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Published online before print March 18, 2008, 10.1101/gr.072850.107
Genome Res. 18:676-682, 2008
©2008 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/08 $5.00
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RECOMB Special/Methods

Effect of genetic divergence in identifying ancestral origin using HAPAA

Andreas Sundquist1, Eugene Fratkin1, Chuong B. Do, and Serafim Batzoglou2

Department of Computer Science, Stanford University, Stanford, California 94305, USA

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.

1 These authors contributed equally to the work.

2 Corresponding author.

E-mail serafim{at}cs.stanford.edu; fax (650) 725-1449.

[HAPAA is available at http://hapaa.stanford.edu.]

Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.072850.107.


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