Retracing Human Genetic Histories and Natural Selection Using Precise Local Ancestry Inference

Abstract

In an increasingly diverse world, including admixed individuals in genomic studies is imperative for equity and portability. A crucial first step is precise local ancestry inference (LAI). We have developed Orchestra, a LAI model with unprecedented accuracy, and trained on over 10,000 single-origin individuals from 35 worldwide populations. We employed Orchestra to delve into genetic relationships and demographic histories, with a focus on Latin Americans, a prime example of admixture, and the Ashkenazi Jewish, whose origins have long been debated. Finally, Orchestra enabled us to map signatures of selection, notably identifying trace Scandinavian ancestry in British samples and unveiling an immune-rich region linked to respiratory infections. Our work advances the field of LAI and holds promise for improvements in future applications for admixed populations.

Optimization of Multi-Ancestry Polygenic Risk Score Disease Prediction Models

“…Next, we proceeded to add ancestry information to the PRS algorithms. We applied an iterative approach, settling on the use of global ancestry information as deduced by Orchestra 77 in addition to the first four genotyping principal components (PCs) (Fig. 3).…”