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k-Recombination haplotype inference in pedigrees

Published: 22 May 2005 Publication History

Abstract

Haplotyping under the Mendelian law of inheritance on pedigree genotype data is studied. Because genetic recombinations are rare, research has focused on Minimum Recombination Haplotype Inference (MRHI), i.e. finding the haplotype configuration consistent with the genotype data having the minimum number of recombinations. We focus here on the more realistic k-MRHI, which has the additional constraint that the number of recombinations on each parent-offspring pair is at most k.
Although k-MRHI is NP-hard even for k = 1, we give an algorithm to solve k-MRHI efficiently by dynamic programming in O(nm03k+12m0) time on pedigrees with n nodes and at most m0 heterozygous loci in each node. Experiments on real and simulated data show that, in most cases, our algorithm gives the same haplotyping results but runs much faster than other popular algorithms.

References

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The CEPH genotype database. http://www.cephb.fr/.
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Murray, J.C. et al. A comprehensive human linkage map with centimorgan density. Science, 265, 2049-2054 (1994).
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A. G. Clark. Inference of haplotypes from -PCR}-amplified samples of diploid populations. Mol. Biol. Evol, 7(2):111-122, 1990.
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K. Doi, J. Li, and T. Jiang. Minimum recombinant haplotype configuration on tree pedigree. In Proceedings of the Third International Workshop on Algorithms in Bioinformatics (WABI'03). Lecture Notes in Computer Science no. 2812, pages 339-353, 2003.
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Griffiths, W. Gelbart, R. Lewontin, and J. Miller. Modern Genetic Analysis: Integrating Genes and Genomes. W. H. Freeman and Company, N.Y., 2002.
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D. Gusfield. Inference of haplotypes from samples of diploid populations: complexity and algorithms. J. Computational Biology, 8:305-323, 2001.
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J. Li and T. Jiang. Efficient rule-based haplotyping algorithms for pedigree data. In Proceedings of the Ninth Annual International Conference on Research in Computational Molecular Biology (RECOMB'03), pages 197-206, 2003.
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P. Tapadar, S. Ghosh, and P. P. Majumder. Haplotyping in pedigrees via a genetic algorithm. Hum Hered, 50(1):43-56, 2000.

Cited By

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  • (2007)Fast elimination of redundant linear equations and reconstruction of recombination-free mendelian inheritance on a pedigreeProceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms10.5555/1283383.1283454(655-664)Online publication date: 7-Jan-2007

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    Published In

    cover image Guide Proceedings
    ICCS'05: Proceedings of the 5th international conference on Computational Science - Volume Part II
    May 2005
    1088 pages
    ISBN:3540260439
    • Editors:
    • Vaidy S. Sunderam,
    • Geert Dick Albada,
    • Peter A. Sloot,
    • Jack J. Dongarra

    Sponsors

    • INTEL: Intel Corporation
    • SGI: SGI Silicon Graphics Inc.
    • Springer-Verlag
    • Microsoft Research: Microsoft Research
    • IBM Corporation

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    Springer-Verlag

    Berlin, Heidelberg

    Publication History

    Published: 22 May 2005

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    • (2007)Fast elimination of redundant linear equations and reconstruction of recombination-free mendelian inheritance on a pedigreeProceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms10.5555/1283383.1283454(655-664)Online publication date: 7-Jan-2007

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