Genome-Scale DNA Methylome and Transcriptome Profiles of Prostate Cancer Recurrence After Prostatectomy

Prostate cancer (PCa) is a major health burden world-wide and despite early treatment, a very large proportion of patients present with biochemical recurrence (BCR) post-treatment, reflected by a rise in PSA over a clinical threshold. Novel transcriptomic and epigenomic biomarkers can provide a powerful tool for clinical management of PCa. Here we provide matched high-depth RNA-Sequencing and array-based genome-wide DNA methylome data of PCa patients (n = 17) with, or without, evidence of BCR following early radical prostatectomy. We have utilized Formalin-Fixed Paraffin-Embedded tissues to generate this data and included technical replicates to provide further validity of the data. We describe the sample features, experimental design, methods and bioinformatic pipeline for processing these multi-omic data. Importantly, we provide comprehensive clinical, histopathological, and follow-up data for each patient to enable correlating transcriptome and methylome features with clinical features. Our data will contribute towards the efforts of developing epigenomic and transcriptomic markers for BCR and also facilitate a deeper understanding of the molecular basis of PCa recurrence. Herein we aimed to generate the methylomic and transcriptomic profiles of PCa patients with, or without, evidence of BCR following early radical prostatectomy. DNA and RNA was extracted from FFPE tissues from a cohort of 17 radical prostatectomy patients. We have generated matched, high-depth, genome-scale profiles of the DNA methylome (MethylationEPIC v2.0 array) and RNA transcriptome (RNA-Seq). Six samples showed a mean detection p-value >0.05 and hence were not considered for MethylationEPIC v2.0 array analysis. Additionally, we have also added technical replicates for methylome and RNA-Seq samples for assessing reproducibility.