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Haplotype Inference for Pedigrees with Few Recombinations

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Bioinformatics Research and Applications (ISBRA 2016)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9683))

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Abstract

Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with n individuals genotyped at every site, a set of Mendelian-consistent haplotypes that have the minimum number of recombinations. This is an \(\mathsf {NP}\)-hard problem and some pedigrees can have thousands of individuals and hundreds of thousands of sites.

This paper formulates this problem as a optimization on a graph and introduces a tailored algorithm with a running time of \(O(n^{(k+2)}m^{6k})\) for n individuals, m sites, and k recombinations. Since there are generally only 1-2 recombinations per chromosome in each meiosis, k is small enough to make this algorithm practically relevant.

Full Manuscript. Pre-print publication of the full manuscript is available at arXiv [10].

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Acknowledgments

BK thanks M. Mnich at the Cluster of Excellence, Saarland University, Saarbrücken, Germany for critical reading of the manuscript. BK thanks arXiv for pre-print publication of the full manuscript [10].

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Authors and Affiliations

  1. Intrepid Net Computing, Dillon, MT, USA

    B. Kirkpatrick

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  1. B. Kirkpatrick
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Correspondence to B. Kirkpatrick .

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Editors and Affiliations

  1. Dept. of Computer Science, Georgia State University, Atlanta, Georgia, USA

    Anu Bourgeois

  2. Centre for Disease Control & Prevention, Atlanta, Georgia, USA

    Pavel Skums

  3. Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong

    Xiang Wan

  4. Georgia State University, Atlanta, Georgia, USA

    Alex Zelikovsky

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Kirkpatrick, B. (2016). Haplotype Inference for Pedigrees with Few Recombinations. In: Bourgeois, A., Skums, P., Wan, X., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2016. Lecture Notes in Computer Science(), vol 9683. Springer, Cham. https://doi.org/10.1007/978-3-319-38782-6_23

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  • DOI: https://doi.org/10.1007/978-3-319-38782-6_23

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-38781-9

  • Online ISBN: 978-3-319-38782-6

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