Phylogenetic Trees for <i>VEGF</i> Haplotypes and Association with Bladder Cancer Risk among 926 Cases and 900 Controls with DNA in the iPLEX Assay, Spanish Bladder Cancer Study

<div><p>See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0030029#pgen-0030029-g001" target="_blank">Figure 1</a> for block definitions. Of the 29 <i>VEGF</i> SNPs determined, two had low genotypic variation in our population; therefore, haplotype analyses were based on the remaining 27 SNPs. Polymorphic bases are in 5′ to 3′ order: Block 1(<b>rs833052</b> and rs866236); Block 2 (<b>rs1109324</b>, <b>rs1547651</b>, rs833060, rs699947, rs1005230, rs833061, rs1570360, rs2010963, <b>rs25648</b>, rs833067, rs3025042, rs833068, <b>rs3024994</b>, rs735286, rs3024998, rs3025000, and rs3025006); and Block 3 (rs3025030, rs3025033, rs3025035, and rs3025036). Bolded rs numbers are for individual SNPs significantly associated with bladder cancer risk.</p><p>Eleven cases and 13 controls with missing data on more than 15 of the 17 SNPs in Block 2 were excluded from haplotype analyses because their inclusion resulted in lack of convergence. Nucleotide changes significantly associated with risk in the individual genotype analyses are shown in boxes. The most common haplotye is the reference category. Haplotypes with the common variant for each individual SNP are CC for Block 1, GAGCCGTGCTGGCCCCC for Block 2, and GACC for Block 3.</p></div

Gene Map and LD Plot of <i>VEGF</i> Gene

<p>Color scheme is based on D′ and logarithm of the odds of linkage (LOD) score values: white D′ < 1 and LOD < 2, blue D′ = 1 and LOD < 2, shades of pink/red: D′ < 1 and LOD ≥ 2, and bright red D′ = 1 and LOD ≥ 2. Numbers in squares are D′ values (values of 1.0 are not shown). Block definition is based on the Gabriel et al. method [34]. Two (rs3024989 and rs367173) of the 29 SNPs determined are not shown because of low variation in this population. Red rectangles in the gene map represent exons.</p

LINE-1 methylation in granulocyte DNA and trihalomethane exposure is associated with bladder cancer risk

<div><p>DNA methylation changes contribute to bladder carcinogenesis. Trihalomethanes (THM), a class of disinfection by-products, are associated with increased urothelial bladder cancer (UBC) risk. THM exposure in animal models produces DNA hypomethylation. We evaluated the relationship of LINE-1 5-methylcytosine levels (LINE-1%5mC) as outcome of long-term THM exposure among controls and as an effect modifier in the association between THM exposure and UBC risk. We used a case-control study of UBC conducted in Spain. We obtained personal lifetime residential THM levels and measured LINE-1%5mC by pyrosequencing in granulocyte DNA from blood samples in 548 incident cases and 559 hospital controls. Two LINE-1%5mC clusters (above and below 64%) were identified through unsupervised hierarchical cluster analysis. The association between THM levels and LINE-1%5mC was evaluated with β regression analyses and logistic regression was used to estimate odds ratios (OR) adjusting for covariables. LINE-1%5mC change between percentiles 75^th and 25^th of THM levels was 1.8% (95% confidence interval (CI): 0.1, 3.4%) among controls. THM levels above vs. below the median (26 μg/L) were associated with increased UBC risk, OR = 1.86 (95% CI: 1.25, 2.75), overall and among subjects with low levels of LINE-1%5mC (n = 975), OR = 2.14 (95% CI: 1.39, 3.30), but not associated with UBC risk among subjects’ high levels of LINE-1%5mC (n = 162), interaction <i>P</i> = 0.03. Results suggest a positive association between LINE-1%5mC and THM levels among controls, and LINE-1%5mC status may modify the association between UBC risk and THM exposure. Because reverse causation and chance cannot be ruled out, confirmation studies are warranted.</p></div

Summary of genes in the Clathrin-mediated vesicle pathways used for pathway-based analysis of multi-study bladder cancer GWAS.

1<p>Number of SNPs genotyped in the gene region (20 kb 5′ upstream and 10 kb 3′ downstream from the gene's coding region).</p>2<p>The SNP representing the gene in the pathway analysis after the removal of SNPs with heterogeneous effects.</p>3<p>The rank of the SNP among all SNPs in the gene's region based on their p-values.</p>4<p>Minor allele frequency among controls.</p>5<p>Per allele odds ratios +95% confidence intervals from logistic regression models adjusting for age, sex, study center, DNA source, and smoking.</p>6<p>1 d.f. trend test.</p

Summary of genes in the NAD metabolism pathways used for pathway-based analysis of multi-study bladder cancer GWAS.

1<p>Number of SNPs genotyped in the gene region (20 kb 5′ upstream and 10 kb 3′ downstream from the gene's coding region).</p>2<p>The SNP representing the gene in the pathway analysis after the removal of SNPs with heterogeneous effects.</p>3<p>The rank of the SNP among all SNPs in the gene's region based on their p-values.</p>4<p>Minor allele frequency among controls.</p>5<p>Per allele odds ratios +95% confidence intervals from logistic regression models adjusting for age, sex, study center, DNA source , and smoking.</p>6<p>1 d.f. trend test.</p

Summary of genes in the aromatic amine metabolism pathway used for pathway-based analysis of multi-study bladder cancer GWAS.

1<p>Number of SNPs genotyped in the gene region (20 kb 5′ upstream and 10 kb 3′ downstream from the gene's coding region).</p>2<p>The SNP representing the gene in the pathway analysis after the removal of SNPs with heterogeneous effects.</p>3<p>The rank of the SNP among all SNPs in the gene's region based on their p-values.</p>4<p>Minor allele frequency among controls.</p>5<p>Per allele odds ratios +95% confidence intervals from logistic regression models adjusting for age, sex, study center, DNA source , and smoking.</p>6<p>1 d.f. trend test.</p

Summary of genes in the Mitotic Metaphase/Anaphase Transition pathway used for pathway-based analysis of multi-study bladder cancer GWAS.

1<p>Number of SNPs genotyped in the gene region (20 kb 5′ upstream and 10 kb 3′ downstream from the gene's coding region).</p>2<p>The SNP representing the gene in the pathway analysis after the removal of SNPs with heterogeneous effects.</p>3<p>The rank of the SNP among all SNPs in the gene's region based on their p-values.</p>4<p>Minor allele frequency among controls.</p>5<p>Per allele odds ratios +95% confidence intervals from logistic regression models adjusting for age, sex, study center, DNA source , and smoking.</p>6<p>1 d.f. trend test.</p

Pathways enriched with bladder cancer susceptibility loci at a <i>P</i>≤0.01 level using GSEA and ARTP.

<p>Results of the top ranked pathways (<i>P</i><0.01) using GSEA and ARTP. In parenthesis are results prior of removal SNPs displaying heterogeneous signals.</p>1<p>The number of genes in the pathway.</p>2<p>The number of genes underlying the enrichment signal in the pathway.</p>3<p><i>P</i>-value of the enrichment score based on 10,000 permutations.</p>4<p>False-discovery rate calculated based on the normalized statistics of the permutation data to account for the variable sizes of genes and pathways.</p