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Research Project: Pediatric Clinical Nutrition

Location: Children's Nutrition Research Center

Title: Detecting structure of haplotypes and local ancestry

item GUAN, YONGTAO - Children'S Nutrition Research Center (CNRC)

Submitted to: Genetics
Publication Type: Review Article
Publication Acceptance Date: 12/31/2013
Publication Date: 3/1/2014
Citation: Guan, Y. 2014. Detecting structure of haplotypes and local ancestry. Genetics. 196(3):625-642.

Interpretive Summary:

Technical 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