Prostatic Neoplasms study with RNA-Seq, WGS + 1 more data on dbGaP (58 participants)

phs001988 — Molecular Characterization of Prostate Cancer Specimens by Bulk and    Single Cell Analysis

Version 1: We performed single-cell RNA-sequencing (scRNA-seq) of fresh biopsies from metastatic castration resistant prostate cancer. Additionally, where available, we performed matched bulk whole exome sequencing (WXS; tumor and normal paired) and whole transcriptome sequencing for the same individuals. We also performed bulk whole exome (WXS) and RNA-sequencing (RNA-Seq) from FFPE pre-treatment biopsies from patients with clinically localized high-risk prostate cancer.Version 2: We added data from a randomized phase 2 trial of radium-223 with or without pembrolizumab in patients with Metastatic Castration-Resistant Prostate Cancer (mCRPC) to bone. After enrollment, study participants underwent bone biopsy and were randomized 2:1 to receive radium-223 at 55 kBq/kg every 4 weeks + pembrolizumab at 200 mg every 3 weeks (Arm A, R223+P) or radium-223 at 55 kBq/kg every 4 weeks alone (Arm B, R223). Stratification factors were alkaline phosphatase ≥220 vs. &#x3C;220 U/L and high vs. low volume bony metastases by CHAARTED criteria. Participants then underwent repeat biopsy after 8 weeks of therapy (+ 3-week window) or after 2 doses of radium-223 if delays occurred. The primary endpoint was differences in CD4+ and CD8+ T-cell infiltrate after 8 weeks of treatment vs. baseline biopsy. Key secondary endpoints were safety/tolerability, radiographic progression-free survival (rPFS), and overall survival (OS). Exploratory endpoints included rate of symptomatic skeletal events (SSEs) and PSA response.Data generated includes bulk whole exome sequencing (WXS), ultra-low pass whole genome sequencing (WGS) at 0.1X coverage, and targeted-capture sequencing. The ultra-low pass sequencing was used as part of the selection criteria for the target capture sequencing. Note: Two subjects in this study are linked to <a href="https://www.ncbi.nlm.nih.gov/gap/advanced_search/?TERM=phs001577">phs001577</a> and <a href="https://www.ncbi.nlm.nih.gov/gap/advanced_search/?TERM=phs000915">phs000915</a> respectively.