Development of a Custom NGS Panel for the Determination of Bladder Cancer Risk

Abstract Backgound Bladder cancer (BCa) is a heterogeneous disease caused by the interaction between environmental and genetic risk factors. The objective of this study was to design a panel that evaluates the role of some selected variants in BCa susceptibility. We are also interested in studying the interaction between environmental and genetic risk factors. Methods The case/controls cohort was composed with 249 BCa cases and 255 controls. The designed Bladder cancer hereditary panel (BCHP) is composed of 139 selected variants. These variants were genotyped by an amplification-based targeted Next-Generation Sequencing (NGS) on the Ion Torrent Proton sequencer (Life Technologies, Ion Torrent technology). Results We have found that rs162555, rs2228000, rs10936599, rs710521, rs3752645, rs804276, rs4639, rs4881400 and rs288980 were significantly associated with decreased risk of bladder cancer. However the homozygous genotypes for VPS37C (rs7104333, A/A), MPG (rs1013358, C/C) genes or the heterozygous genotype for ARNT gene (rs1889740, rs2228099, rs2256355, rs2864873), GSTA4 (rs17614751) and APOBR/IL27 (rs17855750) were significantly associated with increased risk of bladder cancer development compared to reference group (OR=2.53, 2.34, 1.99, 2.00, 2.00, 1.47, 1.96 and 2.27 respectively). We have also found that non–smokers patients harboring heterozygous genotypes for ARNT/rs2864873 (A>G), ARNT/ rs1889740 (C>T) or GSTA4/rs17614751 (G to A) were respectively at 2.775, 3.069 and 6.608 –folds increased risk of Bca development compared to non-smokers controls with wild genotypes. Moreover the ARNT CT (rs1889740), ARNT CG (rs2228099), ARNT TC (rs2864873) and GSS GA genotypes were associated with an increased risk of BCa even in absence of professional risk factors. Finally the decision-tree analysis produced a three major BCa class. These three classes were essentially characterized by an intensity of tobacco use more than 20 pack years (PY) and the CYP1A2 (rs762551) genotype. Conclusions The determined association between genetic variations in BCa and environmental factors, as well as the effect of studied pathway SNPs in comparison with environmental exposition may provide urologists additional genetic information that may help for clinical assessment and treatment decisions. Nevertheless, the underlying mechanisms through which these genes or SNPs affect the clinical behavior of BCas require further studies.