Publication-only abstracts (abstract number preceded by an "e"), published in conjunction with the 2018 ASCO Annual Meeting but not presented at the Meeting, can be found online only.
NGS for cancer testing: A clinical laboratory’s perspective.
Molecular Diagnostics and Imaging
2018 ASCO Annual Meeting
J Clin Oncol 36, 2018 (suppl; abstr e24158)
Author(s): Yassmine Akkari; Legacy Health, Portland, OR
Background: In the last few years, molecular cancer diagnostics using next generation sequencing (NGS) has become an integral part of disease detection, management and treatment. As an inherently complex process, NGS still requires extensive quality management and technical qualifications in clinical practice, both at the wet bench and bioinformatics levels. To address these challenges while meeting the goal of providing best-in-class patient care, we sought an integrated workflow, and implemented tumor NGS testing utilizing the GeneReader NGS System and a “necessary and sufficient” targeted panel. Methods: Our validation algorithm was initiated by determining appropriate referred specimen types to be tested, and diagnostic/prognostic information to be evaluated and reported. Following discussions with our pathologists and oncologists, we opted to focus on a small set of core genes deemed necessary and sufficient to maximize clinical utility of our NGS testing service. We then validated each step of the workflow by testing commercially available reference samples, conducting inter-laboratory comparisons and analyzing precision, reproducibility and limit of detection. Results: We set up a workflow in our CLIA-licensed laboratory, tested 100+ samples of various tissue sources and disease characteristics, and validated all components of this NGS testing. The integration of this workflow from a single vendor allowed rapid integration, increased efficiency, accurate reporting and effective troubleshooting. The availability of an integrated bioinformatics pipeline enabled us to provide analysis and interpretation of variant findings with up-to-date and clinically relevant information to guide individualized cancer care. Conclusions: As a regionally-based, seven-hospital system providing cancer care to surrounding communities, we successfully implemented an NGS workflow with direct impact to improve cancer care. As other healthcare systems in the US adopt similar models, we can collectively drive towards personalized medicine with molecular testing that is local, timely and cost-effective.