Gene duplications and deletions are critical to understanding cancer biology. Deletion in SMAD4, MAP2K4, RB1 and CDKN2A genes are known to play important roles in certain types of cancer or cancer states. Characterization of such mutations in different tumor cells provide insight into the study of novel biomarkers of cancer susceptibility, initiation, progression and metastases and help identify them as risk factors for various types of cancer. We demonstrated a quantitative method to detect multiple gene deletions in human tumor cells by multiplex PCR. We designed four TaqMan® Copy Number Assays to interrogate common deletion mutations in SMAD4, MAP2K4, RB1 and CDKN2A genes and performed multiplex PCR alongside with endogenous controls on representative human tumor and normal cells in different tissues. Since the detection of multiple deletion targets were performed in one single reaction, we were able to profile multiple deletion mutations in one single sample. This method can potentially be applied to the study of Copy Number Variations (CNV) on biological samples with limited quantity such as FFPE samples, as well as enables the characterization of multiple targets on samples in exactly the same condition and state.

Citation Format: Cora Woo, Joyce Wilde, Sunali Patel. Detection of SMAD4, MAP2K4, RB1 and CDKN2A gene deletions in human tumor cells by multiplex qPCR. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1517. doi:10.1158/1538-7445.AM2014-1517