Actionable Structural Variant Detection via RNA-NGS and DNA-NGS in Patients With Advanced Non–Small Cell Lung Cancer

Abstract

ImportanceThe National Comprehensive Cancer Network (NCCN) guidelines for non–small cell lung cancer suggest that RNA next-generation sequencing (NGS) may improve the detection of fusions and splicing variants compared with DNA-NGS alone. However, there is limited adoption of RNA-NGS in routine oncology clinical care today.ObjectiveTo analyze clinical evidence from a diverse cohort of patients with advanced lung adenocarcinoma and compare the detection of NCCN-recommended actionable structural variants (aSVs; fusions and splicing variants) via concurrent DNA and RNA-NGS vs DNA-NGS alone.Design, Setting, and ParticipantsThis multisite, retrospective cohort study examined patients sequenced between February 2021 and October 2023 within the deidentified, Tempus multimodal database, consisting of linked molecular and clinical data. Participants included patients with advanced lung adenocarcinoma and sufficient tissue sample quantities for both RNA-NGS and DNA-NGS testing.ExposuresReceived results from RNA-NGS and DNA-NGS solid-tissue profiling assays.Main Outcomes and MeasuresDetection rates of NCCN guideline–based structural variants (ALK, ROS1, RET and NTRK1/2/3 fusions, as well as MET exon 14 skipping splicing alterations) found uniquely by RNA-NGS.ResultsIn the evaluable cohort of 5570 patients, median (IQR) age was 67.8 (61.3-75.4) years, and 2989 patients (53.7%) were female. The prevalence of actionable structural variants detected by either RNA-NGS or DNA-NGS was 8.8% (n = 491), with 86.7% (n = 426) of these detected by DNA-NGS. Concurrent RNA-NGS and DNA-NGS identified 15.3% more patients harboring aSVs compared with DNA-NGS alone (491 vs 426 patients, respectively), including 14.3% more patients harboring actionable fusions (376 vs 329 patients) and 18.6% more patients harboring MET exon 14 skipping alterations (115 vs 97 patients). There was no significant association between the assay used for aSV detection and aSV-targeted therapeutic adoption or clinical outcome. Emerging structural variants (eSVs) were found to have a combined prevalence to be 0.7%, with only 47.5% of eSVs detected by DNA-NGS.Conclusions and RelevanceIn this cohort study, the detection of structural variants via concurrent RNA-NGS and DNA-NGS was higher across multiple NCCN-guideline recommended biomarkers compared with DNA-NGS alone, suggesting that RNA-NGS should be routinely implemented in the care of patients with advanced NSCLC.