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, Maria Giulia Cangi

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)30592-30603
Number of pages12
JournalOncotarget
Volume6
Issue number31
DOIs
Publication statusPublished - 2015

Keywords

  • High throughput mass-spectrometry
  • Molecular diagnostics
  • Mutations
  • Pathology
  • Solid tumors
  • Target therapy

ASJC Scopus subject areas

  • Oncology

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