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

Simarro Simarro,Ramos Ramos,Murria Murria,Pérez-Simó Pérez-Simó,Juan Juan,Ansótegui Ansótegui,Laiz Laiz,Cases Cases,Salvador Salvador,Aparicio Aparicio,Barragán Barragán,Llop Llop,Gómez-Codina Gómez-Codina,Mancheño Mancheño,Palanca Palanca

doi:10.3390/cancers11081196

Simarro Simarro, Ramos Ramos + Show 13 more

Open Access

https://doi.org/10.3390/cancers11081196

Copy DOI

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.

Highlights

Cancer is a complex and heterogeneous disease with considerable variation in histological and biological features
The College of American Pathologists has suggested the use of expanded panels in its latest guideline [7,8,9] and both the National Comprehensive Cancer Network (NCCN) and the European Society for Medical
MCRC) and analyze its diagnostic potential to characterize molecular heterogeneity and to increase the therapeutic opportunities with targeted therapies; we assess next-generation sequencing (NGS) technology at a technical and economical level; and we describe our experience in clinical practice of an NGS pipeline for cancer molecular diagnostics in the UNE-EN ISO 15189:2013 accreditation scope

Summary

Introduction

Cancer is a complex and heterogeneous disease with considerable variation in histological and biological features. Understanding the role of genetic alterations involved in cancer development has led to its reclassification into different molecular subtypes that reflect biological behavior and may lead to further effective therapeutic targets to achieve improved outcome [1,2]. Laboratories must integrate high-throughput sequencing technologies in routine molecular diagnostics [3] These allow the simultaneous testing of multiple genetic alterations (point mutations, insertions, deletions, copy number variations and translocations) and quantify molecular subclones by procedures that provide accurate, reliable and cost-effective results. In this sense, next-generation sequencing (NGS) has overcome the cited challenges, posing an attractive alternative to traditional molecular diagnostic testing for cancer [4,5,6]. The College of American Pathologists has suggested the use of expanded panels in its latest guideline [7,8,9] and both the National Comprehensive Cancer Network (NCCN) and the European Society for Medical

Objectives

Methods

Results

Conclusion