14. A complete automation and reagent workflow for analysis of cfDNA: from plasma to variants. Roseman N, Parakh S, Lai K, Sheu J, Wei H, Niccum B, Chen T, Huang H, Barnes T, Lewis L, Chakravarty UD, and Potts A. Advances in Genome Biology and Technology (AGBT). (abstract #511). Marco Island, FL. Feb 23-26, 2020
As cost of sequencing continues to drop, the throughput and complexity of NGS assays have risen precipitously. At the same time, the types of samples being used for these assays have expanded as researchers find value in studying low input, degraded biological samples, such as cell free DNA (cfDNA). However, efficient extraction of cfDNA from bodily fluids is challenging due to the very low concentrations of nucleic acid. Manual protocols involved in the NGS workflow – DNA extraction, library preparation, and target enrichment – are often laborious and require significant hands on time, which can increase variability in the downstream analysis. Thus, complete automation workflows can increase throughput, reduce hands-on time, and minimize error. Integrated DNA Technologies (IDT) and Beckman Coulter (BC) have teamed up to provide a complete automation and reagent workflow for analysis of low frequency variants in cfDNA. The Apostle MiniMaxTM High Efficiency Isolation Kit from BC is a magnetic nanoparticle based kit that extracts cfDNA from all bodily fluids. IDT’s xGenTM Prism DNA library prep kit provides novel chemistry to maximize conversion, suppress adapter-dimer formation, reduce chimera rates, and facilitate UMI-based error correction to call ultra-low frequency variants. IDT’s xGenTM target enrichment products maintain high library diversity and on-target rates to enable low frequency variant calling regardless of panel size. The combination of these reagents on the Biomek workstations provides a robust and reproducible solution for the analysis of cfDNA.
• Apostle Minimax, xGen Prism, and xGen hybridization capture provide a complete automated solution from plasma to sequencing on the Beckman Coulter Biomek platforms
• Apostle Minimax provides higher quantity and quality cfDNA extraction compared to a competitor kit
• xGen Prism is specifically designed for low input, degraded samples, such as cfDNA and generates higher coverage and complexity compared to competitor kits
• UMI-based error correction can be used to eliminate nearly all false positive calls and enables accurate low frequency variant calling