High performance multiplexed targeted enrichment sequencing from FFPE tissues

Library construction for Next-Generation Sequencing (NGS) using formalin-fixed paraffin-embedded (FFPE) samples offers unique challenges in acquiring high-quality sequencing data due to wide distribution of sample quality. Specifically, differences in formalin fixation methods lead to crosslinked and/or degraded nucleic acid and inconsistent extraction yields. Hence, FFPE extraction and library construction methods must be carefully considered for target enrichment applications. In collaboration, Covaris and Twist Bioscience demonstrate a complete library preparation and target enrichment solution that generates ready-to-sequence multiplexed libraries directly from FFPE tissue.This workflow leverages the Covaris truXTRAC FFPE total Nucleic Acid Plus Kit and oneTUBE-10 shearing with the world-class performance of Twist Bioscience’s Target Enrichment Solutions. Covaris, the Gold Standard for DNA shearing in NGS, also offers pre-analytical products that leverage Adaptive Focused Acoustics® (AFA)® technology. In this FFPE-specific application, the Covaris truXTRAC FFPE total Nucleic Acid Plus Kit and oneTUBE-10 shearing enable full emulsification of paraffin and disaggregation of tissue for highly efficient nucleic acid extraction and generation of size specific DNA libraries. With the Twist Bioscience Human Core Exome kit, the resulting libraries are indexed, pooled, and target enriched with uniquely optimized DNA probes to generate ready-to-sequence high quality multiplexed libraries.Using the aforementioned workflow, results from processing numerous FFPE tissue types are presented. Sequencing results demonstrate large improvements in general Picard metrics that include uniformity (Fold_80 85% with 100X downsampling), and duplication rates ( Citation Format: Mark Consugar, Leonardo Arbiza, Kristin Butcher, Siyuan Chen, Hutson Chilton, Richard Gantt, Yehudit Hasin-Brumshtein, Jim Laugharn, Jayne Simon, Ulrich Thomann, Christina Thompson, Ramsey Zeitoun. High performance multiplexed targeted enrichment sequencing from FFPE tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3544.