Abstract 5026: Microfluidic capillary electrophoresis optimization of high-throughput cfDNA and pDNA measurements for enabling cancer diagnostics and gene therapy development

Abstract

Abstract Rapid and accurate electrophoresis characterization can be an important tool for cancer researchers and therapy manufacturers. Advances in NGS of low molecular weight cfDNA for diagnostics may benefit from high-throughput checks of cfDNA sample quality with ultra-low quantities of sample. On the other hand, high molecular weight pDNA characterization and separation of supercoiled, linear and open-linear conformations aids in quality control of these payloads for personalized medicine and in particular cancer vaccines and gene therapies. This work shows optimization of established microfluidic capillary electrophoresis to enable the measurement of cfDNA and pDNA. cfDNA study was completed on plasma reformatted from whole blood tubes using Janus G3 Blood iQ workstation. The cfDNA samples were extracted using commercial cfDNA extraction kits. Using a LabChip GX Touch Biologics Characterization system: gel optimization, marker solution dilution, and inclusion of a low molecular weight DNA standard improved the sensitivity of cfDNA detection. This afforded a new electrophoresis assay with linear dynamic range of 50-1000 pg/uL and sensitivity of <25 ng/uL. pDNA, supercoiled DNA and linear DNA standards were prepared according to published procedures and measured on the LabChip GX Touch Biologics Characterization system. A new ladder system was developed along with gel optimization to develop a new High Sensitivity Assay platform capable of baseline resolving each conformation and providing fragment DNA sizing and purity information. Taken together, this work provides researchers new tools to leverage automated microfluidic capillary electrophoresis for DNA analysis in both upstream and manufacturing processes. Citation Format: Dipti Mehta, Gayatri Gautam, Adriana Coll de Pena, Menel Ben Frej, Anubhav Tripathi, James White. Microfluidic capillary electrophoresis optimization of high-throughput cfDNA and pDNA measurements for enabling cancer diagnostics and gene therapy development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5026.