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Issue No.03 - May-June (2013 vol.10)
pp: 688-695
Xiong Li , Coll. of Inf. Sci. & Eng., Hunan Univ., Changsha, China
Bo Liao , Coll. of Inf. Sci. & Eng., Hunan Univ., Changsha, China
Lijun Cai , Coll. of Inf. Sci. & Eng., Hunan Univ., Changsha, China
Zhi Cao , Coll. of Inf. Sci. & Eng., Hunan Univ., Changsha, China
Wen Zhu , Coll. of Inf. Sci. & Eng., Hunan Univ., Changsha, China
ABSTRACT
Currently, there are lots of methods to select informative SNPs for haplotype reconstruction. However, there are still some challenges that render them ineffective for large data sets. First, some traditional methods belong to wrappers which are of high computational complexity. Second, some methods ignore linkage disequilibrium that it is hard to interpret selection results. In this study, we innovatively derive optimization criteria by combining two-locus and multilocus LD measure to obtain the criteria of MaxCorrelation and Min-Redundancy (MCMR). Then, we use a greedy algorithm to select the candidate set of informative SNPs constrained by the criteria. Finally, we use backward scheme to refine the candidate subset. We separately use small and middle (>1,000 SNPs) data sets to evaluate MCMR in terms of the reconstruction accuracy, the time complexity, and the compactness. Additionally, to demonstrate that MCMR is practical for large data sets, we design a parameter w to adapt to various platforms and introduce another replacement scheme for larger data sets, which sharply narrow down the computational complexity of evaluating the reconstruct ratio. Then, we first apply our method based on haplotype reconstruction for large size (>5,000 SNPs) data sets. The results confirm that MCMR leads to promising improvement in informative SNPs selection and prediction accuracy.
INDEX TERMS
Accuracy, Time complexity, Greedy algorithms, Couplings, Prediction algorithms, Predictive models, Bioinformatics,informative SNPs, polymorphism, biological techniques, computational complexity, greedy algorithms, optimisation, informative SNP selection, single nucleotide polymorphism, large size data sets, haplotype reconstruction, computational complexity, two-locus LD measurement, multilocus LD measurement, optimization criteria, linkage disequilibrium, high computational complexity, wrappers, min-redundancy, max-correlation, multilocus linkage disequilibrium, two-locus linkage disequilibrium, Accuracy, Time complexity, Greedy algorithms, Couplings, Prediction algorithms, Predictive models, Bioinformatics, SVM, Haplotypes, single nucleotide polymorphism
CITATION
Xiong Li, Bo Liao, Lijun Cai, Zhi Cao, Wen Zhu, "Informative SNPs Selection Based on Two-Locus and Multilocus Linkage Disequilibrium: Criteria of Max-Correlation and Min-Redundancy", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, no. 3, pp. 688-695, May-June 2013, doi:10.1109/TCBB.2013.61
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