Analytical and Clinical Validation of the Oncomine Dx Express Test, an In Vitro Diagnostic-Labeled Assay, for Genomic Profiling of FFPE Tumor Samples.

Abstract

Background: Genomic profiling of solid tumors by next-generation sequencing (NGS) supports personalized therapy selection, but routine clinical adoption requires robust analytical and clinical validation. The Oncomine™ Dx Express Test (ODxET) is a companion diagnostic and tumor profiling in vitro diagnostic NGS assay for detecting targeted single- and multinucleotide variants (SNVs/MNVs), insertions, deletions, copy number variations (CNVs), and RNA fusions or splice variants in formalin-fixed, paraffin-embedded (FFPE) solid tumor samples.

Methods: In a retrospective, blinded analytical study, 462 FFPE samples representing 15 tumor types and including 76 wild-type samples, were analyzed with ODxET and compared with validated orthogonal methods. Reproducibility and repeatability were evaluated across three sites, each using two operators, two sequencers, three reagent lots, and two replicates. Clinical performance for epidermal growth factor receptor (EGFR) exon 20 insertion detection was assessed using non-small cell lung cancer (NSCLC) samples from the WU-KONG1B sunvozertinib clinical trial and commercially sourced biomarker-negative specimens, with clinical effectiveness evaluated in patients treated with the approved sunvozertinib dose.

Results: The ODxET assay showed high analytical concordance for EGFR exon 20 insertions, with a positive percent agreement (PPA) of 100% and a negative percent agreement (NPA) of 95.5%. Across the reportable range of profiling variant classes, the ODxET assay also showed high analytical concordance with orthogonal methods for SNVs (PPA = 99.5%, NPA = 100%), insertions and deletions (PPA and NPA = 100%), CNVs (PPA = 94.2%, NPA = 99.3%), and RNA variants (PPA = 95.9%, NPA = 100%). DNA variant repeatability was 100%, except for one BRAF p.V600E instance (NPA = 97.1%). RNA repeatability ranged from 88.9% (ALK fusion) to 100%. Similarly, the ODxET assay showed high clinical concordance with the clinical trial assays for EGFR exon 20 insertions, with a PPA of 97.9%, a NPA of 100%, and an overall percent agreement (OPA) of 98.9%. In the ODxET EGFR exon 20 insertion-positive/clinical trial assay-positive subgroup, response rates were consistent with those observed in the overall sunvozertinib trial population.

Conclusions: These findings support the analytical concordance, reproducibility, and clinical utility of the ODxET assay for molecular profiling of FFPE solid tumor samples.