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International Conference on Research in Computational Molecular Biology

RECOMB 2015: Research in Computational Molecular Biology pp 340–353Cite as

Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs

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Part of the Lecture Notes in Computer Science book series (LNBI,volume 9029)

Abstract

The genomes of remotely related individuals occasionally contain long segments that are Identical By Descent (IBD). Sharing of IBD segments has many applications in population and medical genetics, and it is thus desirable to study their properties in simulations. However, no current method provides a direct, efficient means to extract IBD segments from simulated genealogies. Here, we introduce computationally efficient approaches to extract ground-truth IBD segments from a sequence of genealogies, or equivalently, an ancestral recombination graph. Specifically, we use a two-step scheme, where we first identify putative shared segments by comparing the common ancestors of all pairs of individuals at some distance apart. This reduces the search space considerably, and we then proceed by determining the true IBD status of the candidate segments. Under some assumptions and when allowing a limited resolution of segment lengths, our run-time complexity is reduced from \(O(n^3\log n)\) for the naïve algorithm to \(O(n\log n)\), where \(n\) is the number of individuals in the sample.

Keywords

  • Identity by Descent
  • Ancestral Recombination Graphs
  • Population Genetics
  • Simulation

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  • DOI: 10.1007/978-3-319-16706-0_35
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Author information

Authors and Affiliations

  1. Department of Computer Science, Columbia University, New York, NY, 10027, USA

    Shuo Yang, Shai Carmi & Itsik Pe’er

  2. Department of Systems Biology, Columbia University, New York, NY, 10032, USA

    Itsik Pe’er

Authors
  1. Shuo Yang
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  2. Shai Carmi
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  3. Itsik Pe’er
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Correspondence to Itsik Pe’er .

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Editors and Affiliations

  1. National Center of Biotechnology Information, Bethesda, Maryland, USA

    Teresa M. Przytycka

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Yang, S., Carmi, S., Pe’er, I. (2015). Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs. In: Przytycka, T. (eds) Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science(), vol 9029. Springer, Cham. https://doi.org/10.1007/978-3-319-16706-0_35

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  • DOI: https://doi.org/10.1007/978-3-319-16706-0_35

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