Exome And Targeted Sequencing To Discover And Validate Candidate Genes In Advanced And Lethal Prostate Cancer

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Prostate carcinoma is the most common malignancy and the second leading cause of cancer mortality in men. In order to understand the genetic composition of lethal and advanced prostate cancer, we used exome sequencing to identify protein-altering mutations within a panel of 23 prostate cancer xenografts that represent a wide spectrum of advanced disease phenotypes. Although corresponding normal tissue was not available for most tumors, we were able to take advantage of increasingly deep catalogs of human genetic variation to remove most germline variants. On average, each tumor genome contains ∼200 novel nonsynonymous variants, of which the vast majority was specific to individual carcinomas. Based on the prevalence of rare nonsynonymous variants, we identified a subset of 30 genes including TP53, DLK2, GPC6 and SDF4 as putative candidates involved in tumor progression. To ascertain the frequency of mutations in these candidate genes across a large panel of tumors, we developed a molecular inversion probe (MIP) based protocol that enables efficient targeting and sequencing of tens of genes across hundreds to thousands of samples. The method requires as little as 50 nanograms of DNA as input, and is compatible with DNA isolated from both frozen and formalin formalin-fixed paraffin embedded (FFPE) tissues. We have applied this method to capture and deeply sequence the nearly ∼1,000 exons of the 30 candidate genes across 150 prostate cancer metastases on a single lane of an Illumina HiSeq2000 platform. Unexpectedly, our exome survey identified three tumors with substantially higher mutation frequencies, with 2,000-4,000 novel coding variants per exome. We used whole genome sequencing to characterize the global patterns of mutation in one of these tumors, and found a high prevalence of transition mutations within CpG islands. Experiments to determine whether hypermutation is the result of loss of DNA repair pathway function are ongoing. Collectively, our results indicate that exome sequencing combined with efficient screening of candidate genes is a powerful method to understand the genetics of advanced prostate cancer. We also report a previously undescribed subtype of prostate cancers exhibiting “hypermutated” genomes, with potential implications for resistance to cancer therapeutics. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5059. doi:1538-7445.AM2012-5059