Dataset Information

An improved PSO algorithm for generating protective SNP barcodes in breast cancer.

ABSTRACT: BACKGROUND: Possible single nucleotide polymorphism (SNP) interactions in breast cancer are usually not investigated in genome-wide association studies. Previously, we proposed a particle swarm optimization (PSO) method to compute these kinds of SNP interactions. However, this PSO does not guarantee to find the best result in every implement, especially when high-dimensional data is investigated for SNP-SNP interactions. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we propose IPSO algorithm to improve the reliability of PSO for the identification of the best protective SNP barcodes (SNP combinations and genotypes with maximum difference between cases and controls) associated with breast cancer. SNP barcodes containing different numbers of SNPs were computed. The top five SNP barcode results are retained for computing the next SNP barcode with a one-SNP-increase for each processing step. Based on the simulated data for 23 SNPs of six steroid hormone metabolisms and signalling-related genes, the performance of our proposed IPSO algorithm is evaluated. Among 23 SNPs, 13 SNPs displayed significant odds ratio (OR) values (1.268 to 0.848; p<0.05) for breast cancer. Based on IPSO algorithm, the jointed effect in terms of SNP barcodes with two to seven SNPs show significantly decreasing OR values (0.84 to 0.57; p<0.05 to 0.001). Using PSO algorithm, two to four SNPs show significantly decreasing OR values (0.84 to 0.77; p<0.05 to 0.001). Based on the results of 20 simulations, medians of the maximum differences for each SNP barcode generated by IPSO are higher than by PSO. The interquartile ranges of the boxplot, as well as the upper and lower hinges for each n-SNP barcode (n?=?3?10) are more narrow in IPSO than in PSO, suggesting that IPSO is highly reliable for SNP barcode identification. CONCLUSIONS/SIGNIFICANCE: Overall, the proposed IPSO algorithm is robust to provide exact identification of the best protective SNP barcodes for breast cancer.

SUBMITTER: Chuang LY

PROVIDER: S-EPMC3356401 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

An improved PSO algorithm for generating protective SNP barcodes in breast cancer.

Chuang Li-Yeh LY Lin Yu-Da YD Chang Hsueh-Wei HW Yang Cheng-Hong CH

PloS one 20120518 5

<h4>Background</h4>Possible single nucleotide polymorphism (SNP) interactions in breast cancer are usually not investigated in genome-wide association studies. Previously, we proposed a particle swarm optimization (PSO) method to compute these kinds of SNP interactions. However, this PSO does not guarantee to find the best result in every implement, especially when high-dimensional data is investigated for SNP-SNP interactions.<h4>Methodology/principal findings</h4>In this study, we propose IPSO ...[more]

PMID: 22623973

Similar Datasets

Project description:BackgroundBreast cancer predisposition genes identified to date (e.g., BRCA1 and BRCA2) are responsible for less than 5% of all breast cancer cases. Many studies have shown that the cancer risks associated with individual commonly occurring single nucleotide polymorphisms (SNPs) are incremental. However, polygenic models suggest that multiple commonly occurring low to modestly penetrant SNPs of cancer related genes might have a greater effect on a disease when considered in combination.MethodsIn an attempt to identify the breast cancer risk conferred by SNP interactions, we have studied 19 SNPs from genes involved in major cancer related pathways. All SNPs were genotyped by TaqMan 5'nuclease assay. The association between the case-control status and each individual SNP, measured by the odds ratio and its corresponding 95% confidence interval, was estimated using unconditional logistic regression models. At the second stage, two-way interactions were investigated using multivariate logistic models. The robustness of the interactions, which were observed among SNPs with stronger functional evidence, was assessed using a bootstrap approach, and correction for multiple testing based on the false discovery rate (FDR) principle.ResultsNone of these SNPs contributed to breast cancer risk individually. However, we have demonstrated evidence for gene-gene (SNP-SNP) interaction among these SNPs, which were associated with increased breast cancer risk. Our study suggests cross talk between the SNPs of the DNA repair and immune system (XPD-[Lys751Gln] and IL10-[G(-1082)A]), cell cycle and estrogen metabolism (CCND1-[Pro241Pro] and COMT-[Met108/158Val]), cell cycle and DNA repair (BARD1-[Pro24Ser] and XPD-[Lys751Gln]), and within carcinogen metabolism (GSTP1-[Ile105Val] and COMT-[Met108/158Val]) pathways.ConclusionThe importance of these pathways and their communication in breast cancer predisposition has been emphasized previously, but their biological interactions through SNPs have not been described. The strategy used here has the potential to identify complex biological links among breast cancer genes and processes. This will provide novel biological information, which will ultimately improve breast cancer risk management.

Project description:Image contrast enhancement uses the object intensity transformation function to maximize the amount of information to enhance an image. In this paper, the image enhancement problem is regarded as an optimization problem, and the particle swarm algorithm is used to obtain the optimal solution. First, an improved particle swarm optimization algorithm is proposed. In this algorithm, individual optimization, local optimization, and global optimization are used to adjust the particle's flight direction. In local optimization, the topology is used to induce comparison and communication between particles. The sparse penalty term in speed update formula is added to adjust the sparsity of the algorithm and the size of the solution space. Second, the three channels of the color images R, G, and B are represented by a quaternion matrix, and an improved particle swarm algorithm is used to optimize the transformation parameters. Finally, contrast and brightness elements are added to the fitness function. The fitness function is used to guide the particle swarm optimization algorithm to optimize the parameters in the transformation function. This paper verifies via two experiments. First, improved particle swarm algorithm is simulated and tested. By comparing the average values of the four algorithms under the three types of 6 test functions, the average value is increased by at least 15 times in the single-peak 2 test functions: in the multi-peak and multi-peak fixed-dimension 4 test functions, this paper can always search for the global optimal solution, and the average value is either the same or at least 1.3 times higher. Second, the proposed algorithm is compared with other evolutionary algorithms to optimize contrast enhancement, select images in two different data sets, and calculate various evaluation indicators of different algorithms under different images. The optimal value is the algorithm in this paper, and the performance indicators are at least a 5% increase and a minimum 15% increase in algorithm running time. Final results show that the effects the proposed algorithm have obvious advantages in both subjective and qualitative aspects.

Dataset Information

An improved PSO algorithm for generating protective SNP barcodes in breast cancer.

Publications

An improved PSO algorithm for generating protective SNP barcodes in breast cancer.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets