First experiences in a US clinical laboratory with Oncomine Dx Express Test: Evaluation in formalin-fixed...

Formalin-fixed paraffin-embedded (FFPE) tissues are among the most commonly preserved specimen types in pathology. Clinical-grade next-generation sequencing (NGS) tests require extensive method development including nucleic acid extraction, analytic and clinical validation, and independent laboratory verification studies. The recently FDA-approved Oncomine Dx Express Test (ODxET) is an in vitro diagnostic (IVD) amplicon-based NGS test designed for clinical testing. This study evaluated clinical accuracy of the test in an external laboratory from the manufacturer and using an independent reference assay. We assessed 48 serially sectioned FFPE tissue from 13 diverse tumor types using ODxET on the Genexus Integrated System as compared to a reference hybrid capture NGS panel processed at an independent laboratory. Discrepant findings were confirmed with either a validated amplicon-based NGS panel, or with droplet digital polymerase chain reaction (ddPCR). Overall concordance was 98% at the variant level (n = 89/91) and 96% at the sample level (n = 45/47), with VAFs ranging from 0.37 to 87.51%. Transfer of ODxET into the clinical laboratory was executed following the current guidance from the CAP organization. Standardization of procedures, optimization of NGS assays, and harmonization of bioinformatics pipelines critically improved the inter-laboratory comparability of genomic profiling from FFPE tissue samples and allowed for rapid integration into the clinical laboratory.