Oncotarget

Research Papers: Pathology:

Rapid targeted somatic mutation analysis of solid tumors in routine clinical diagnostics

Gilda Magliacane, Greta Grassini, Paola Bartocci, Ilaria Francaviglia, Elena Dal Cin, Gianluca Barbieri, Gianluigi Arrigoni, Lorenza Pecciarini, Claudio Doglioni and Maria Giulia Cangi _

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Oncotarget. 2015; 6:30592-30603. https://doi.org/10.18632/oncotarget.5190

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Abstract

Gilda Magliacane1,*, Greta Grassini1,*, Paola Bartocci2,*, Ilaria Francaviglia1, Elena Dal Cin1, Gianluca Barbieri2, Gianluigi Arrigoni1, Lorenza Pecciarini1, Claudio Doglioni1, Maria Giulia Cangi1

1Unit of Pathology, IRCCS San Raffaele Scientific Institute, Milano, Italy

2Diatech Pharmacogenetics Company, Jesi, Italy

*These authors have contributed equally to this work

Correspondence to:

Maria Giulia Cangi, e-mail: cangi.mariagiulia@hsr.it

Claudio Doglioni, e-mail: doglioni.claudio@hsr.it

Keywords: Pathology, molecular diagnostics, solid tumors, high throughput mass-spectrometry, target therapy, mutations

Received: July 01, 2015     Accepted: August 14, 2015     Published: September 02, 2015

ABSTRACT

Tumor genotyping is an essential step in routine clinical practice and pathology laboratories face a major challenge in being able to provide rapid, sensitive and updated molecular tests.

We developed a novel mass spectrometry multiplexed genotyping platform named PentaPanel to concurrently assess single nucleotide polymorphisms in 56 hotspots of the 5 most clinically relevant cancer genes, KRAS, NRAS, BRAF, EGFR and PIK3CA for a total of 221 detectable mutations. To both evaluate and validate the PentaPanel performance, we investigated 1025 tumor specimens of 6 different cancer types (carcinomas of colon, lung, breast, pancreas, and biliary tract, and melanomas), systematically addressing sensitivity, specificity, and reproducibility of our platform. Sanger sequencing was also performed for all the study samples.

Our data showed that PentaPanel is a high throughput and robust tool, allowing genotyping for targeted therapy selection of 10 patients in the same run, with a practical turnaround time of 2 working days. Importantly, it was successfully used to interrogate different DNAs isolated from routinely processed specimens (formalin-fixed paraffin embedded, frozen, and cytological samples), covering all the requirements of clinical tests.

In conclusion, the PentaPanel platform can provide an immediate, accurate and cost effective multiplex approach for clinically relevant gene mutation analysis in many solid tumors and its utility across many diseases can be particularly relevant in multiple clinical trials, including the new basket trial approach, aiming to identify appropriate targeted drug combination strategies.


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