Schematic representation of the included methods.

<p>GV indicates genetic variant; MV, multivariate; PCHAT, Principal Component of Heritability Association Test; T1, trait 1; T2, trait 2; T3, trait 3; TATES, Trait-based Association Test that uses Extended Simes procedure; UV-MA, meta-analysis of univariate results; UV-PCA, univariate analysis of first principal component.</p

Power of the methods for scenarios with one of three traits associated with the QTL (A), two of three traits associated with the QTL (B) and with all three traits associated with the QTL (C).

<p>The explained variance of the QTL was fixed at 0.1%. For clarity reasons, we have not provided errors bars. Confidence ranges for the power estimates are all between 1 and 5%; exact values are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095923#pone.0095923.s003" target="_blank">Tables S3</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095923#pone.0095923.s005" target="_blank">S5</a>. MAF, minor allele frequency; MV, multivariate; PCHAT, Principal Component of Heritability Association Test; QTL, quantitative trait locus; rE, residual correlation; rG, genetic correlation induced by the QTL; TATES, Trait-based Association Test that uses Extended Simes procedure; UV-MA, meta-analysis of univariate results; UV-PCA, univariate analysis of first principal component; UV T1, univariate analysis of trait 1; UV T2, univariate analysis of trait 2; UV T3, univariate analysis of trait 3.</p

Simulation scenarios.

<p>MAF indicates minor allele frequency; j, trait; QTL, quantitative trait locus; rE, residual correlation; rG, genetic correlation.</p

Prognostic Relevance of Urinary Bladder Cancer Susceptibility Loci

<div><p>In the last few years, susceptibility loci have been identified for urinary bladder cancer (UBC) through candidate-gene and genome-wide association studies. Prognostic relevance of most of these loci is yet unknown. In this study, we used data of the Nijmegen Bladder Cancer Study (NBCS) to perform a comprehensive evaluation of the prognostic relevance of all confirmed UBC susceptibility loci. Detailed clinical data concerning diagnosis, stage, treatment, and disease course of a population-based series of 1,602 UBC patients were collected retrospectively based on a medical file survey. Kaplan-Meier survival analyses and Cox proportional hazard regression were performed, and log-rank tests calculated, to evaluate the association between 12 confirmed UBC susceptibility variants and recurrence and progression in non-muscle invasive bladder cancer (NMIBC) patients. Among muscle-invasive or metastatic bladder cancer (MIBC) patients, association of these variants with overall survival was tested. Subgroup analyses by tumor aggressiveness and smoking status were performed in NMIBC patients. In the overall NMIBC group (n = 1,269), a statistically significant association between rs9642880 at 8q24 and risk of progression was observed (GT vs. TT: HR = 1.08 (95% CI: 0.76–1.54), GG vs. TT: HR = 1.81 (95% CI: 1.23–2.66), P for trend = 2.6×10⁻³). In subgroup analyses, several other variants showed suggestive, though non-significant, prognostic relevance for recurrence and progression in NMIBC and survival in MIBC. This study provides suggestive evidence that genetic loci involved in UBC etiology may influence disease prognosis. Elucidation of the causal variant(s) could further our understanding of the mechanism of disease, could point to new therapeutic targets, and might aid in improvement of prognostic tools.</p></div

Association between rs9642880 (<i>MYC</i> locus) and progression-free survival in NMIBC patients.

<p>Kaplan-Meier survival plot showing association between rs9642880 genotype and progression-free survival (PFS) of non-muscle invasive bladder cancer (NMIBC) patients.</p

Association between rs798766 (<i>TACC3/FGFR3</i> locus) and recurrence-free survival in NMIBC patients by smoking status.

<p>Kaplan-Meier survival plots showing association between rs798766 genotype and recurrence-free survival (RFS) in <b>A</b>) never cigarette smokers (Logrank P  =  3.0×10⁻⁵) and <b>B</b>) ever cigarette smokers (Logrank P  =  0.84) with non-muscle invasive bladder cancer (NMIBC).</p

Extensively replicated germline UBC susceptibility loci.

<p>OR: odds ratio; <i>TP63</i>: tumor protein p63; <i>TERT</i>: telomerase reverse transcriptase; <i>CLPTM1L</i>: CLPTM1-like; <i>PSCA</i>: prostate stem cell antigen; <i>CBX6</i>: chromobox homolog 6; <i>APOBEC3A</i>: apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A; <i>CCNE1</i>: cyclin E1; <i>SLC14A1</i>: solute carrier family 14 (urea transporter), member 1</p>a<p>for <i>NAT2</i> and <i>GSTM1</i> these do not refer to the risk allele but to the risk genotype;</p>b<p>risk allele frequency among controls as published in candidate-gene study/GWAS paper</p

Association of confirmed UBC susceptibility variants with overall mortality among MIBC patients.

<p>CNV: copy number variant; HR: hazard ratio; CI: confidence interval;</p>a<p>with adjustment for extended/metastasized (<i>i.e.</i>, primary stage T4(b) ór any T with N+/N≥1 and/or M1) <i>vs.</i> localized disease (<i>i.e.</i>, primary stage T2-T4a with N0/NX and M0/MX) in multivariable Cox proportional hazard regression analyses;</p>b<p>P for trend (unadjusted) for independent rs2978974 SNP at the 8q24.3 locus is 0.16;</p>c<p>P for trend (unadjusted) for causal risk variant (rs17863783) at the 2q37.1 locus is 0.92;</p>d<p>rs1495741: tag SNP for <i>NAT2</i> acetylation status (GG  =  rapid, AG  =  intermediate, AA  =  slow)</p

Demographic and clinicopathological characteristics of included NMIBC and MIBC patients

<p>UCC: urothelial cell carcinoma; SCC: squamous cell carcinoma; AC: adenocarcinoma; p.o.: post-operative; i.v.: intravesical; CT: chemotherapy; IT: immunotherapy</p>a<p>curative intent corresponds to treatment of tumors of stage T2-T4a with N0/NX and M0/MX; palliative intent corresponds to treatment of tumors of stage T4(b) ór any T with N≥1/N+ and/or M1</p

Association of selected UBC susceptibility variants with NMIBC recurrence and progression by smoking status.

<p>CNV: copy number variant; del.  =  deletion; C.E.: converging error; HR: hazard ratio; CI: confidence interval</p>a<p>Presented effect estimates and statistical significance are based on multivariable Cox proportional hazard regression analyses with adjustment for treatment (TURT + both adjuvant i.v. CT and IT <i>vs.</i> TURT + adjuvant i.v. IT <i>vs.</i> TURT + adjuvant i.v. CT <i>vs.</i> TURT only (± one direct p.o. i.v. CT instillation));</p>b<p>rs1495741: tag SNP for <i>NAT2</i> acetylation status (GG  =  rapid, AG  =  intermediate, AA  =  slow);</p>c<p>based on exploratory analysis</p