Molecular Profiling in Non-Squamous Non-Small Cell Lung Carcinoma: Towards a Switch to Next-Generation Sequencing Reflex Testing

Abstract

Molecular diagnosis of lung cancer is a constantly evolving field thanks to major advances in precision oncology. The wide range of actionable molecular alterations in non-squamous non-small cell lung carcinoma (NS-NSCLC) and the multiplicity of mechanisms of resistance to treatment resulted in the need for repeated testing to establish an accurate molecular diagnosis, as well as to track disease evolution over time. While assessing the increasing complexity of the molecular composition of tumors at baseline, as well as over time, has become increasingly challenging, the emergence and implementation of next-generation sequencing (NGS) testing has extensively facilitated molecular profiling in NS-NSCLC. In this review, we discuss recent developments in the molecular profiling of NS-NSCLC and how NGS addresses current needs, as well as how it can be implemented to address future challenges in the management of NS-NSCLC.

A Real-World Experience from a Single Center (LPCE, Nice, France) Highlights the Urgent Need to Abandon Immunohistochemistry for ROS1 Rearrangement Screening of Advanced Non-Squamous Non-Small Cell Lung Cancer

“…In conclusion, the present study demonstrated that performing IHC to evaluate the ROS1 rearrangement status in advanced NS-NSCLC should be abandoned nowadays in favor of ultrafast RNA NGS reflex testing [ 16 , 17 , 43 ]. ROS1 FISH is still useful for validation of the diagnosis in the case of uncertain NGS results and/or of very small tissue biopsies with a few tumor cells.…”

Current challenges and practical aspects of molecular pathology for non-small cell lung cancers

“…However, the developments in digital pathology may encounter several problems, depending on the institution and laboratories, notably with respect to different interfaces of information systems, the software and the work of the laboratory technicians and the pathologist. An increase in the automation of procedures including nucleic acid extraction (from tissue or liquids), quality control, the preparation of libraries and sequencing, and bioinformatic tools should allow in-house adoption of more and more complex genomic analyses [ 80 ]. The pathologist must be one of the essential players in therapeutic decision making in multidisciplinary boards [ 11 ].…”

“…However, the regular participation at molecular boards is time consuming and requires the pathologist to reorganize the workload. Another challenge concerns the setup of reflex NGS, without waiting for the request from the clinician, in particular for advanced staged tumors [ 80 ]. Managing the impact on laboratory staff and costs also needs to be addressed, as well as the storage, analysis, and application of complex data, including also data protection [ 80 , 81 ].…”

Actionable mutational profiling in solid tumors using hybrid‐capture‐based next‐generation sequencing in a real‐world setting in Spain

“…3,4 Compared with other sequencing modalities, NGS holds many advantages, for instance, high throughput to fully sequence all types of mutations for many genes (hundreds to thousands), the sensitivity and the speed. 1,2,5 Moreover, testing in a single assay is both timely and costeffective as it can detect all four main classes of genomic alterations: base substitutions insert and deletions, copy number alterations, and rearrangements or fusions. 1,2,6,7 NGS has identified novel genetic alterations contributing to oncogenesis, cancer progression, and metastasis.…”

“…Next‐generation sequencing (NGS) is a high complex molecular technique that makes it possible to simultaneously test for a very large panel of genes by allowing parallel sequencing of numerous small nucleic acid fragments 3,4 . Compared with other sequencing modalities, NGS holds many advantages, for instance, high throughput to fully sequence all types of mutations for many genes (hundreds to thousands), the sensitivity and the speed 1,2,5 . Moreover, testing in a single assay is both timely and cost‐effective as it can detect all four main classes of genomic alterations: base substitutions insert and deletions, copy number alterations, and rearrangements or fusions 1,2,6,7 …”