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A simple greedy algorithm for reconstructing pedigrees

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  • Cowell, Robert G.

Abstract

This paper introduces a simple greedy algorithm for searching for high likelihood pedigrees using micro-satellite (STR) genotype information on a complete sample of related individuals. The core idea behind the algorithm is not new, but it is believed that putting it into a greedy search setting, and specifically the application to pedigree learning, is novel. The algorithm does not require age or sex information, but this information can be incorporated if desired. The algorithm is applied to human and non-human genetic data and in a simulation study.

Suggested Citation

  • Cowell, Robert G., 2013. "A simple greedy algorithm for reconstructing pedigrees," Theoretical Population Biology, Elsevier, vol. 83(C), pages 55-63.
    • Handle: RePEc:eee:thpobi:v:83:y:2013:i:c:p:55-63
    DOI: 10.1016/j.tpb.2012.11.002
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    1. Katta G. Murty, 1968. "Letter to the Editor—An Algorithm for Ranking all the Assignments in Order of Increasing Cost," Operations Research, INFORMS, vol. 16(3), pages 682-687, June.
    2. Almudevar, Anthony & LaCombe, Jason, 2012. "On the choice of prior density for the Bayesian analysis of pedigree structure," Theoretical Population Biology, Elsevier, vol. 81(2), pages 131-143.
    3. Cowell, Robert G., 2009. "Efficient maximum likelihood pedigree reconstruction," Theoretical Population Biology, Elsevier, vol. 76(4), pages 285-291.
    4. Eugene L. Lawler, 1972. "A Procedure for Computing the K Best Solutions to Discrete Optimization Problems and Its Application to the Shortest Path Problem," Management Science, INFORMS, vol. 18(7), pages 401-405, March.
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    Cited by:

    1. Sheehan, Nuala A. & Bartlett, Mark & Cussens, James, 2014. "Improved maximum likelihood reconstruction of complex multi-generational pedigrees," Theoretical Population Biology, Elsevier, vol. 97(C), pages 11-19.
    2. Sun, M. & Jobling, M.A. & Taliun, D. & Pramstaller, P.P. & Egeland, T. & Sheehan, N.A., 2016. "On the use of dense SNP marker data for the identification of distant relative pairs," Theoretical Population Biology, Elsevier, vol. 107(C), pages 14-25.

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