Oncotarget

Research Papers:

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

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Oncotarget. 2018; 9:22749-22768. https://doi.org/10.18632/oncotarget.25229

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Abstract

Duarte Mendes Oliveira1,6, Teresa Mirante1,6, Chiara Mignogna2, Marianna Scrima1,8, Simona Migliozzi1, Gaetano Rocco3, Renato Franco4, Francesco Corcione7, Giuseppe Viglietto1,6, Donatella Malanga1,6 and Antonia Rizzuto5

1Department of Experimental and Clinical Medicine, University “Magna Graecia”, Catanzaro, Italy

2Department of Health Sciences, University “Magna Graecia”, Catanzaro, Italy

3Pathology Unit, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS, Naples, Italy

4Pathology Unit, Second University of Naples, Italy

5Department of Medical and Surgical Sciences, University “Magna Graecia”, Catanzaro, Italy

6Interdepartmental Center of Services (CIS), University “Magna Graecia”, Catanzaro, Italy

7UOC Chirurgia Generale, Azienda Ospedaliera dei Colli, Napoli, Italy

8Biogem scarl, Institute of Genetic Research, Ariano Irpino (AV), Italy

Correspondence to:

Giuseppe Viglietto, email: viglietto@unicz.it

Donatella Malanga, email: malanga@unicz.it

Keywords: solid tumors; oncomine focus assay; copy number variation; gene fusions

Received: December 09, 2017     Accepted: April 05, 2018     Published: April 27, 2018

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.


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