A deeper knowledge of cancer biology, alongside advances in diagnostic technologies, has led to much more effective therapeutic strategies in Indeed, over the last decade or so, the incessant quest for new genetic alterations capable of predicting patient response to treatments, has given rise to the development of highly sophisticated molecular tests Accordingly, many sequencing platforms can nowadays detect multiple driver mutations simultaneously thanks to fully automated procedures which drastically reduce turnaround time and costs. A case in point is the Idylla™ system (Biocartis NV, Mechelen, Belgium. This system is a fully automated sample-to-result Real-Time PCR with all reagents integrated in a single-use cartridge; it consists of a console which displays results as either "mutation" or "no mutation" when DNA quality is adequate, or as "invalid" when it is. What is most striking about this platform is that the cartridge can run multiple sample types, including solid and liquid biopsies, yielding results within approximately two hours. Another advantage is its ease of use taking up only a couple of minutes of hands-on time to prepare samples and load the cartridge. This fascinating assay has been validated for the identification of many driver genes, both on tissue and on plasma specimens. In particular Idylla™ EGFR, Idylla™ BRAF, Idylla™ KRAS, Idylla™ NRAS-BRAF, and Idylla™ MSI have been validated on formalin fixed paraffin embedded (FFPE) samples; instead, Idylla™ ctKRAS and Idylla™ ctNRAS-BRAF have been validated on plasma samples. Many more are currently in the pipeline. The aim of my PhD project was to develop and validate novel clinical applications of the the Idylla™ system. I divided my thesis into four chapters.
The first chapter focuses on the performance of the Idylla™ EGFR Assay on cytological non-small cell lung cancer samples. This test was specifically designed to process formalin-fixed, paraffin-embedded sections without requiring preliminary DNA extraction. On the other hand, my PhD work has demonstrated that this assay can also be used to process archival smears from patients with NSCLC by scraping the stained cellular material directly into the cartridge.
The second chapter focuses on the viable application of Idylla™ NRAS-BRAF Assay to cytological thyroid fine-needle aspirates (FNAs) with undetermined morphology. Our research demonstrated that FNA needle rinses can be genotyped by the same cytopathologist who performs the FNA, a procedure that is commonly called rapid on-site molecular evaluation (ROME).
The third chapter, instead, discusses the feasibility of using Idylla™ to analyze liquid biopsy specimens. Such application is highly important, given the scant availability of tissue specimens in advanced NSCLC patients. Our laboratory results have indeed demonstrated the efficiency of the Idylla™ ctKRAS Assay in detecting plasma the KRAS p.G12C mutation, a novel target in NSCLC patients.
Finally, in the fourth chapter, I explore the analytical and clinical performance of the Idylla™ SARS-CoV-2 test on previously tested SARS-CoV-2 people by conventional RT-PCR based approach in different settings, including initial diagnosis and clinical follow-up. In this regard, I provide substantial evidence that this assay may represent a valid, fast, and highly sensitive and specific RT-PCR test for the identification of SARS-CoV-2 infection
