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Minimum Conflict Individual Haplotyping from SNP Fragments and Related Genotype

By Xiang-Sun Zhang, Rui-Sheng Wang, Ling-Yun Wu and Wei Zhang


The Minimum Error Correction (MEC) is an important model for haplotype reconstruction from SNP fragments. However, this model is effective only when the error rate of SNP fragments is low. In this paper, we propose a new computational model called Minimum Conflict Individual Haplotyping (MCIH) as an extension to MEC. In contrast to the conventional approaches, the new model employs SNP fragment information and also related genotype information, thereby a high accurate inference can be expected. We first prove the MCIH problem to be NP-hard. To evaluate the practicality of the new model we design an exact algorithm (a dynamic programming procedure) to implement MCIH on a special data structure. The numerical experience indicates that it is fairly effective to use MCIH at the cost of related genotype information, especially in the case of SNP fragments with a high error rate. Moreover, we present a feed-forward neural network algorithm to solve MCIH for general data structure and large size instances. Numerical results on real biological data and simulation data show that the algorithm works well and MCIH is a potential alternative in individual haplotyping

Topics: Original Research
Publisher: Libertas Academica
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Provided by: PubMed Central
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    1. (2005). A parsimonious tree-grow method for haplotype inference.
    2. (2002). Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem.
    3. (2000). An SNP map of the human genome generated by reduced representation shotgun sequencing.
    4. (2002). Generating samples under a Wright-Fisher neutral model of genetic variation.
    5. (2001). Genome research:Map of the human genome 3.0.
    6. (2003). Haploptye inference by maximum parsimony.
    7. (2004). Haplotype reconstruction from genotype data using imperfect phylogeny. Bioinformatics,
    8. (2005). Haplotype reconstruction from SNP fragment by Minimum Error Correction.
    9. (2004). Haplotype reconstructon from SNP alignment.
    10. (2001). Haplotype variation and linkage disequilibrium in 313 human genes.
    11. (2002). Haplotyping as perfect phylogeny: conceptual framework and effi cient solu tions.
    12. (2001). High-resolution haplotype structure in hu man genome.
    13. (1990). Inference of haplotypes from PCR-amplified samples of dipoid populations.
    14. (1998). It’s raining, hallelujah? Nature Genetics,
    15. (1986). Learning internal representations by error propagarion,
    16. (2000). Neural Networks in Optimization.
    17. (2004). Optimally phasing long genomic regions using local haplotype prediction.
    18. (2002). Practical algorithms and fixed-parameter tractability for the single individual SNP haplotyping problem.
    19. (2000). Sequence variability and candidate gene analysis in complex disease: associa tion of µ opoid receptor gene variation with substance dependence. Human Molecular Genetic,
    20. (1999). Sequence variation in the human an giotensim converting enzyme. Nature genetics,
    21. (2001). SNPs problems, complexity, and algorithms.
    22. (2001). The sequence of the human genome.

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