Detecting structure of haplotypes and local ancestry.
Publication
, Journal Article
Guan, Y
Published in: Genetics
March 2014
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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Published In
Genetics
DOI
EISSN
1943-2631
ISSN
0016-6731
Publication Date
March 2014
Volume
196
Issue
3
Start / End Page
625 / 642
Related Subject Headings
- Software
- Polymorphism, Single Nucleotide
- Phylogeny
- Models, Genetic
- Mexico
- Markov Chains
- Linkage Disequilibrium
- Humans
- Haplotypes
- Genomics
Citation
APA
Chicago
ICMJE
MLA
NLM
Guan, Y. (2014). Detecting structure of haplotypes and local ancestry. Genetics, 196(3), 625–642. https://doi.org/10.1534/genetics.113.160697
Guan, Yongtao. “Detecting structure of haplotypes and local ancestry.” Genetics 196, no. 3 (March 2014): 625–42. https://doi.org/10.1534/genetics.113.160697.
Guan Y. Detecting structure of haplotypes and local ancestry. Genetics. 2014 Mar;196(3):625–42.
Guan, Yongtao. “Detecting structure of haplotypes and local ancestry.” Genetics, vol. 196, no. 3, Mar. 2014, pp. 625–42. Epmc, doi:10.1534/genetics.113.160697.
Guan Y. Detecting structure of haplotypes and local ancestry. Genetics. 2014 Mar;196(3):625–642.
Published In
Genetics
DOI
EISSN
1943-2631
ISSN
0016-6731
Publication Date
March 2014
Volume
196
Issue
3
Start / End Page
625 / 642
Related Subject Headings
- Software
- Polymorphism, Single Nucleotide
- Phylogeny
- Models, Genetic
- Mexico
- Markov Chains
- Linkage Disequilibrium
- Humans
- Haplotypes
- Genomics