Analysis of high-order SNP barcodes in mitochondrial D-loop for chronic dialysis susceptibility |
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| Affiliation: | 1. Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan;2. Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan;3. Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung, Taiwan;4. Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan |
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| Abstract: | 
ObjectivesPositively identifying disease-associated single nucleotide polymorphism (SNP) markers in genome-wide studies entails the complex association analysis of a huge number of SNPs. Such large numbers of SNP barcode (SNP/genotype combinations) continue to pose serious computational challenges, especially for high-dimensional data.MethodsWe propose a novel exploiting SNP barcode method based on differential evolution, termed IDE (improved differential evolution). IDE uses a “top combination strategy” to improve the ability of differential evolution to explore high-order SNP barcodes in high-dimensional data.ResultsWe simulate disease data and use real chronic dialysis data to test four global optimization algorithms. In 48 simulated disease models, we show that IDE outperforms existing global optimization algorithms in terms of exploring ability and power to detect the specific SNP/genotype combinations with a maximum difference between cases and controls. In real data, we show that IDE can be used to evaluate the relative effects of each individual SNP on disease susceptibility.ConclusionIDE generated significant SNP barcode with less computational complexity than the other algorithms, making IDE ideally suited for analysis of high-order SNP barcodes. |
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| Keywords: | Single nucleotide polymorphism Differential evolution SNP barcode |
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