Application of multi-SNP approaches Bayesian LASSO and AUC-RF to detect main effects of inflammatory-gene variants associated with bladder cancer risk

Evangelina López De Maturana, Yuanqing Ye, M. Luz Calle, Nathaniel Rothman, Víctor Urrea, Manolis Kogevinas, Sandra Petrus, Stephen J. Chanock, Adonina Tardón, Montserrat García-Closas, Anna González-Neira, Gemma Vellalta, Alfredo Carrato, Arcadi Navarro, Belén Lorente-Galdós, Debra T. Silverman, Francisco X. Real, Xifeng Wu, Núria Malats

Research output: Contribution to journalArticle

Abstract

The relationship between inflammation and cancer is well established in several tumor types, including bladder cancer. We performed an association study between 886 inflammatory-gene variants and bladder cancer risk in 1,047 cases and 988 controls from the Spanish Bladder Cancer (SBC)/EPICURO Study. A preliminary exploration with the widely used univariate logistic regression approach did not identify any significant SNP after correcting for multiple testing. We further applied two more comprehensive methods to capture the complexity of bladder cancer genetic susceptibility: Bayesian Threshold LASSO (BTL), a regularized regression method, and AUC-Random Forest, a machine-learning algorithm. Both approaches explore the joint effect of markers. BTL analysis identified a signature of 37 SNPs in 34 genes showing an association with bladder cancer. AUC-RF detected an optimal predictive subset of 56 SNPs. 13 SNPs were identified by both methods in the total population. Using resources from the Texas Bladder Cancer study we were able to replicate 30% of the SNPs assessed. The associations between inflammatory SNPs and bladder cancer were reexamined among non-smokers to eliminate the effect of tobacco, one of the strongest and most prevalent environmental risk factor for this tumor. A 9 SNP-signature was detected by BTL. Here we report, for the first time, a set of SNP in inflammatory genes jointly associated with bladder cancer risk. These results highlight the importance of the complex structure of genetic susceptibility associated with cancer risk.

Original languageEnglish (US)
Article numbere83745
JournalPloS one
Volume8
Issue number12
DOIs
StatePublished - Dec 31 2013

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    De Maturana, E. L., Ye, Y., Calle, M. L., Rothman, N., Urrea, V., Kogevinas, M., Petrus, S., Chanock, S. J., Tardón, A., García-Closas, M., González-Neira, A., Vellalta, G., Carrato, A., Navarro, A., Lorente-Galdós, B., Silverman, D. T., Real, F. X., Wu, X., & Malats, N. (2013). Application of multi-SNP approaches Bayesian LASSO and AUC-RF to detect main effects of inflammatory-gene variants associated with bladder cancer risk. PloS one, 8(12), [e83745]. https://doi.org/10.1371/journal.pone.0083745