B-020 Fully Automated and Scalable cfDNA Extraction Solution from up to 10 mL Samples

Abstract

Abstract Background The use of circulating, cell-free DNA (cfDNA) is rapidly evolving in the clinical landscape, becoming one of the fastest growing areas in recent years. It offers tremendous clinical potential as a screening method for tumor, cancer, disease progression, treatment response, and more. Circulating DNA is found in low quantities and often requires large sample input volumes to isolate the less abundant cfDNA to sufficient amounts needed for downstream analysis. The existing methods for extraction are often silica spin column-based, which involve an extensive amount of hands-on work, and they require large volumes of binding buffers, making it unsuitable for extractions involving sample volumes as large as 10 mL. These existing workflows impose certain limitations in terms of the sample volume and number of samples that they can process. Methods To tackle this necessity, Omega Bio-tek has developed a fully automated solution using Mag-Bind® cfDNA Kit (M3298) to extract cfDNA from up to 10 mL volumes from 48 samples in 2.75 h when integrated on Hamilton’s Microlab® STAR™ platform. Results The system is scalable and can extract from sample volumes ranging from 1–10 mL without any hardware modification or additional, expensive accessories on the Hamilton workstation. Here, we elucidate the workings of this automated protocol using Omega Bio-tek’s Mag-Bind® cfDNA Kit and compare its performance to a manual extraction protocol from 4 mL of plasma processed using the same kit. We also present additional solutions using the Mag-Bind® cfDNA kit to showcase extraction of fragments as small as 50 bp with minimal genomic DNA contamination. Conclusion Omega Bio-tek’s custom workflows provides the customers with different protocols to fit their different application needs. Thus, this kit offers researchers and scientists the flexibility to use the same kit for not only large volume sample processing but also for recovering short cfDNA fragments.