Genome-wide gene expression profiles of primary prostate cancer

Prognostic biomarkers are useful to screen patients with clinically localized prostate cancer (PCa) who are at high risk of metastatic progression. The tumor transcriptome can be used to evaluate the aggressiveness of PCa and predict adverse patient outcomes. Genomewide gene expression levels were measured in primary tumor samples of 503 patients in a population‐based cohort. Formalin‐fixed, paraffin‐embedded (FFPE) PCa tumor tissue blocks were obtained from radical prostatectomy samples and used to make H&E‐stained slides, which were reviewed by a PCa pathologist to confirm the presence of and the location of prostate adenocarcinoma. For each patient, two 1‐mm tumor tissue cores were taken from the areas enriched with ≥ 75% tumor cells from the dominant lesion. The RNeasy® FFPE Kit (Qiagen Inc., Valencia, CA, USA) was used to isolate the RNA from tissue cores, and the samples were quantified with RiboGreen, aliquoted (200 ng per patient) onto 96‐well plates, and shipped to Illumina for gene expression profiling. Tumor RNA samples from patients with various outcomes were randomly distributed across the plates and laboratory personnel were blinded to this information.