Single haplotype admixture models using large scale HLA genotype frequencies to reproduce human admixture

The Human Leukocyte Antigen (HLA) is the most polymorphic region in humans. Anthropologists use HLA to trace populations9 migration and evolution. However, recent admixture between populations masks the ancestral haplotype frequency distribution. We present an HLA-based method based on high-resolution HLA haplotype frequencies to resolve population admixture using a non-negative matrix factorization formalism and validated using haplotype frequencies from 56 populations. The result is a minimal set of original populations decoding roughly 90% of the total variance in the studied admixtures. These original populations agree with the geographical distribution, phylogenies and recent admixture events of the studied groups. With the growing population of multi-ethnic individuals, the matching process for stem-cell and solid organ transplants is becoming more challenging. The presented algorithm provides a framework that facilitates the breakdown of highly admixed populations into original groups, which can be used to better match the rapidly growing population of multi-ethnic individuals worldwide.