Use of eQTL Analysis for the Discovery of Target Genes Identified by GWAS
Final rept. 1 Apr 2011-31 Mar 2014
MAYO CLINIC ROCHESTER MN
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The goal of this grant proposal was to 1 construct a prostate tissue-specific expression quantitative trait loci eQTL dataset and 2 utilize this dataset to identify candidate genes for existing prostate cancer PC risk-single nucleotide polymorphisms SNPs that could then be followed up in future studies. To accomplish this goal we performed a genomewide SNP analysis Illumina Human Omni 2.5M SNP array and a genome-wide mRNA expression analysis RNA sequencing on a common set of 500 samples of normal prostate tissue sampled from men with PC. Of 500 processed samples, 471 samples passed stringent quality control QC and were available for further analysis. Our primary analysis focused on identifying eQTLs for 146 PC risk-SNPs, including all SNPs in linkage disequilibrium with each risk-SNP r2 0.5, resulting in 100 unique risk-intervals. Furthermore, we focused on cis-acting associations only where the transcript was located within 2Mb -1Mb of the risk-SNP interval. Of all SNPs located in the 100 risk-intervals N6324 SNPs, 1,718 demonstrated a significant eQTL signal after adjustment for sample histology lymphocytes and epithelial cells and meeting a Bonferroni-adjusted p-value threshold of 1.96 e-7 ranged from 1.96 e-7 to 1.52 e-91. Of the 100 PC riskintervals, 31 31 demonstrated a significant eQTL signal and these were associated with 54 genes.
- Medicine and Medical Research