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

Full Text

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


  • eng

Conference Location

  • United States