Abstract 2100: Cancer biomarker research using castPCR technology

Abstract

Abstract Cancer Biomarkers have applications in the diagnosis, staging, prognosis and monitoring of disease progression, as well as in the predication and monitoring of drug response. Profiling and validation research tools are needed that exhibit the combined features of high sensitivity and high specificity for cancers. However, the sensitivity of molecular methods such as DNA sequencing and conventional genotyping in tumor samples is limited, typically ranging from 5-20%. We have recently developed TaqMan® Mutation Detection Assays using our competitive allele specific TaqMan® PCR (castPCR) technology for cancer biomarker research. castPCR assays were tested with >300 tumor research samples (either fresh/frozen or formalin-fixed, paraffin-embedded samples) and cell lines to assess mutation status. The results showed that castPCR technology can robustly detect mutations as low as 0.1% and has >99% concordance to other technologies including PCR-based technology and sequencing. In this study, a large panel of castPCR assays for AKT1, APC, BRAF, CTNNB1, HRAS, KRAS, NRAS, PIK3CA, PTEN and TP53 genes were used for investigating somatic mutations in breast tumor research samples. Initially, 4 model FFPE cell lines were used to validate the assays. Mutant DNAs were titrated in the wild type DNAs from 50% to 0.1%. Mutations were identified down to 0.1% titration with high reproducibility. No false positives were found in non-tumor samples. The results obtained by castPCR assays for 20 breast tumor samples were concordant to those reported by other methods. Our data showed that castPCR technology provides an excellent tool for identifying cancer biomarkers or confirming potential cancer markers such as those obtained by next-generation sequencing and other technologies. 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 2100. doi:1538-7445.AM2012-2100