Inferring ancestry in admixed populations using microarray probe intensities

Abstract

Numerous methods exist for inferring the ancestry mosaic of an admixed individual based on its genotypes and those of its ancestors. These methods rely on bialleic SNPs obtained from genotype calling algorithms, which classify each marker as belonging to one of four states (reference allele, alternate allele, heterozygous, or no call) based on probe hybridization intensity signals. We demonstrate that this conversion of probe intensities to discrete genotypes can lead to a loss of information and introduce errors via incorrect genotype calls.