Identifying Cancer Mutations in Neuroendocrine Prostate Cancer through Massively Parallel DNA-Sequencing of Formalin-Fixed Paraffin Embedded Tissue
Himisha Beltran, Kyung Park, Theresa Y MacDonald, Roman Yelensky, Garrett Frampton, Doron Lipson, Philip J Stephens, Maureen T Cronin, Scott T Tagawa, David M Nanus, Juan Miguel Mosquera, Mark A Rubin. Weill Medical College of Cornell University, New York, NY; Foundation Medicine, Cambridge, MA
Background: Neuroendocrine prostate cancer (NEPC) is an aggressive lethal variant of prostate cancer that most commonly arises from existing prostate adenocarcinoma (PCa). Despite chemotherapy, most patients survive less than one year. Little is known about the underlying biology of NEPC, as metastases are rarely biopsied. The purpose of this study was to determine the spectrum of somatic mutations in NEPC by using a novel DNA sequencing platform and to evaluate for targetable molecular alterations.
Design: 44 NEPC and mixed NEPC/PCa were evaluated by study pathologist and 77 high density foci of NEPC, PCa, and benign areas were selected for DNA extraction. Massively parallel sequencing via HiSeq2000 (Illumina, San Diego, CA) was performed using indexed seq libraries constructed by adapter ligation followed by hybridization with optimized capture probes (Agilent, Cupertino, CA). Data was processed using publicly available and newly validated software tools (Foundation Medicine, Cambridge, MA) to make mutation assignments for base alterations, indels and CNAs in 182 cancer associated genes and common sites of rearrangement for 15 genes.
Results: 5/8 biopsies and 62/65 (overall 93%) of prostate foci yielded sufficient DNA (>50 ng) for analysis from 40m of formalin-fixed paraffin embedded tissue (FFPE) tissue. Average median sequence coverage was 934x. TMPRSS2-ERG fusion was present in 28% of NEPC. Recurrent homozygous deletions involving PTEN and RB1 were seen, and 1 tumor with BRCA2 loss. Several high confidence non-synonymous mutations were identified including TP53 (40%), CTNNB1 (12%), and less frequently mutations involving PTEN, PIK3CA, AR, as well as other novel mutations/fusions. There was high concordance between NEPC and PCa foci in mixed tumors, as well as between primary tumor and metastases. High confidence lesions were validated with exome sequencing and FISH.
Conclusions: This study shows feasibility of an in-depth DNA analysis using FFPE tissue, and even biopsy material. Comprehensive genome sequencing has nominated novel biologic pathways and provides insight into disease progression from PCa to NEPC, as well as potential new drug targets for a tumor that is currently lethal. This is a useful and comprehensive sequencing tool to evaluate tumors such as NEPC and other metastatic tumors, where obtaining tissue is challenging.
Category: Special Category - Pan-genomic/Pan-proteomic approaches to Cancer
Tuesday, March 20, 2012 1:30 PM
Platform Session: Section H1, Tuesday Afternoon