Abstract 213: Demonstration of the genexus integrated sequencing system with the oncomine precision assay
Authors: Jian Gu, Ru Cao, Jeff Schageman, Kris Lea, Priyanka Kshatriya, Amir Marcovitz, Paul Williams, Rasika Sunnadeniya, Varun Bagai, Khalid Hanif, Jose L. Costa, Kelli Bramlett
Journal: Cancer Research (2020)

Abstract Introduction: We describe the development and performance of a new sample-to-report targeted sequencing solution for testing solid tissue cancers using the Genexus Integrated Sequencing System and accompanying software. The assay is designed for research applications from either formalin fixed paraffin embedded (FFPE) solid tumor samples or cell-free total nucleic acid (cfTNA) from liquid biopsy samples. The Genexus Integrated Sequencer is a fully automated system requiring minimal touch points and hands on time allowing a novice user to go from nucleic acid to variant calls for somatic variant testing across multiple cancer types in less than two days. Methods: The Oncomine Precision Assay is a new amplicon-based assay targeting specific somatic variants in 50 genes with coverage for multiple cancer types. The assay uses AmpliSeq HD chemistry capable of distinguishing true sample biological variants from errors generated during library preparation, templating, and sequencing through incorporation of molecular tags during target amplification. With about 15 minutes of hands on time, a run is set-up using pre-filled reagent strips for a fully automated run that includes library prep, templating, sequencing, variant calling, and a final report if desired. Results: Reported here are the results generated from an early external test site along with development data. The Oncomine Precision Assay is designed to detect somatic variants in 50 unique genes testing all major variant types important in the oncology research. The content was selected based on published accounts of target actionability and prevalence across multiple cancer types. All major variant types are targeted including SNVs, insertions, deletions, copy number variation, fusion transcripts and alternate splice forms. Data is shared from an external test lab using the Oncomine Precision Assay on the Genexus Integrated Sequencer with control and research samples. Results from both multiplexed FFPE and liquid biopsy runs are presented. Data demonstrates use of a single assay and system to effectively call variants from both FFPE and liquid biopsy sample types with a turn-around time of less than 30 hours. Conclusion: The Oncomine Precision Assay and Genexus Integrated Sequencer enable detection of key oncology variants in 50 genes using either solid tissue or liquid biopsy samples as input. This fully automated solution for oncology research generates variant calls from nucleic acid input in less than 2 days with minimal hands-on time and touch-points from the user. Many features of the automated system increase success rates by ensuring the appropriate reagents are properly installed before a run. The user friendly, highly automated, and fully optimized sample to answer system described here has great potential for targeted oncology sequencing in the research setting. Citation Format: Jian Gu, Ru Cao, Jeff Schageman, Kris Lea, Priyanka Kshatriya, Amir Marcovitz, Paul Williams, Rasika Sunnadeniya, Varun Bagai, Khalid Hanif, Jose L. Costa, Kelli Bramlett. Demonstration of the genexus integrated sequencing system with the oncomine precision assay [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 213.