Detecting structure of haplotypes and local ancestry.
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.
SubjectChromosomes, Human, Pair 6
Chromosomes, Human, Pair 8
Polymorphism, Single Nucleotide
Published Version (Please cite this version)10.1534/genetics.113.160697
Publication InfoGuan, 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.
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