RNAseq Analysis of Formalin-Fixed Paraffin-Embedded Prostate Cancer Tissues

In an effort to identify biomarkers of recurrence, we have performed global RNA-sequencing on 106 formalin-fixed, paraffin-embedded (FFPE) prostatectomy samples from 100 patients at three independent sites, and identified a new set of biomarkers of biochemical recurrence composed of a 24-gene panel. We validated this 24-gene panel on an independent publicly available dataset of 140 patients and this new panel outperformed previously published markers based on cell proliferation gene sets in terms of prediction of biochemical recurrence (BCR). In addition we identified differences in gene expression between Gleason Pattern 4+3 and Gleason Pattern 3+4 tumors.

Dataset features

Information

Specifications

Application:	RNA-seq analysis
Number of samples:	106
Release date:	Apr 11 2014
Last update date:	Oct 18 2018
Access:	Public
Diseases:	Neoplasms, Prostatic Neoplasms
Dataset link	RNAseq Analysis of Formalin-Fixed Paraffin-Embedded Prostate Cancer Tissues

Experimental Protocol

106 samples from 100 patients were sequenced. Six samples were sequenced from two independent RNA preps and libraries. All samples were taken from FFPE Radical Prostatectomies. Samples were obtained from Atlanta VA Medical Center, U. Toronto Sunnybrook Research Centre, and Moffitt Cancer Center.

Repositories

GEO

ArrayExpress

ENA

BioProject

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Contact

Carlos Moreno