Using Allele Sharing Distance for Detecting Human Population Stratification

There is a long history of using allele sharing distance (ASD) and closely related metrics for population stratification analysis. However, the theory for this practical usage has not been reported. In this paper, we describe the theoretical background for using ASD on single nucleotide polymorphism (SNP) genetic data for human population stratification analysis. In showing the proof, we lay the ground work for a general distance-based method for classifying subpopulations using SNPs and ASD. We also show its relation to other closely related distance metrics using HapMap Phase I SNP data.