Detecting structure of haplotypes and local ancestry.
Journal Article (Journal Article)
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.
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Duke Authors
Cited Authors
- Guan, Y
Published Date
- March 2014
Published In
Volume / Issue
- 196 / 3
Start / End Page
- 625 - 642
PubMed ID
- 24388880
Pubmed Central ID
- PMC3948796
Electronic International Standard Serial Number (EISSN)
- 1943-2631
Digital Object Identifier (DOI)
- 10.1534/genetics.113.160697
Language
- eng
Conference Location
- United States