(1082-C) Automating cell-free and formalin-fixed paraffin-embedded DNA library preparation for Next Generation Sequencing workflows on the Biomek® NGeniuS® System

Abstract: Automation in laboratories is advantageous for generating highly reproducible next generation sequencing (NGS) sample libraries, while reducing error potential and sample variation. Integrated DNA Technologies’ (IDT) xGen™ cfDNA & FFPE DNA Library Prep kit utilizes novel chemistry to maximize sample input conversion, suppress adapter-dimer formation, and facilitate consensus analysis, allowing researchers to identify and characterize variants occurring in malignant samples. Automation on Beckman Coulter’s Biomek NGeniuS Next Generation Library Prep System shows comparable results to manual DNA preparations, while reducing hands-on time and lowering the likelihood of user-introduced errors. Together these methods provide a walk away NGS automation solution for researchers directly upon instrument installation with no optimization required due to the fixed deck layout and closed-box system. To demonstrate the workflow’s utility in precision genomics, Apostle MiniMax™ High Efficiency cfDNA Isolation Kit was used to isolate cfDNA from plasma from unhealthy individuals who had varying cancer diagnoses. IDT’s xGen™ cfDNA & FFPE DNA Library Prep kit was run on Beckman Coulter’s Biomek NGeniuS Next Generation Library Prep System to prepare cfDNA libraries from 10ng of plasma extraction, then whole genome sequencing (WGS) was performed on an Illumina NextSeq 550 instrument. Qubit fluorometric and Agilent 4200 TapeStation quantification measured an average of 2,801ng yield from the low input/degraded samples with uniform fragment sizing. Whole genome sequencing analysis demonstrated a high percent reads aligned (99.6%) with a low percentage of dimer (0.08%) and an adapter percentage non-detectable by bioinformatics. The combination of IDT’s xGen library preparation on the Biomek NGeniuS Next Generation Library Prep System provides a reliable and consistent solution that is comparable to manual performance and has demonstrated utility in the production of reliable and consistent sample libraries from low input and/or degraded samples resulting in high quality WGS data.

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