Simultaneous identification of clinically relevant single nucleotide variants, copy number alterations and gene fusions in solid tumors by targeted next-generation sequencing.

Duarte Mendes Oliveira,Chiara Mignogna,Francesco Corcione,Antonia Rizzuto,Teresa Mirante,Gaetano Rocco,Marianna Scrima,Giuseppe Viglietto,Renato Franco,Simona Migliozzi,Donatella Malanga

doi:10.18632/oncotarget.25229

Abstract

In this study, we have set-up a routine pipeline to evaluate the clinical application of Oncomine™ Focus Assay, a panel that allows the simultaneous detection of single nucleotide hotspot mutations in 35 genes, copy number alterations (CNAs) in 19 genes and gene fusions involving 23 genes in cancer samples. For this study we retrospectively selected 106 patients that were submitted to surgical resection for lung, gastric, colon or rectal cancer.We found that 56 patients out of 106 showed at least one alteration (53%), with 47 patients carrying at least one relevant nucleotide variant, 10 patients carrying at least one CNA and 3 patients carrying one gene fusion. On the basis of the mutational profiles obtained, we have identified 22 patients (20.7%) that were potentially eligible for targeted therapy.The most frequently mutated genes across all tumor types included KRAS (30 patients), PIK3CA (16 patients), BRAF (6 patients), EGFR (5 patients), NRAS (4 patients) and ERBB2 (3 patients) whereas CCND1, ERBB2, EGFR and MYC were the genes most frequently subjected to copy number gain. Finally, gene fusions were identified only in lung cancer patients and involved MET [MET(13)–MET(15) fusion] and FGFR3 [FGFR3(chr 17)–TACC3(chr 11)].In conclusion, we demonstrate that the analysis with a multi-biomarker panel of cancer patients after surgery, may present several potential advantages in clinical daily practice, including the simultaneous detection of different potentially druggable alterations, reasonable costs, short time of testing and automated interpretation of results.

Highlights

Precision Medicine is a term that is used to describe how genetic information about patients is used to diagnose and treat their disease [1, 2]
We have set-up a routine pipeline to evaluate the clinical application of OncomineTM Focus Assay, a panel that allows the simultaneous detection of single nucleotide hotspot mutations in 35 genes, copy number alterations (CNAs) in 19 genes and gene fusions involving 23 genes in cancer samples
Predicting the response to trastuzumab in breast cancer patients is dictated by positivity to HER2 [6,7,8], sensitivity to the anti-EGFR inhibitor gefitinib in NSCLC patients is predicted by EGFR mutations [9, 10] and resistance to the anti-EGFR monoclonal antibody cetuximab in advanced colorectal cancer patients is predicted by KRAS mutations [11]

Summary

Introduction

Precision Medicine is a term that is used to describe how genetic information about patients is used to diagnose and treat their disease [1, 2]. The success of precision medicine relies on validated biomarkers that allow accurate prognosis and prediction of response to therapy [3]. The use of genetic biomarkers to direct therapy of oncological patients has been hampered by the necessity to analyse one biomarker at a time [4, 5]. The introduction of Generation Sequencing (NGS) techniques has allowed the development of assays for the simultaneous analysis of multiple biomarkers [12]. Due to the huge amount of data generated by these type of studies, the identification of clinically relevant alterations in specific patients is often doubtful, which has delayed the introduction of NGS in the clinical setting [15]. NGS is expensive, time consuming and presents important technical challenges including source, quantity and quality of the DNA to be sequenced [16]

Methods

Results

Conclusion