Transcriptome-wide gene expression analysis of prostate cancer (PCa) needle biopsies

We assessed transcriptome-wide gene expression in needle biopsies of PCa patients prior to radical prostatectomy (RP) by next-generation sequencing (HiSeq 2500). We applied Cox proportional hazard models to the cohorts from different platforms and specimen types and combined the evidence from these by fixed effect meta-analysis to identify genes predictive for time to DoD (death of disease). Genes were combined by a weighted median approach into a prognostic score. Tumor cell content and GS from the biopsy cores were evaluated by pathologists. If applicable, the hospital provided tissue sections from the biopsy with the highest tumor cell content. If multiple biopsy cores were used for analysis, the average tumor cell content of all the samplings (typically 2 o 3 cores) was calculated. The primary clinical endpoint of the cohort was death of disease (DoD). Total RNA of FFPE needle biopsies of 16 PCa patients was assessed for gene expression profiling by strand-specific total RNASeq. ------------------------------------------------ Raw data not submitted to GEO due to patient privacy issues