Stroma-Based Prognosticators Incorporating Differences between African and European Americans
Abstract
Our objective is to identify and validate RNA prognosticators for prostate cancer in European Americans (EA) and African Americans (AA), and port these to DNA methylation and protein-based prognosticators, where possible. The unique aspect of this project is that it uses tumor-adjacent stroma as a source of markers, and uses standard Formalin-fixed Paraffin-embedded (FFPE) tissue, which is a challenge for molecular biology. In the first year we accumulated 70 AA prostatectomy samples, and matched them with 140 EA by Gleason Score, chemical relapse status, and approximate age. We generated both RNA and DNA from 40 AA and 70 EA samples. We can profile the higher quality and higher yield RNA and DNA samples by array card RT-PCR, and bisulfite sequencing, respectively. For the EA samples, we chose the better quality among more than one EA sample mapped to the same AA sample. Exploiting the recent three-fold reduction in the cost of sequencing per read, we developed sequencing methods to extract expression and DNA methylation information from samples in the bottom half of quality and yield, which would otherwise be lost to the study. Many of these samples are among the more important older samples and AA samples.
Document Details
- Document Type
- Technical Report
- Publication Date
- Oct 01, 2016
- Accession Number
- AD1034631
Entities
People
- Dan Mercola
- Michael Mcclelland
- Mike Lilly
Organizations
- University of California, Irvine