Abstract
Abstract The discovery of circulating tumor DNA (ctDNA) in the blood, urine and other bodily fluids of cancer patients has led to a new type of non-invasive method of characterizing cancer-causing mutations, the liquid biopsy. With NGS technologies becoming increasingly sensitive, down to a 0.1% Limit of Detection (LOD), they are rapidly gaining traction as a valid assay for cancer genotyping and have potential to direct cancer treatment plans. The wide-angle view provided by NGS panels, combined with dPCR’s zoomed-in precision detection of DNA provide a comprehensive picture of a cancer’s genetic makeup. By applying these complementary techniques at the appropriate time based on the disease type and stage, cancer treatment will become quicker, more precise and more cost-effective in the future. NGS and digital PCR together provide a complete picture of the cancer genome. As part of our research, we wet-lab tested a subset of Rare Mutation Assays corresponding to the Oncomine cfDNA panel for next generation sequencing. Synthetic plasmid (GeneArt) carrying the mutation was spiked into wild-type genomic DNA to reflect a mutation rate of 0.1%. Wild-type genomic DNA was used as negative control. Thermal cycling was performed according to protocol for digital PCR using the QuantStudio 3D. In this study, we tested a pilot set of samples using AcroMetrix Oncology Hotspot Control and Horizon cfDNA Reference Standard with both NGS using Oncomine cfDNA panel and digital PCR with Rare Mutation Assays. Comparison of NGS and digital PCR results for the same sample showed excellent correlation in the low mutation range around 0.1%. This study confirms that digital PCR using QuantStudio 3D and Rare Mutation Assays is effective as a method for orthogonal validation of NGS data using the Oncomine cfDNA panel. Additionally, TaqMan Rare Mutation Assays offer a sensitive and precise solution for downstream mutation tracking over a time course. For Research Use Only. Not for use in diagnostic procedures. Citation Format: Vidya Venkatesh, Marion Laig, Kamini Varma, Yanchun Li, Kelli Bramlett, Dalia Dhingra, Richard Chien. Orthogonal validation of oncomine cfDNA panel data with digital PCR using TaqMan Rare Mutation Assays [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 739. doi:10.1158/1538-7445.AM2017-739
Published Version
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