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Improved branch and bound algorithm for detecting SNP-SNP interactions in breast cancer.

ABSTRACT: BACKGROUND:Single nucleotide polymorphisms (SNPs) in genes derived from distinct pathways are associated with a breast cancer risk. Identifying possible SNP-SNP interactions in genome-wide case-control studies is an important task when investigating genetic factors that influence common complex traits; the effects of SNP-SNP interaction need to be characterized. Furthermore, observations of the complex interplay (interactions) between SNPs for high-dimensional combinations are still computationally and methodologically challenging. An improved branch and bound algorithm with feature selection (IBBFS) is introduced to identify SNP combinations with a maximal difference of allele frequencies between the case and control groups in breast cancer, i.e., the high/low risk combinations of SNPs. RESULTS:A total of 220 real case and 334 real control breast cancer data are used to test IBBFS and identify significant SNP combinations. We used the odds ratio (OR) as a quantitative measure to estimate the associated cancer risk of multiple SNP combinations to identify the complex biological relationships underlying the progression of breast cancer, i.e., the most likely SNP combinations. Experimental results show the estimated odds ratio of the best SNP combination with genotypes is significantly smaller than 1 (between 0.165 and 0.657) for specific SNP combinations of the tested SNPs in the low risk groups. In the high risk groups, predicted SNP combinations with genotypes are significantly greater than 1 (between 2.384 and 6.167) for specific SNP combinations of the tested SNPs. CONCLUSIONS:This study proposes an effective high-speed method to analyze SNP-SNP interactions in breast cancer association studies. A number of important SNPs are found to be significant for the high/low risk group. They can thus be considered a potential predictor for breast cancer association.

SUBMITTER: Chuang LY

PROVIDER: S-EPMC3626712 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature

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Improved branch and bound algorithm for detecting SNP-SNP interactions in breast cancer.

Chuang Li-Yeh LY Chang Hsueh-Wei HW Lin Ming-Cheng MC Yang Cheng-Hong CH

Journal of clinical bioinformatics 20130214 1

<h4>Background</h4>Single nucleotide polymorphisms (SNPs) in genes derived from distinct pathways are associated with a breast cancer risk. Identifying possible SNP-SNP interactions in genome-wide case-control studies is an important task when investigating genetic factors that influence common complex traits; the effects of SNP-SNP interaction need to be characterized. Furthermore, observations of the complex interplay (interactions) between SNPs for high-dimensional combinations are still comp ...[more]

PMID: 23410245

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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.

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Improved branch and bound algorithm for detecting SNP-SNP interactions in breast cancer.

Publications

Improved branch and bound algorithm for detecting SNP-SNP interactions in breast cancer.

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