title: 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.
authors.affiliation: Department of Pediatrics and Department of Molecular and Human Genetics, U.S. Department of Agriculture/Agricultural Research Service, Children's Nutrition Research Center, Baylor College of Medicine, Houston, Texas 77030.
authors.forename: Yongtao
authors.initials: Y
authors.lastname: Guan
mesh_terms: D002896:Chromosomes, Human, Pair 6; D002898:Chromosomes, Human, Pair 8; D019143:Evolution, Molecular; D014644:Genetic Variation; D015894:Genome, Human; D023281:Genomics; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D008390:Markov Chains; D008800:Mexico; D008957:Models, Genetic; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012984:Software
keywords: admixture; haplotype; linkage disequilibrium (LD); local ancestry; two-layer clustering