Identification of a novel susceptibility locus at 13q34 and refinement of the 20p12.2 region as a multi-signal locus associated with bladder cancer risk in individuals of European ancestry

Abstract

Candidate gene and genome-wide association studies (GWAS) have identified 15 independent genomic regions associated with bladder cancer risk. In search for additional susceptibility variants, we followed up on four promising single-nucleotide polymorphisms (SNPs) that had not achieved genome-wide significance in 6911 cases and 11 814 controls (rs6104690, rs4510656, rs5003154 and rs4907479, P < 1 × 10(-6)), using additional data from existing GWAS datasets and targeted genotyping for studies that did not have GWAS data. In a combined analysis, which included data on up to 15 058 cases and 286 270 controls, two SNPs achieved genome-wide statistical significance: rs6104690 in a gene desert at 20p12.2 (P = 2.19 × 10(-11)) and rs4907479 within the MCF2L gene at 13q34 (P = 3.3 × 10(-10)). Imputation and fine-mapping analyses were performed in these two regions for a subset of 5551 bladder cancer cases and 10 242 controls. Analyses at the 13q34 region suggest a single signal marked by rs4907479. In contrast, we detected two signals in the 20p12.2 region-the first signal is marked by rs6104690, and the second signal is marked by two moderately correlated SNPs (r(2) = 0.53), rs6108803 and the previously reported rs62185668. The second 20p12.2 signal is more strongly associated with the risk of muscle-invasive (T2-T4 stage) compared with non-muscle-invasive (Ta, T1 stage) bladder cancer (case-case P ≤ 0.02 for both rs62185668 and rs6108803). Functional analyses are needed to explore the biological mechanisms underlying these novel genetic associations with risk for bladder cancer.

Figure 1.

Forest plots of meta-analyses results with bladder cancer risk for SNPs rs6104690 at 20p12.2 and rs4907479 at 13q34. Metaplots for SNPs rs6104690 at 20p12.2 (A) and rs4907479 at 13q34 (B). Details of individual studies are presented in Supplementary Material, Table S1. The New England Bladder Cancer Study (NEBCS) represents a single study comprised of Maine (ME) and Vermont (VT) components genotyped in NCI-GWAS1, and the New Hampshire (NH) component genotyped in NCI-GWAS2. Fixed-effects meta-analysis by study was used to calculate the combined OR, 95% CI and P-trend for the variant allele.

Figure 2.

Association results and LD plot for the 13q34 region. The −log₁₀(P-value) (left Y-axis) for NCI-GWAS1 and NCI-GWAS2 genotyped SNPs (blue) and imputed SNPs (gray) plotted on the genomic coordinates (X axis; NCBI genome build 37). The combined data for NCI-GWAS1, NCI-GWAS2, TXBCS-GWAS, IBCS-GWAS, NBCS-GWAS and TaqMan study data for the 13q34 locus marked by SNP rs4907479, are shown in red. Right Y-axis presents LR of putative recombination hotspots based on 5 sets of 100 randomly selected controls from NCI-GWAS1 and NCI-GWAS2 and shown as connected blue lines.

Figure 3.

Fine-mapping association analysis of the 20p12.2 region. The results are shown for five SNPs of interest: validated GWAS candidate rs6104690 (19), novel finding rs6108803, previously reported rs62185668 and rs4813953 associated with bladder cancer (18), and rs1327235 associated with systolic blood pressure (23). The plots are based on the combined NCI-GWAS1 and NCI-GWAS2 dataset, which includes 5551 bladder cancer cases and 10 242 controls of European origin. (A) Association results for bladder cancer risk (Y-axis) are presented as −log10(P-value) for logistic regression models, assuming additive genetic effect and adjusting for age, gender, 11 study groups, significant eigenvectors, smoking (ever/never) and specified SNPs. SNPs of interest are marked as filled diamonds: rs6104690 (red), rs6108803 (brown), rs62185668 (green), rs4813953 (blue) and rs1327235 (orange); corresponding proxy SNPs (r² ≥ 0.8) are presented as color-matched, un-filled diamonds. (B) Pairwise LD (r² and D′) of SNPs of interest across the 33 Kb in the 20p12.2 region.