Abstract 5677: Performance of a robust and sensitive liquid biopsy workflow for mutation detection in plasma

Abstract

The discovery of circulating tumor DNA (ctDNA) and the development of highly sensitive technologies have made the utility of liquid biopsies in clinical practice more feasible. Potential applications for liquid biopsies include early cancer detection, tumor genotyping in the absence of tissue biopsies, disease monitoring, and identification of drug resistance markers. However, there is a multitude of technical challenges to accurately detect ctDNA with high sensitivity and reproducibility. Various methods have been established by research centers and companies, each with its advantages and limitations. We have developed a sensitive NGS-based liquid biopsy assay, called the AVENIO ctDNA Analysis Kits (research use only), which includes three panels targeting biomarkers for solid tumors. The AVENIO ctDNA Analysis Kits include cfDNA extraction from up to 5ml plasma input, optimized reagents and workflow for NGS library preparation and target enrichment. It is accompanied with an intuitive software and data analysis package to easily obtain results. The assay sensitively detects 4 cancer relevant mutation classes - single nucleotide variations (SNVs), insertions/deletions, copy number variations and structural rearrangements. We conducted a study with 200+ samples of plasma-derived cfDNA, cell line blends containing relevant cancer mutations, and clinical samples, with which we demonstrate the analytical sensitivity of the three distinct AVENIO gene panels (covering 17, 77 and 197 genes). We demonstrate >95% sensitivity for SNVs at 0.5% mutant allele frequency; >95% sensitivity for 1% indels; >95% sensitivity for 1% structural variants. We also demonstrate assay robustness through multiple replicates, day-to-day, and operator-to-operator reproducibility. In conclusion, the AVENIO ctDNA Analysis Kits for solid tumors encompasses a comprehensive assay and analysis workflow aimed to provide researchers with robust, reliable, highly sensitive and ease to use liquid biopsy assays to conduct the necessary studies to demonstrate the utility of circulating biomarkers in routine clinical testing. Citation Format: Jonathan Choi, Cindy Choi, Jorge Dinis, Jingchuan Li, Sean Chien, Bosun Min, Abraham Munoz, Janet Jin, Amrita Pati, Liang Feng, Johnny Wu, Ashla Singh, Fergal Casey. Performance of a robust and sensitive liquid biopsy workflow for mutation detection in plasma [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 5677. doi:10.1158/1538-7445.AM2017-5677