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Genetics. 2014 Mar;196(3):625-42. doi: 10.1534/genetics.113.160697. Epub 2014 Jan 3.

Detecting structure of haplotypes and local ancestry.

Author information

1
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.

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.

KEYWORDS:

admixture; haplotype; linkage disequilibrium (LD); local ancestry; two-layer clustering

PMID:
24388880
PMCID:
PMC3948796
DOI:
10.1534/genetics.113.160697
[Indexed for MEDLINE]
Free PMC Article

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