Use of eQTL Analysis for the Discovery of Target Genes Identified by GWAS
Abstract
The goals of this grant proposal are 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 can then be followed up in future studies. To accomplish this goal, we will perform a genome-wide SNP analysis (Illumina Human Omni 2.5M SNP array) and a genome-wide mRNA expression analysis (Illumina humanht-12 BeadChip) on a common set of 500 samples of normal prostate tissue sampled from men with PC. To date, we have pre-screened normal prostate tissue with the use of H&E stained sections from 4000 men having a radical prostatectomy in order to identify those cases meeting our strict selection criteria for further processing (tissue localized to the posterior region of the prostate, no tumor, no high grade PIN, no BPH, <1% lymphocytes, and the final percent of epithelial cells present >40%). Following this initial evaluation, 565 tissue samples were selected and further processed into 10 micron thick sections (cryostat) and reevaluated (H&E stained sections) prior to final processing for RNA and DNA extraction. Of the 565, 524 samples have been selected for RNA and DNA extraction, which is now in progress and should be completed shortly.
Document Details
- Document Type
- Technical Report
- Publication Date
- Apr 01, 2012
- Accession Number
- ADA561870
Entities
People
- Stephen Thibodeau
Organizations
- Mayo Clinic