Clinical feasibility of NGS liquid biopsy analysis in NSCLC patients

Abstract

BackgroundAnalysis of circulating tumor nucleic acids in plasma of Non-Small Cell Lung Cancer (NSCLC) patients is the most widespread and documented form of "liquid biopsy" and provides real-time information on the molecular profile of the tumor without an invasive tissue biopsy.MethodsLiquid biopsy analysis was requested by the referral physician in 121 NSCLC patients at diagnosis and was performed using a sensitive Next Generation Sequencing assay. Additionally, a comparative analysis of NSCLC patients at relapse following EGFR Tyrosine Kinase Inhibitor (TKIs) treatment was performed in 50 patients by both the cobas and NGS platforms.ResultsAt least one mutation was identified in almost 49% of the cases by the NGS approach in NSCLC patients analyzed at diagnosis. In 36 cases with paired tissue available a high concordance of 86.11% was observed for clinically relevant mutations, with a Positive Predictive Value (PPV) of 88.89%. Furthermore, a concordance rate of 82% between cobas and the NGS approach for the EGFR sensitizing mutations (in exons 18, 19, 21) was observed in patients with acquired resistance to EGFR TKIs, while this concordance was 94% for the p.T790M mutation, with NGS being able to detect this mutation in three 3 additional patients.ConclusionsThis study indicates the feasibility of circulating tumor nucleic acids (ctNA) analysis as a tumor biopsy surrogate in clinical practice for NSCLC personalized treatment decision making. The use of new sensitive NGS techniques can reliably detect tumor-derived mutations in liquid biopsy and provide clinically relevant information both before and after targeted treatment in patients with NSCLC. Thus, it could aid physicians in treatment decision making in clinical practice.

Next Generation Sequencing-Based Profiling of Cell Free DNA in Patients with Advanced Non-Small Cell Lung Cancer: Advantages and Pitfalls

“…Moreover, the concordance was significantly higher in patients at diagnosis than in patients at progression, being 88.9% and 70.2%, respectively [ 24 ]. In contrast, a 60–70% overall concordance rate has been reported in studies in which all the genetic alterations identified in tumor specimens and plasma samples were considered, including TP53 and KRAS mutations [ 39 , 40 , 51 , 53 ]. Importantly, the overall concordance rates were higher when the time elapsed between tissue and plasma sampling was short (62.5% vs. 43.3%; cut-off 1.3 months) [ 51 ].…”

Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review

“…Nucleic acid purification is a crucial step also for liquid biopsies and it can be hampered by an inappropriate plasma separation, most studies directly use ctDNA [ 24 , 65 ], but in some cases gene fusion analysis requires ctRNA and specific purification procedures [ 66 ].…”

“…This assay allowed to characterize ALK, ROS1 and RET fusions together with the most common genetic alterations by preparing a ctDNA and a ctRNA library. Moreover, such an assay uses random molecular tags as a unique molecular identifier to uniquely label each molecule prior to library amplification, thus increasing the test performance [ 66 ].…”

Current Achievements and Applications of Transcriptomics in Personalized Cancer Medicine

“…The first approach is limited by the uncommonness of cancer cells in the bloodstream (around one CTC per billion blood cells) [ 162 ], which significantly reduce the clinical application of this method. Alternatively, analysis of nucleic components of tumor cells—cell free DNA (cfDNA) and circulating RNA (circRNA, including miRNA)—is gaining an increasing interest, demonstrated in numerous studies and clinical trials [ 159 , 163 , 164 , 165 ]. Rapid advancement of novel technologies, enables to detect cancerous DNA/RNA with high accuracy for diagnosis, prognosis and therapeutic monitoring [ 166 ].…”