On the Inference of Ancestries in Admixed Populations

  • Sriram Sankararaman
  • Gad Kimmel
  • Eran Halperin
  • Michael I. Jordan
Conference paper

DOI: 10.1007/978-3-540-78839-3_37

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4955)
Cite this paper as:
Sankararaman S., Kimmel G., Halperin E., Jordan M.I. (2008) On the Inference of Ancestries in Admixed Populations. In: Vingron M., Wong L. (eds) Research in Computational Molecular Biology. RECOMB 2008. Lecture Notes in Computer Science, vol 4955. Springer, Berlin, Heidelberg

Abstract

Inference of ancestral information in recently admixed populations, in which every individual is composed of a mixed ancestry (e.g., African Americans in the US), is a challenging problem. Several previous model-based approaches have used hidden Markov models (HMM) to model the problem, however, the Markov Chain Monte Carlo (MCMC) algorithms underlying these models converge slowly on realistic datasets. While retaining the HMM as a model, we show that a combination of an accurate fast initialization and a local hill-climb in likelihood results in significantly improved estimates of ancestry. We studied this approach in two scenarios—the inference of locus-specific ancestries in a population that is assumed to originate from two unknown ancestral populations, and the inference of allele frequencies in one ancestral population given those in another.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Sriram Sankararaman
    • 1
  • Gad Kimmel
    • 1
    • 2
  • Eran Halperin
    • 2
  • Michael I. Jordan
    • 1
    • 3
  1. 1.Computer Science DivisionUniversity of CaliforniaBerkeleyUSA
  2. 2.International Computer Science InstituteBerkeleyUSA
  3. 3.Department of StatisticsUniversity of CaliforniaBerkeleyUSA

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