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.
journal_name
Geneticsjournal_title
Geneticsauthors
Guan Ydoi
10.1534/genetics.113.160697subject
Has Abstractpub_date
2014-03-01 00:00:00pages
625-42issue
3eissn
0016-6731issn
1943-2631pii
genetics.113.160697journal_volume
196pub_type
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