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Multiple-Ancestor Localization for Recently Admixed Individuals

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Algorithms in Bioinformatics (WABI 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9289))

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Abstract

Inference of ancestry from genetic data is a fundamental problem in computational genetics, with wide applications in human genetics and population genetics. The treatment of ancestry as a continuum instead of a categorical trait has been recently advocated in the literature. Particularly, it was shown that a European individual’s geographic coordinates of origin can be determined up to a few hundred kilometers of error using spatial ancestry inference methods. Current methods for the inference of spatial ancestry focus on individuals for whom all ancestors originated from the same geographic location.    In this work we develop a spatial ancestry inference method that aims at inferring the geographic coordinates of ancestral origins of recently admixed individuals, i.e. individuals whose recent ancestors originated from multiple locations. Our model is based on multivariate normal distributions integrated into a two-layered Hidden Markov Model, designed to capture both long-range correlations between SNPs due to the recent mixing and short-range correlations due to linkage disequilibrium. We evaluate the method on both simulated and real European data, and demonstrate that it achieves accurate results for up to three generations of admixture. Finally, we discuss the challenges of spatial inference for older admixtures and suggest directions for future work.

Y. Margalit and Y. Baran—Contributed equally to this work.

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Acknowledgements

E.H. is a faculty fellow of the Edmond J. Safra Center at Tel Aviv University. Y.B. was supported in part by a fellowship from the Edmond J. Safra Center for Bioinformatics at Tel-Aviv University. E.H. and Y.B. were also supported in part by the United States Israel Binational Science Foundation (grant 2012304), and by the National Science Foundation (grant III-1217615), and by the Israeli Science Foundation (grant 989/08). E.H, Y.B, and Y.M were partially supported by the German-Israeli Foundation (grant 1094-33.2/ 2010). E.H was also supported by the Israel Science Foundation (grant 1425/13).

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Authors and Affiliations

  1. The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel

    Yaron Margalit, Yael Baran & Eran Halperin

  2. Department of Molecular Microbiology and Biotechnology, Tel-Aviv University, Tel Aviv, Israel

    Eran Halperin

  3. International Computer Science Institute, Berkeley, CA, 94704, USA

    Eran Halperin

Authors
  1. Yaron Margalit
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  2. Yael Baran
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  3. Eran Halperin
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Correspondence to Eran Halperin .

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Editors and Affiliations

  1. University of Maryland, College Park, Maryland, USA

    Mihai Pop

  2. University of Lille, Lille, France

    Hélène Touzet

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Margalit, Y., Baran, Y., Halperin, E. (2015). Multiple-Ancestor Localization for Recently Admixed Individuals. In: Pop, M., Touzet, H. (eds) Algorithms in Bioinformatics. WABI 2015. Lecture Notes in Computer Science(), vol 9289. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-48221-6_9

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  • DOI: https://doi.org/10.1007/978-3-662-48221-6_9

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