Implementing molecular characterisation of prostate cancer tissue from patients recruited to the multi-centre STAMPEDE trial: The STRATOSPHERE consortium
Authors: E. Grist, M.A. Parry, L. Mendes, S. Santos Vidal, S. Kudahetti, C. Gilson, M. Anjum, N. Atako, F. Ingleby, N. James, N.W. Clarke, M. Sydes, M.K.B. Parmar, S. Chowdhury, R.J. Jones, H. Leung, R. Eeles, D. Waugh, D. Berney, G. Attard
Journal: Annals of Oncology (2018)

Background: STAMPEDE is a multi-arm, multi-stage (MAMS) platform protocol. It has recruited more than 10,000 patients since 2005. Hormone-sensitive metastatic or locally advanced prostate cancer patients starting androgen deprivation therapy (ADT) have been randomised between a number of experimental treatment pairings, including docetaxel or abiraterone, shown to improve overall survival. Funded by PCUK, the STRATOSPHERE consortium (Stratification for rational treatment-oncomarker pairings of STAMPEDE patients starting long-term hormone treatment) has established a framework to enable molecular analyses of archival tissue from these patients. We present the optimised work-flow and preliminary data on feasibility of next-generation sequencing (NGS) of FFPE archival samples. Methods: Approximately 95% of patients participating in STAMPEDE have consented to donate their archival tissue for research. Retrospective tumour block acquisition started in March 2017 and is ongoing. To date, FFPE blocks from 1310 (35%) consenting patients randomised between ADT and abiraterone and docetaxel +/- zoledronic acid comparison arms (3909 total participants) have been retrieved from 64/112 STAMPEDE sites. Results: Morphological review has identified cancer in 86% of cores. DNA and RNA from alternate sections have been extracted using the Zymo Quick-DNA and Quick-RNA FFPE kits. The mean amount of DNA obtained per core was 23ng (range: 0-82ng) from a mean of 8 sections (range 2-14) at 10um thickness per block. DNA has been subjected to low-pass whole genome sequencing and analyses of the first 100 cores from participants recruited to the SOC arm is ongoing. RNA is being extracted from cores with >50% cellularity and >60% tumour content to assess transcriptomic changes and integrate with genomic data. Conclusions: The STRATOSPHERE consortium is addressing the challenge of exploiting FFPE material with low-output, poor-quality nucleic acids from a clinically-important randomised cohort with long-term follow-up. Molecular data will be linked to clinical outcome to test differences in treatment effect by molecular sub-type. Legal entity responsible for the study: University College London. Funding: Prostate Cancer UK. Disclosure: C. Gilson: Grant support from Clovis Oncology. N. James: Grant support, drug supplies and distribution, lecture fees, and advisory board fees from Astellas Pharma and Novartis, grant support, drug supplies and distribution, and lecture fees from Pfizer, grant support, drug supplies and distribution from Clovis Oncology, and grant support, discounted drug supplies, lecture fees, advisory board fees, and travel assistance from Sanofi-Aventis. N.W. Clarke: Receives consulting fees, fees for serving on an advisory board, and lecture fees from Janssen Pharmaceuticals. M. Sydes, M.K.B. Parmar: Grant support and drug supplies and distribution from Astellas Pharma, Clovis Oncology, Novartis, Pfizer, and Sanofi-Aventis. S. Chowdhury: Honoraria, lecture fees, and travel support from Janssen Pharmaceuticals. R.J. Jones: Lecture fees, fees for serving on an advisory board, and publication and writing support from Janssen and grant support, lecture fees, and fees for serving on an advisory board from Astellas Pharma. D. Berney: Has acted as advisor for AstraZeneca, Merck and Roche and has been paid a grant by Myriad genetics for validation of their Prolaris RNA based test for early prostate cancer. G. Attard: Consulting fees from Veridex, Novartis, and Millennium Pharmaceuticals, consulting fees, lecture fees, and travel support from Roche/Ventana Medical Systems and Astellas Pharma, consulting fees and travel support from Medivation, Abbott Laboratories, ESSA Pharma, and Bayer HealthCare Pharmaceuticals, lecture fees from Sanofi-Aventis and Takeda, grant support from AstraZeneca, Arno Therapeutics, and Innocrin Pharmaceuticals, and royalties for a patent on “17-substituted steroids useful in cancer treatment” (GB9305269) being licensed by Janssen Pharmaceuticals. All other authors have declared no conflicts of interest.