Supplementary Data from Identification of Novel Susceptibility Loci and Genes for Prostate Cancer Risk: A Transcriptome-Wide Association Study in Over 140,000 European Descendants

Supplementary file including three sup figures and 11 sup tables, and Supplementary Note including consortia PIs, Funding Acknowledgements, and references. Supplementary Figure 1. Model external performance using data from the Mayo Clinic study by the internal performance (R2) of models built using GTEx data for (A) prostate tissue models, and (B) cross tissue models. Supplementary Figure 2. Model external performance using data from the TCGA study by the internal performance (R2) of models built using GTEx data for (A) prostate tissue models, and (B) cross tissue models. Supplemental Figure 3. Validation of knockdown in (A) PC-3, (B) DU-145, and (C) LNCaP cells. Supplementary Table 1. Primer sequences Supplementary Table 2. siRNA sequences for examined protein-coding genes Supplemental Table 3. siRNA sequences for examined long non-coding RNAs Supplementary Table 4. Internal performance of prostate and cross-tissue gene expression prediction models built using GTEx data Supplementary Table 5. Forty-eight gene expression-trait associations with p > 0.05 after conditioning on reported prostate cancer risk variants for genes located at genomic loci within 500kb of previous GWAS-identified prostate cancer risk variants Supplementary Table 6. Thirty-four expression-trait associations for genes previously reported as potential target genes of GWAS-identified prostate cancer risk variants Supplementary Table 7. Full list of risk SNPs adjusted for in conditional analyses, and their distances with the associated genes Supplementary Table 8. Associations of predicted gene expression using either prostate models or Cross Tissue models with prostate cancer risk for all 137 identified genes Supplementary Table 9. Patterns of 137 identified prostate cancer risk associated genes in human cancer tissues, cell lines, and normal tissues, as well as prognostic utility in human cancers, based on The Human Protein Atlas Supplementary Table 10. Independent predicting SNPs for identified associated genes using prostate tissue models, their weight values in prostate tissue gene expression prediction models, and associations with prostate cancer risk Supplementary Table 11. Independent predicting SNPs for identified associated genes using cross tissue models, their weight values in cross tissue gene expression prediction models, and associations with prostate cancer risk