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

Simarro J1,2, Murria R1,2, Pérez-Simó G1,2, Llop M1, Mancheño N3, Ramos D3, Juan I1,2, Barragán E1, Laiz B1, Cases E4, Ansótegui E4, Gómez-Codina J2,5, Aparicio J2,5, Salvador C2,5, Juan Ó5, Palanca S6,7.

Author information

1: Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain.
2: Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain.
3: Department of Pathology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain.
4: Department of Pulmonology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain.
5: Department of Medical Oncology, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain.
6: Molecular Biology Unit, Service of Clinical Analysis, University and Polytechnic La Fe Hospital, 46026 Valencia, Spain. palanca_sar@gva.es.
7: Clinical and Translational Cancer Research Group, Health Research Institute La Fe, 46026 Valencia, Spain. palanca_sar@gva.es.

Abstract

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 TP53 (49%), followed by KRAS (31%) and EGFR (13%); in mCRC, TP53 (50%), KRAS (48%) and PIK3CA (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 >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.