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An Iterative Algorithm for tagSNP Selection Based on Information Entropy Analysis

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Abstract

In this research, an iterative algorithm based on information entropy analysis is proposed for tagSNPs selection. Dynamic programming algorithm is employed to partition haplotypes into blocks with the first constraint, the minimum total block entropy. Missing SNPs are inferred with the second constraint, the minimum number of tagSNPs. The proposed algorithm iterates between these two phases with the above two constraints until the number of tagSNPs reaches its minimum. The proposed algorithm is simulated with two data sets, including Daly et al. 2001, and Patil et al. 2001. Experimental results show that the proposed scheme reduces the number of tagSNPs required in haplotypes significantly.

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References

  1. Johnson, G. C., Esposito, L., Barratt, B. J., et al. (2001). Haplotype tagging for the identification of common disease genes. Natural Genetic, 29, 233–237.

    Article  Google Scholar 

  2. Daly, M., Rious, J., Schaffner, S., Hudson, T., & Lander, E. (2001). High-resolution haplotype structure in the human genome. Natural Genetic, 29, 229–232.

    Article  Google Scholar 

  3. Sved, J. A. (1971). Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theoretical Population Biology, 2, 125–141.

    Article  Google Scholar 

  4. http://www.ncbi.nlm.nih.gov/projects/SNP/.

  5. Chen, W. -P., Lee, T. -C., & Lin, Y. -L. (2006). Haplotype block partitioning and tagSNP selection on human chromosome 21. International Computer Symposium, 1278–1283.

  6. Patil, N., Berno, A. J., Hinds, D. A., et al. (2001). Blocks of limited haplotype diversity revealed by high resolution scanning of human chromosome 21. Science, 294, 1719–1723.

    Article  Google Scholar 

  7. Zhang, K., Deng, M., Chen, T., Waterman, M. S., & Sun, F. (2002). A dynamic programming algorithm for haplotype block partitioning. The National Academy of Science, 99, 7335–7339.

    Article  MATH  Google Scholar 

  8. Zhang, K., Qin, Z. S., Liu, J. S., Chen, T., Waterman, M. S., & Sun, F. (2004). Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Research, 14, 908–916.

    Article  Google Scholar 

  9. Sun, C. -L., Yang, C. -B., Shiue, Y. -L., & Ann, H. -Y. (2005). An effective algorithm for SNP haplotype block inference. Proc. National Computer Symposium.

  10. Su, S.-C., Kuo, C.-C. Jay, & Chen, T. (2005). Inference of missing SNPs and information quantity measurements for haplotype blocks. Bioinformatics, 21, 2001–2007.

    Article  Google Scholar 

  11. Liu, Q., Yang, J., Chen, Z., Yang, M. Q., Sung, A. H., & Huang, X. (2008). Supervised learning-based tagSNP selection for genome-wide disease classifications. BMC Genomics, 9, 1–9.

    Article  Google Scholar 

  12. Guo, M.-Z., Wang, J., & Liu, Y. (2009). A hybrid clustering and graph based algorithm for tagSNP selection. Soft Computing, 13, 1143–1151.

    Article  Google Scholar 

Download references

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Authors and Affiliations

  1. Department of Electrical Engineering, National Sun Yat-Sen University, No. 70, Lien-hai Road, Kushan District, Kaohsiung, 804, Taiwan, Republic of China

    Chia-Hung Yeh

  2. Institude of Electrical Engineering, National Dong Hwa University, 1, Sec. 2, Da Hsueh Rd., Shou-Feng, Hualien, 974, Taiwan, Republic of China

    Jing-Wun Jheng

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  1. Chia-Hung Yeh
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  2. Jing-Wun Jheng
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Correspondence to Chia-Hung Yeh.

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Yeh, CH., Jheng, JW. An Iterative Algorithm for tagSNP Selection Based on Information Entropy Analysis. J Sign Process Syst 64, 233–239 (2011). https://doi.org/10.1007/s11265-009-0440-6

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  • DOI: https://doi.org/10.1007/s11265-009-0440-6

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