RT Journal
A1 Sundquist, Andreas
A1 Fratkin, Eugene
A1 Do, Chuong B.
A1 Batzoglou, Serafim
T1 Effect of genetic divergence in identifying ancestral origin using HAPAA
JF Genome Research 
JO Genome Research 
YR 2008 
FD April 01 
VO 18 
IS 4 
SP 676 
OP 682 
DO 10.1101/gr.072850.107 
UL http://genome.cshlp.org/content/18/4/676.abstract 
AB The genome of an admixed individual with ancestors from isolated populations is a mosaic of chromosomal blocks, each following the statistical properties of variation seen in those populations. By analyzing polymorphisms in the admixed individual against those seen in representatives from the populations, we can infer the ancestral source of the individual’s haploblocks. In this paper we describe a novel approach for ancestry inference, HAPAA (HMM-based analysis of polymorphisms in admixed ancestries), that models the allelic and haplotypic variation in the populations and captures the signal of correlation due to linkage disequilibrium, resulting in greatly improved accuracy. We also introduce a methodology for evaluating the effect of genetic divergence between ancestral populations and time-to-admixture on inference accuracy. Using HAPAA, we explore the limits of ancestry inference in closely related populations.