Bayesian Multi-Population Haplotype Inference via a Hierarchical Dirichlet Process Mixture

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Bayesian Multi-Population Haplotype Inference via a Hierarchical Dirichlet Process Mixture (2006)

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by Eric P. Xing , Kyung-Ah Sohn , Michael I. Jordan , Yee-Whye Teh

Venue:	In Proceedings of the 23st International Conference on Machine Learning
Citations:	12 - 6 self

BibTeX

@INPROCEEDINGS{Xing06bayesianmulti-population,
    author = {Eric P. Xing and Kyung-Ah Sohn and Michael I. Jordan and Yee-Whye Teh},
    title = {Bayesian Multi-Population Haplotype Inference via a Hierarchical Dirichlet Process Mixture},
    booktitle = {In Proceedings of the 23st International Conference on Machine Learning},
    year = {2006},
    pages = {1049--1056},
    publisher = {ACM Press}
}

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Abstract

Uncovering the haplotypes of single nucleotide polymorphisms and their population demography is essential for many biological and medical applications. Methods for haplotype inference developed thus far---including methods based on coalescence, finite and infinite mixtures, and maximal parsimony--- ignore the underlying population structure in the genotype data. As noted by Pritchard (2001), di#erent populations can share certain portion of their genetic ancestors, as well as have their own genetic components through migration and diversification. In this paper, we address the problem of multipopulation haplotype inference. We capture cross-population structure using a nonparametric Bayesian prior known as the hierarchical Dirichlet process (HDP) (Teh et al., 2006), conjoining this prior with a recently developed Bayesian methodology for haplotype phasing known as DP-Haplotyper (Xing et al., 2004). We also develop an e#cient sampling algorithm for the HDP based on a two-level nested Polya urn scheme. We show that our model outperforms extant algorithms on both simulated and real biological data.

Keyphrases

bayesian multi-population haplotype inference hierarchical dirichlet process mixture extant algorithm medical application hierarchical dirichlet process real biological data genotype data haplotype inference cross-population structure genetic ancestor di erent population single nucleotide polymorphism two-level nested polya urn scheme genetic component multipopulation haplotype inference infinite mixture population demography maximal parsimony bayesian methodology population structure share certain portion

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