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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

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Chicago
ICMJE
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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