Stroma-Based Prognosticators Incorporating Differences between African and European Americans
Technical Report,30 Sep 2015,29 Sep 2016
University of California, Irvine Irvine United States
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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.
- Medicine and Medical Research
- Genetic Engineering and Molecular Biology