Fig. 1.

Results from the univariate analysis relating the methylation M-value at each of the 2,670 smoking-related CpG sites and the bladder cancer case/control status. The volcano plot (a) represents, for each of the 2670 CpG site separately, the effect size estimate (β; X-axis) representing the estimated methylation difference (on the logit scale) between cases and controls, and the p-value (Y-axis) for the null hypothesis of no association ($H_0:\beta =0$) on the log₁₀ scale. Horizontal red dashed line represents the Bonferroni-corrected significance level ensuring an FWER < 0.05 (n = 28). CpG sites found differentially methylated at an FDR level of 0.05 (N = 191) are presented in yellow. The associations between the 2670 smoking-related CpG sites and smoking status in our data are summarised in panel B by their p-values and are plotted against the p-value for the association with bladder cancer status. The (n = 200) CpG sites associated to smoking status are above the horizontal dashed line, which represent the Bonferroni-corrected significance level ensuring an FWER < 0.05. The (N = 24) CpG found associated to both smoking and bladder cancer status are presented in dark red, those exclusively associated to bladder cancer (N = 4) and smoking (N = 176) are plotted in light red and orange respectively. The marginal histogram along the axis summarise the number of CpG sites associated to bladder cancer (along the Y-axis) or to smoking (along the X-axis) in a given range of p-values for smoking (Y axis) and bladder cancer (X-axis). Panel C represents the 37 CpG sites with bladder p-values ranging from ${10}^{-10}$ and ${10}^{-4}$, and smoking p-values between ${10}^{-23}$ and ${10}^{-1}$. Among these, 17 are associated with both smoking and bladder cancer status, 4 are associated with bladder cancer but not smoking and 9 are associated with smoking but not bladder. Panel D represents the 92 CpG sites with bladder cancer p-values between ${10}^{-5}$ and ${10}^{-2}$ and smoking p-values between ${10}^{-17}$ and ${10}^{-4.5}$. Among these, 3 are associated with both smoking and bladder cancer and 82 are associated with smoking but not bladder cancer