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

Vitamin-D related single nucleotide polymorphisms (SNPs) with p-values <0.05 and risk of pancreatic cancer from PanScan I-III (3,583 cases and 7,053 controls).

<p>^a After bonferroni correction (0.05/213) p-values < 0.0002 were considered significant</p><p>^b Odds ratios (ORs) were adjusted for age (≤50, 51–60, 61–70, 71–80, ≥81 years), sex, study, and population stratification by 5 eigenvectors for ethnic ancestry.</p><p>^c Odds ratios (ORs) are for the number of copies of the minor allele.</p><p>^d Phase refers to participation in PanScan I, II or III. For rs4668123 data was available only from PanScan phases II and III.</p><p>Vitamin-D related single nucleotide polymorphisms (SNPs) with p-values <0.05 and risk of pancreatic cancer from PanScan I-III (3,583 cases and 7,053 controls).</p

Pathway analysis for risk of pancreatic cancer and gene sets in the vitamin D pathway (3,583 cases and 7,053 controls)

<p>^aP-values account for number of SNPs within genes or within the overall pathway, but not for the total number of genes; Models were adjusted for age (≤50, 51–60, 61–70, 71–80, ≥81 years), sex, study and population stratification by 5 eigenvectors for ethnic ancestry.</p><p>Pathway analysis for risk of pancreatic cancer and gene sets in the vitamin D pathway (3,583 cases and 7,053 controls)</p