Detecting structure of haplotypes and local ancestry.
Abstract
We present a two-layer hidden Markov model to detect the structure of haplotypes for
unrelated individuals. This allows us to model two scales of linkage disequilibrium
(one within a group of haplotypes and one between groups), thereby taking advantage
of rich haplotype information to infer local ancestry of admixed individuals. Our
method outperforms competing state-of-the-art methods, particularly for regions of
small ancestral track lengths. Applying our method to Mexican samples in HapMap3,
we found two regions on chromosomes 6 and 8 that show significant departure of local
ancestry from the genome-wide average. A software package implementing the methods
described in this article is freely available at http://bcm.edu/cnrc/mcmcmc.
Type
Journal articleSubject
Chromosomes, Human, Pair 6Chromosomes, Human, Pair 8
Humans
Markov Chains
Genomics
Evolution, Molecular
Phylogeny
Haplotypes
Linkage Disequilibrium
Polymorphism, Single Nucleotide
Genome, Human
Models, Genetic
Software
Mexico
Genetic Variation
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https://hdl.handle.net/10161/17276Published Version (Please cite this version)
10.1534/genetics.113.160697Publication Info
Guan, Yongtao (2014). Detecting structure of haplotypes and local ancestry. Genetics, 196(3). pp. 625-642. 10.1534/genetics.113.160697. Retrieved from https://hdl.handle.net/10161/17276.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Yongtao Guan
Assistant Professor of Biostatistics & Bioinformatics

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