Histogram of the posterior probabilities of having a positive (negative) SNP effect by Bayesian Threshold LASSO model (BTL) in the total population.

<p>The dot point line indicates the cut-off point of 80% above which SNPs were considered.</p

Venn diagrams showing the overlapping between the SNPs selected by Bayesian Threshold model (BTL) and AUC-Random Forest (AUC-RF).

<p>(A) Number of SNPs detected by each method in the total population. (B) Number of SNPs detected by each method in the non-smoker subset. (C) Number of common SNPs detected by BTL in the total population and non-smoker subset, with posterior probabilities of at least 80% and 75% of having an effect different from 0. (D) Number of SNPs detected by AUC-RF in both the total population and the non-smoker subset.</p

Risk estimates from Bayesian Threshold LASSO model (BTL), considering a posterior probability of 75%, and from logistic regression analyses among non-smokers.

a<p>Posterior mean of the OR, calculated from the BTL analyses. Similar values for the median were obtained for each SNP.</p>b<p>It corresponds to , where .</p>c<p>OR obtained from the adjusted logistic regression.</p>d<p><i>p</i>-value of the trend obtained from the adjusted logistic regression.</p><p>SNPs also selected by AUC-RF are bold-faced.</p

Relative variable importance for the top 12 polymorphisms selected by AUC-RF in the total population.

a<p>Calculated by dividing the raw variable importance measurement by that with the highest MDG, that of smoking status.</p

Risk estimates of Bayesian Threshold LASSO model (BTL), considering a posterior probability higher than 80%, and from logistic regression for the total population.

<p>^a Posterior mean of the OR, calculated from the BTL analyses Similar values for the median were obtained for each SNP.</p><p>^b It corresponds to , where .</p><p>^c OR obtained from the adjusted logistic regression.</p><p>^d<i>p</i>-value of the trend obtained from the adjusted logistic regression.</p><p>SNPs also selected by AUC-RF are bold-faced.</p

Main effect <i>p-values</i> for bladder cancer risk (overall and for each subphenotype) for each tag-SNP under the additive mode of inheritance.

<p>A SNP <i>p-value</i> above the red line is considered as associated with the phenotype after multiple testing correction by Bonferroni (4.2 for main effects and 3.6 for subtypes). All models are adjusted for age, gender, region and cigarette smoking status.</p

Significant SNPs at α = 0.05 in the logistic regression main effect models.

<p><i>MAF(a)</i>, minor allele frequency); <i>pHWE</i>, <i>p-value</i> from the Hardy Weinberg equilibrium test; <i>MOI</i>, Mode of Inheritance.</p><p><i>Repr. (%)</i>, percentage reproducibility assessing the robustness of each SNP by LASSO.</p><p>All models are adjusted for age, gender, region and smoking status.</p><p>Odd ratio and 95%CI under the model of inheritance that provided the lowest <i>p-value</i>, and percentage reproducibility from LASSO under the additive mode of inheritance.</p

SNPs in <i>TP53</i> and bladder cancer risk.

<p><i>Repr. (%)</i>,percentage reproducibility assessing the robustness of each SNP by LASSO.</p><p>AA, Aa and aa represent common-homozygotes, heterozygotes and rare-allele homozygotes, respectively.</p><p>OR, odds ratio; CI, confidence interval; OR(Aa) and OR(aa) were estimated relative to genotype AA.</p>1<p>Arg72Pro polymorphism.</p><p>All models were adjusted for age, gender, region and cigarette smoking status.</p

Demographics and smoking status of patients included in the study.

1<p><i>p-value</i> from Pearson's χ² test for association.</p