Biomarker testing for advanced lung cancer by next-generation sequencing; a valid method to achieve a comprehensive glimpse at mutational landscape

Abstract

Background Next-generation sequencing (NGS) based assay for finding an actionable driver in non-small-cell lung cancer is a less used modality in clinical practice. With a long list of actionable targets, limited tissue, arduous single-gene assays, the alternative of NGS for broad testing in one experiment looks attractive. We report here our experience with NGS for biomarker testing in hundred advanced lung cancer patients. Methods Predictive biomarker testing was performed using the Ion AmpliSeq™ Cancer Hotspot Panel V2 (30 tumors) and Oncomine™ Solid Tumor DNA and Oncomine™ Solid Tumor Fusion Transcript kit (70 tumors) on Ion-Torrent sequencing platform. Results One-seventeen distinct aberrations were detected across 29 genes in eighty-six tumors. The most commonly mutated genes were TP53 (43% cases), EGFR (23% cases) and KRAS (17% cases). Thirty-four patients presented an actionable genetic variant for which targeted therapy is presently available, and fifty-two cases harbored non-actionable variants with the possibility of recruitment in clinical trials. NGS results were validated by individual tests for detecting EGFR mutation, ALK1 rearrangement, ROS1 fusion, and c-MET amplification. Compared to single test, NGS exhibited good agreement for detecting EGFR mutations and ALK1 fusion (sensitivity- 88.89%, specificity- 100%, Kappa-score 0.92 and sensitivity- 80%, specificity- 100%, Kappa-score 0.88; respectively). Further, the response of patients harboring tyrosine kinase inhibitor (TKI) sensitizing EGFR mutations was assessed. The progression-free-survival of EGFR positive patients on TKI therapy, harboring a concomitant mutation in PIK3CA-mTOR and/or RAS-RAF-MAPK pathway gene and/or TP53 gene was inferior to those with sole-sensitizing EGFR mutation (2 months vs. 9.5 months, P = 0.015). Conclusions This is the first study from South Asia looking into the analytical validity of NGS and describing the mutational landscape of lung cancer patients to study the impact of co-mutations on cancer biology and treatment outcome. Our study demonstrates the clinical utility of NGS testing for identifying actionable variants and making treatment decisions in advanced lung cancer.

Molecular characterization of advanced non-small cell lung cancer patients by cfDNA analysis: experience from routine laboratory practice

“…However, NGS was used in the vast majority of patients, with various other methodologies used in the rest of the patients. All methods are adequate in terms of sensitivity and specificity (36,37) with the main difference being that NGS covers all possible mutations in the EGFR gene while the other methods are limited to specific EGFR mutations.…”

Adopting Molecular Testing for Solid Tumors in Latin America: Challenges and Opportunities

“…[26] Following TT discovery for EGFRmutant lung adenocarcinoma, many other driver genes and respective therapies have become available, and there is a growing list of potential new candidate genes. [27] Survival is improved in patients with tumors with altered driver genes and access to TT than in those without access. [28] For example, mortality from metastatic driver-positive NSCLC decreased by 6.3% annually from 2013 to 2016, corresponding to the approval of several TTs.…”

State legislative trends related to biomarker testing

“…In contrast, a next-generation sequencing (NGS) panel can identify multiple genetic alterations with a single test that identifies several to hundreds of genetic alterations. 11 There…”

“…Multiple single‐gene assays, each of which identifies a single analyte, are needed to select the appropriate targeted agent or immunotherapy; however, if this is done in sequence, it can result in significant delays in initiating either novel or conventional therapies according to the testing outcomes. In contrast, a next‐generation sequencing (NGS) panel can identify multiple genetic alterations with a single test that identifies several to hundreds of genetic alterations 11 . There is increased clinical interest in incorporating NGS into clinical practice, with 75% of oncologists nationally reporting the use of NGS testing in 2017 and with 27% reporting incorporating NGS results into their treatment decisions 12 .…”