The AVENIO Edge System is Roche's fully automated system for NGS library preparation, target enrichment, library QC, and sample pooling. With integrated workflows, trusted KAPA reagents, and end-to-end connectivity, the AVENIO Edge System* is designed to enable reliable, high-quality results without the need for constant instrument monitoring. In this demo, we will highlight key features and benefits of the AVENIO Edge System*, and demonstrate the simplicity of system setup by sharing the step-by-step process for a user-defined library preparation workflow.
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Speaker: Scott Verrow
Senior Automation Support Scientist
Roche Sequencing and Life Science
Presenter: Emma White, Automation Scientist NGS, Roche Diagnostics, Wilmington, MA 01887
Co-Authors: Joshua Tjokrosurjo1*, Marsha McMakin1, Rachel Kasinskas1, Nicole Madamba2, Dawn Obermoeller2
1Roche Diagnostics, 200 Ballardvale St #250, Wilmington, MA 01887
2Perkin Elmer, Inc. 940 Winter Street, Waltham, MA 02451 USA
*Author no longer employee of Roche
Abstract: Genomes hold an abundance of information, both invaluable and inscrutable. Whole-genome sequencing with Next-Generation Sequencing (NGS) technology has driven a wide diversity of investigations and applications, especially in the field of human health. Technological advances have improved throughput capacity and decreased cost-per-base, thereby increasing the feasibility of large-scale studies and sequencing-based diagnostic tools. Even so, the financial and computational costs of sequencing remain non-trivial. NGS can be economized by limiting the sequencing libraries to specific genomic regions during preparation in a process called target enrichment. Using a target enrichment approach allows for higher throughput and more replicates for equivalent sequencing and computational resources.
Expanding the scope and scale of sequencing-based experiments through targeted enrichment adds logistical complexity to sample preparation. Larger sample sizes impose greater labor demands, longer processing time, and more opportunities for errors. Automating sample preparations on liquid handling instruments resolves many of these issues. Standardized NGS liquid handling platforms, such as the Sciclone G3 NGSx and NGSx iQ workstations from Perkin Elmer, expedite implementation of NGS workflows by offering out-of-the box solutions for many popular reagent kits, including the Roche KAPA NGS workflows. The KAPA HyperCap v3 workflow is a protocol for high-quality, automation-friendly library preparation and target enrichment and has been implemented on both the Sciclone G3 NGSx and NGSx iQ systems. Sequencing libraries are constructed by using either the KAPA HyperPrep kit or the KAPA HyperPlus kit, ligation-based preparations with an optional upfront enzymatic fragmentation step in the KAPA HyperPlus kit. Libraries are then enriched using the KAPA Target Enrichment Kit, an in-solution probe hybridization process compatible with the KAPA HyperExome human exome probe panel or other custom probe panels.
The automated workflow was demonstrated on the Sciclone G3 NGSx workstation with 96 replicates of 100 ng of intact human gDNA, using the KAPA HyperPlus kit. The pre-capture sequencing libraries were combined into pools of 8 libraries each for target enrichment using the KAPA HyperExome panel. The libraries were assessed for quantity and fragment distribution before and after target enrichment, demonstrating consistent yields and expected fragment.