Usefulness of Two Independent DNA and RNA Tissue-Based Multiplex Assays for the Routine Care of Advanced NSCLC Patients

Abstract

Personalized medicine is nowadays a paradigm in lung cancer management, offering important benefits to patients. This study aimed to test the feasibility and utility of embedding two multiplexed genomic platforms as the routine workup of advanced non-squamous non-small cell lung cancer (NSCLC) patients. Two parallel multiplexed approaches were performed based on DNA sequencing and direct digital detection of RNA with nCounter® technology to evaluate gene mutations and fusions. The results were used to guide genotype-directed therapies and patient outcomes were collected. A total of 224 advanced non-squamous NSCLC patients were prospectively included in the study. Overall, 85% of samples were successfully characterized at DNA and RNA levels and oncogenic drivers were found in 68% of patients, with KRAS, EGFR, METΔex14, BRAF, and ALK being the most frequent (31%, 19%, 5%, 4%, and 4%, respectively). Among all patients with complete genotyping results and follow-up data (n = 156), the median overall survival (OS) was 1.90 years (confidence interval (CI) 95% 1.69–2.10) for individuals harbouring an actionable driver treated with a matched therapy, compared with 0.59 years (CI 95% 0.39–0.79) in those not eligible for any targeted therapy and 0.61 years (CI 95% 0.12–1.10) in patients with no drivers identified (p < 0.001). Integrating DNA and RNA multiplexing technologies into the routine molecular testing of advanced NSCLC patients is feasible and useful and highlights the necessity of widespread integrating comprehensive molecular diagnosis into lung cancer care.

EBUS-TBNA Cytological Samples for Comprehensive Molecular Testing in Non–Small Cell Lung Cancer

“…For controversial cases, a consensus was reached over a double headed microscope. References [ 18 , 20 , 21 , 22 , 23 ] are cited in the supplementary material .…”

“…This situation prompted us to investigate the yield of EBUS-TBNA specimens, a cytological methodology, using a comprehensive multiplex genotyping based on combined next-generation sequencing (NGS) (DNA) and nCounter (RNA) multiplex testing [ 18 ], as well as PD-L1, in a series of patients with newly diagnosed NSCLC at our institution. We also aimed to assess the reproducibility of results between cytological specimens and paired tissue biopsies taken from the same tumor.…”

RNA-Based Multiplexing Assay for Routine Testing of Fusion and Splicing Variants in Cytological Samples of NSCLC Patients

“…The use of multiplexed panels for the detection of mutations and fusions in the lung cancer clinical environment has been exponentially increasing over the last few years [ 10 , 13 ]. Previous studies have shown that cytological smears and cell blocks are suitable for performing DNA and RNA massive sequencing [ 14 , 15 , 16 ].…”

“…We have previously reported the use of nCounter for simultaneous detection of fusions in ALK, ROS1, and RET [ 9 , 10 ] and, more recently, for MET alterations [ 11 ]. In this article, we analyze the prospective use of the nCounter technology for the detection of fusions, MET Δ ex14 splicing and MET very high expression in NSCLC cytological samples and we compare the results with FFPE biopsies.…”

Multiplex RNA‐based detection of clinically relevant MET alterations in advanced non‐small cell lung cancer

“…The NanoString nCounter™ Analysis System is a high-throughput, quantitative transcript-based hybridization technology that allows for the simultaneous analysis of the expression of hundreds of target genes [26] and can be easily incorporated in the routine molecular testing workflow of tumor samples [27].…”