Prostate Cancer Biobanking Protocol for the Cancer Genome Atlas (TCGA) and High Quality Clinical Care
R Esgueva, R Kim, M Shevchuk, AK Tewari, MA Rubin. Weill Cornell Medical College, New York, NY
Background: The Cancer Genome Atlas (TCGA) program is a comprehensive effort by the National Cancer Institute and the National Human Genome Research Institute (NHGRI) to elucidate the molecular basis of cancer using genome analysis technologies, including deep genome sequencing. TCGA launched a pilot project on three tumor types in 2006 to explore the feasibility of a full-scale effort to explore the entire spectrum of genomic changes involved in human cancers. Problems with sample quality hindered the early phases of this study. We present a biobanking protocol that should allow for prostate cancer to be included in the next phase of TGCA program without compromising clinical care.
Design: We developed a protocol to rapidly acquire prostate tumor samples from a robotic prostatectomy (RP) cohort. To assess the clinical impact of implementing this biobanking (BB) protocol, we evaluated 100 consecutive RP specimens that were processed for both clinical review (CR) and BB procurement after obtaining patient consent. Alternate levels of the prostate, including the apical/base margins and seminal vesicles, were submitted for CR as formalin fixed paraffin embedded blocks. The remaining BB levels were processed into snap frozen OCT blocks and sectioned. Every H&E slide was reviewed histologically by two independent pathologists. All tumor foci identified on the BB tissue were classified using criteria for high- or low-density tumor cell populations; high density tissue cores were used for DNA and RNA sequencing. Differences in reported pathological evaluations (Gleason score (GS), surgical margin status (SM), extraprostatic extension (EPE)) between the CR and the BB specimens were compared.
Results: After comparing the BB and CR specimens, we identified four cases with higher focal GS within the frozen BB, although this did not affect the overall GS. One BB case was diagnosed with equivocal EPE, and three cases contained equivocal positive SM calls. After reevaluating these cases the pT stage was not affected. Of these 100 frozen samples, approximately 90% contained cancer, and 25% contained high density tumor areas that passed rigorous Q/C for DNA and RNA sequencing.
Conclusions: Clinical staging and grading were not affected by implementing a BB protocol. This protocol confirms the feasibility of considering prostate cancer for TCGA program and also ensures important clinical quality assessment for all samples.
Category: Genitourinary (including renal tumors)
Tuesday, March 23, 2010 1:00 PM
Poster Session IV # 119, Tuesday Afternoon