Abstract
Targeted therapies are a new paradigm in lung cancer management. Next-generation sequencing (NGS) techniques have allowed for simultaneous testing of several genes in a rapid and efficient manner; however, there are other molecular diagnostic tools such as the nCounter® Vantage 3D single nucleotide variants (SNVs) solid tumour panel which also offer important benefits regarding sample input and time-to-response, making them very attractive for daily clinical use. This study aimed to test the performance of the Vantage panel in the routine workup of advanced non-squamous non-small cell lung cancer (NSCLC) patients and to validate and compare its outputs with the Oncomine Solid Tumor (OST) panel DNA kit, the standard technique in our institution. Two parallel multiplexed approaches were performed based on DNA NGS and direct digital detection of DNA with nCounter® technology to evaluate SNVs. A total of 42 advanced non-squamous NSCLC patients were prospectively included in the study. Overall, 95% of samples were successfully characterized by both technologies. The Vantage panel accounted for a sensitivity of 95% and a specificity of 82%. In terms of predictive values, the probability of truly presenting the SNV variant when it is detected by the nCounter panel was 82%, whereas the probability of not presenting the SNV variant when it is not detected by the platform was 95%. Finally, Cohen’s Kappa coefficient was 0.76, indicating a substantial correlation grade between OST and Vantage panels. Our results make nCounter an analytically sensitive, practical and cost-effective tool.
Highlights
Lung cancer is the leading cause of cancer worldwide, being responsible for more than 1.6 million deaths per year; more than breast, colon and prostate cancers combined [1]
Regarding the molecular diagnosis of the 41 patients submitted to both Next-Generation Sequencing (NGS) and nCounter testing, diagnostic correlation was studied by classifying patients into three different categories: complete correlation, partial correlation and no correlation
Complete correlation was assumed when a determined single nucleotide variants (SNVs) was identified by both platforms or when no mutation was detected; partial correlation corresponded to patients in which a SNV was detected by one platform but could not be assessed by the other technique since it was not included in the panel; patients were classified as “no correlation”
Summary
Lung cancer is the leading cause of cancer worldwide, being responsible for more than 1.6 million deaths per year; more than breast, colon and prostate cancers combined [1]. Several targeted therapies have been approved for the treatment of identified mutations in the EGFR [3,4,5], BRAF [6], or MET genes [7,8], as well as for gene rearrangements of ALK [9,10,11,12,13], ROS1 [14,15], NTRK [16,17], and more recently, RET [18,19]. Several guidelines endorse routine genetic testing of the five leading oncogenes EGFR, ALK, ROS1, BRAF and NTRK in newly metastatic non-squamous NSCLC patients, while other molecular targets, such as HER2 and KRAS mutations are approaching clinical practice [20,21,22]. RET rearrangements and MET exon 14 skipping (MET∆ex14) mutations hopefully will be added soon to the list of mandatory testing genes
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