Development, Implementation and Assessment of Molecular Diagnostics by Next Generation Sequencing in Personalized Treatment of Cancer: Experience of a Public Reference Healthcare Hospital

• Main Authors: Javier Simarro, Rosa Murria, Gema Pérez-Simó, Marta Llop, Nuria Mancheño, David Ramos, Inmaculada de Juan, Eva Barragán, Begoña Laiz, Enrique Cases, Emilio Ansótegui, José Gómez-Codina, Jorge Aparicio, Carmen Salvador, Óscar Juan, Sarai Palanca
• Format: Article
• Language: English
• Published: MDPI AG 2019-08-01
• Series: Cancers
• Subjects: next generation sequencing; non-small cell lung cancer; metastatic colorectal cancer; molecular diagnostics; UNE-EN ISO 15189 accreditation
• Online Access: https://www.mdpi.com/2072-6694/11/8/1196

The establishment of precision medicine in cancer patients requires the study of several biomarkers. Single-gene testing approaches are limited by sample availability and turnaround time. Next generation sequencing (NGS) provides an alternative for detecting genetic alterations in several genes with low sample requirements. Here we show the implementation to routine diagnostics of a NGS assay under International Organization for Standardization (UNE-EN ISO 15189:2013) accreditation. For this purpose, 106 non-small cell lung cancer (NSCLC) and 102 metastatic colorectal cancer (mCRC) specimens were selected for NGS analysis with Oncomine Solid Tumor (ThermoFisher). In NSCLC the most prevalently mutated gene was <i>TP53</i> (49%), followed by <i>KRAS</i> (31%) and <i>EGFR</i> (13%); in mCRC, <i>TP53</i> (50%), <i>KRAS</i> (48%) and <i>PIK3CA</i> (16%) were the most frequently mutated genes. Moreover, NGS identified actionable genetic alterations in 58% of NSCLC patients, and 49% of mCRC patients did not harbor primary resistance mechanisms to anti-EGFR treatment. Validation with conventional approaches showed an overall agreement &gt;90%. Turnaround time and cost analysis revealed that NGS implementation is feasible in the public healthcare context. Therefore, NGS is a multiplexed molecular diagnostic tool able to overcome the limitations of current molecular diagnosis in advanced cancer, allowing an improved and economically sustainable molecular profiling.