Tumor molecular profiling of NSCLC patients using next generation sequencing

Abstract

Non‑small cell lung cancer (NSCLC) is the most common type of lung cancer and a tumor with a broad spectrum of targeted therapies already available or in clinical trials. Thus, molecular characterization of the tumor using next generation sequencing (NGS) technology, has become a key tool for facilitating treatment decisions and the clinical management of NSCLC patients. The performance of a custom 23 gene multiplex amplification hot spot panel, based on Ion AmpliSeq™ technology, was evaluated for the analysis of tumor DNA extracted from formalin-fixed and paraffin-embedded (FFPE) tissues. Furthermore, the Ion AmpliSeq™ RNA Fusion Lung Cancer Research Panel was used for fusion RNA transcript analysis. The mutation spectrum of the tumors was determined in a cohort of 502 patients with NSCLC using the aforementioned targeted gene panels. The panel used for tumor DNA analysis in this study exhibited high rates (100%) of sensitivity, specificity and reproducibility at a mutation allelic frequency of 3%. At least one DNA mutation was detected in 374 patients (74.5%) and an RNA fusion was identified in 16 patients, (3.2%). In total, alterations in a cancer-driver gene were identified (including point mutations, gene rearrangements and MET amplifications) in 77.6% of the tumors tested. Among the NSCLC patients, 23% presented a mutation in a gene associated with approved or emerging targeted therapy. More specifically, 13.5% (68/502) presented a mutation in a gene with approved targeted therapy (EGFR, ALK, ROS1) and 9.4% (47/502) had an alteration in a gene related to emerging targeted therapies (ERBB2, BRAF, MET and RET). Furthermore, 51.6% of the patients had a mutation in a gene that could be related to an off label therapy or indicative for access to a clinical trial. Thus, the targeted NGS panel used in this study is a reliable approach for tumor molecular profiling and can be applied in personalized treatment decision making for NSCLC patients.

Figure 1.

Percentage of tumors with one, two, three or more detectable mutations among the 374 NSCLC tumors with detected mutations.

Figure 2.

Bar chart showing the distribution of mutated genes in 502 NSCLC patients.

Figure 3.

Bar chart showing mutation frequency among male (blue) and female (red) NSCLC patients.

Figure 4.

Pie chart showing the epidermal growth factor receptor EGFR mutation spectrum in NSCLC patients. Percentages were calculated out of the total mutated tumors.

Figure 5.

Bar chart showing mutation frequency according to the NSCLC patient histology.

Figure 6.

Bar chart showing gene CNA (copy number amplification) in 502 NSCLC patients.

Figure 7.

Bar chart showing gene fusion frequencies in 502 NSCLC tumors.

Figure 8.

(A) Percentage of patients with mutations associated with approved, emerging and clinical trial biomarkers. (B) Distribution of somatic gene alterations among NSCLC patients eligible for approved or emerging therapies for NSCLC patients.