J. Comput. Biol. - Ancestry inference in complex admixtures via variable-length Markov chain linkage models.

Tópicos

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Resumo

Inferring the ancestral origin of chromosomal segments in admixed individuals is key for genetic applications, ranging from analyzing population demographics and history, to mapping disease genes. Previous methods addressed ancestry inference by using either weak models of linkage disequilibrium, or large models that make explicit use of ancestral haplotypes. In this paper we introduce ALLOY, an efficient method that incorporates generalized, but highly expressive, linkage disequilibrium models. ALLOY applies a factorial hidden Markov model to capture the parallel process producing the maternal and paternal admixed haplotypes, and models the background linkage disequilibrium in the ancestral populations via an inhomogeneous variable-length Markov chain. We test ALLOY in a broad range of scenarios ranging from recent to ancient admixtures with up to four ancestral populations. We show that ALLOY outperforms the previous state of the art, and is robust to uncertainties in model parameters.

Resumo Limpo

infer ancestr origin chromosom segment admix individu key genet applic rang analyz popul demograph histori map diseas gene previous method address ancestri infer use either weak model linkag disequilibrium larg model make explicit use ancestr haplotyp paper introduc alloy effici method incorpor general high express linkag disequilibrium model alloy appli factori hidden markov model captur parallel process produc matern patern admix haplotyp model background linkag disequilibrium ancestr popul via inhomogen variablelength markov chain test alloy broad rang scenario rang recent ancient admixtur four ancestr popul show alloy outperform previous state art robust uncertainti model paramet

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