Abstract LB049: Novel and user-friendly hybridization capture workflow for low quality samples on small gene panels

Abstract Hybridization capture targeted sequencing is a valuable and cost-effective method for in-depth sequencing of specific areas of interest to detect desired low allele frequency variants. While this approach has many advantages over WGS, commercially available workflows are notoriously complex and tend to have a long hands-on time and challenging hot liquid washes. Integrated DNA Technologies (IDT) novel xGen™ Hyb and Wash v3 (xGen v3) workflow overcomes the laboratory challenges of hybridization capture. xGen v3 has no pre-heating, no hot-liquid handling, and no temperature-sensitive urgency. This workflow reduces significantly the amount of time users must spend at their lab bench while executing the protocol. The simple and user-friendly workflow increases throughput, decreases hands-on time and easily adaptable for automation.In this study we demonstrate xGen v3 workflow performance with non-GIAB Formalin-Fixed Paraffin-Embedded (FFPE) input samples using panels of varying sizes from 11Mb target bed size to custom panel smaller than 200Kb with different probe design strategies. Libraries were constructed from Horizon Discovery FFPE standard, formalin compromised standards and NA12878 using IDT’s xGen cfDNA & FFPE DNA Library Prep Kit. This was followed by 1-plex hybridization capture using xGen v3 kit workflow with library total input into capture from 500ng to 100ng and sequenced on Illumina’s NextSeq2000 sequencer. xGen v3 workflow performance remains high regardless of input type, quality or input amount into capture. We also demonstrate consistently high performance across all panels tested regardless of probe design strategy. IDT’s unique hybridization and capture technology eliminates hot liquid handling while demonstrating excellent performance with input and hybridization time flexibility. The simple and user-friendly workflow increases throughput and decreases hands-on time. This workflow supports large gene panels and more focused specific gene monitoring, which could be leveraged for a variety of NGS oncology research applications. Citation Format: Ekaterina Star, Daniel Saatman, Jinglie Zhou, Alexandra Wang. Novel and user-friendly hybridization capture workflow for low quality samples on small gene panels [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB049.