Concordance analyses of a rapid, targeted, and comprehensive genomic profiling panel for the detection of guideline-recommended biomarkers in non-small cell lung cancer

Targeted therapies and immunotherapies have improved survival in non-small cell lung cancer (NSCLC). For advanced and early-stage disease, clinical guidelines emphasize timely biomarker results to optimize outcomes. Laboratories face challenges in meeting expanding biomarker demands while conserving tissue and maintaining turnaround times suitable for clinical use and trial enrollment. This study evaluated concordance between the targeted Oncomine™ Precision Assay (OPA), a rapid, low-input NGS panel, and the OmniSeq® INSIGHT (OSI) comprehensive genomic profiling (CGP) assay and assessed OPA's feasibility for expedited biomarker reporting in routine practice. We retrospectively selected 200 advanced NSCLC samples with residual nucleic acid previously tested by OSI. DNA and RNA were re-run using OPA on the Genexus instrument with inter-assay controls. Concordance analyses focused on DNA variants in BRAF , EGFR , ERBB2(HER2) , KRAS , and MET , and RNA fusions in ALK , MET , RET , ROS1 , and NTRK1-NTRK3 . Sensitivity and specificity of OPA relative to OSI were calculated. Workflow metrics including ease-of-use and hands-on time were also evaluated.In a preliminary cohort of 37 samples, OPA showed Assay-QC pass rates of 95% (DNA) and 100% (RNA). Five samples that failed OSI RNA QC passed OPA, though no additional fusions were detected; these were excluded from concordance calculations. Averaged sequencing metrics were 1.07M DNA mapped reads and 125,180 RNA fusion mapped reads. Inter-assay controls were 100% concordant for SNV/Indels (20/20) and fusions (44/44). In the clinical cohort, OPA showed 96.7% for SNV/Indels (29/30), 100% for CNVs (3/3) and fusions (2/2). Specificity was 99.89%, with one potential false positive possibly below OSI's limit of detection (LOD). Turnaround time was 1 day with <1-hour hands-on time. OPA demonstrated high concordance with OSI for a defined set of actionable NSCLC biomarkers. While not all clinically relevant biomarkers (e.g., TMB, MSI, or genes outside the OPA panel) were assessed, results showed strong analytical agreement for overlapping targets. CGP assays like OSI remain the standard for broad biomarker testing in advanced NSCLC, but OPA's rapid turnaround and low-input requirements offer a practical option for timely detection of select actionable biomarkers, making it a useful complement to CGP when time or tissue is limited.