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Efficient maximum likelihood pedigree reconstruction

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  • Cowell, Robert G.

Abstract

A simple and efficient algorithm is presented for finding a maximum likelihood pedigree using microsatellite (STR) genotype information on a complete sample of related individuals. The computational complexity of the algorithm is at worst (O(n32n)), where n is the number of individuals. Thus it is possible to exhaustively search the space of all pedigrees of up to thirty individuals for one that maximizes the likelihood. A priori age and sex information can be used if available, but is not essential. The algorithm is applied in a simulation study, and to some real data on humans.

Suggested Citation

  • Cowell, Robert G., 2009. "Efficient maximum likelihood pedigree reconstruction," Theoretical Population Biology, Elsevier, vol. 76(4), pages 285-291.
    • Handle: RePEc:eee:thpobi:v:76:y:2009:i:4:p:285-291
    DOI: 10.1016/j.tpb.2009.09.002
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    References listed on IDEAS

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    1. A. P. Dawid & J. Mortera & V. L. Pascali & D. Van Boxel, 2002. "Probabilistic Expert Systems for Forensic Inference from Genetic Markers," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 29(4), pages 577-595, December.
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    Cited by:

    1. Anderson, Eric C. & Ng, Thomas C., 2016. "Bayesian pedigree inference with small numbers of single nucleotide polymorphisms via a factor-graph representation," Theoretical Population Biology, Elsevier, vol. 107(C), pages 39-51.
    2. Cowell, Robert G., 2013. "A simple greedy algorithm for reconstructing pedigrees," Theoretical Population Biology, Elsevier, vol. 83(C), pages 55-63.
    3. Almudevar, Anthony, 2016. "An information theoretic approach to pedigree reconstruction," Theoretical Population Biology, Elsevier, vol. 107(C), pages 52-64.
    4. 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.
    5. 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.
    6. Riester, Markus & Stadler, Peter F. & Klemm, Konstantin, 2010. "Reconstruction of pedigrees in clonal plant populations," Theoretical Population Biology, Elsevier, vol. 78(2), pages 109-117.
    7. 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.

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