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 (RNA sequencing) 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%). Furthermore, the RNA / DNA purification and DNA genotyping / RNA expression analyses proposed have also been completed. We are now in the final phase of the project. We have completed the quality-control analysis of the genotyping and RNA sequencing results and are now completing the statistical analysis required for the construction of the eQTL dataset.
Document Details
- Document Type
- Technical Report
- Publication Date
- Apr 01, 2013
- Accession Number
- ADA591115
Entities
People
- Stephen Thibodeau
Organizations
- Mayo Clinic