature of our approach is that it incorporates the admixed genomes themselves jointly with public datasets, such as 1000 Genomes, to improve the accuracy of CSV calling. We use simulations to show that our approach attains accuracy similar to widely used computationally intensive haplotype-based approaches with large decreases in runtime. Most importantly, we show that our method recovers comparable local ancestries, as the 1000 Genomes consensus local ancestry calls in the real admixed individuals from the 1000 Genomes Project. We extend our approach to account for low-coverage sequencing and show that accurate local ancestry inference can be attained at low sequencing coverage. Finally, we generalize CSVs to sub-continental population-specific variants (sCSVs) and show that in some cases it is possible to determine the sub-continental ancestry for short chromosomal segments on the basis of sCSVs.Author Summary: Advances in sequencing technologies are dramatically changing the volume and type of data collected in genetic studies. Although most genetic studies so far have focused on individuals of European ancestry, recent studies are increasingly being performed in individuals of admixed ancestry (i.e., with recent ancestors from multiple continents, e.g., Latino Americans). A key component in such studies is the accurate inference of continental ancestry at each segment in the genome of these individuals. In this work we present accurate and robust methods that use continent-specific variants (i.e., genetic variants observed only in individuals of a given continent), now readily accessible through sequencing technology, to perform extremely fast and accurate inference of the ancestral origin of each genomic segment in recently admixed individuals.