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Ion Torrent next-generation sequencing for routine identification of clinically relevant mutations in colorectal cancer patients
  1. Umberto Malapelle1,
  2. Elena Vigliar1,
  3. Roberta Sgariglia1,
  4. Claudio Bellevicine1,
  5. Lorenzo Colarossi2,3,
  6. Domenico Vitale2,
  7. Pierlorenzo Pallante4,5,
  8. Giancarlo Troncone1
  1. 1Department of Public Health, Pathological section, University of Naples Federico II, Naples, Italy
  2. 2Mediterranean Institute of Oncology (IOM), Catania, Italy
  3. 3PhD Programme in Biotechnology and Clinical Medicine, Sapienza University, Rome, Italy
  4. 4CNR/IEOS, Institute of Experimental Endocrinology and Oncology, National Research Council, Naples, Italy
  5. 5Department of Molecular Medicine and Medical Biotechnology (DMMBM), University of Naples Federico II, Naples, Italy
  1. Correspondence to Professor Giancarlo Troncone, Pathological section, Department of Public Health, University of Naples Federico II, via Sergio Pansini 5, Naples I-80131, Italy; giancarlo.troncone{at}unina.it

Abstract

Aims To evaluate the accuracy, consumable cost and time around testing (TAT) of a next-generation sequencing (NGS) assay, the Ion Torrent AmpliSeq Colon and Lung Cancer Panel, as an alternative to Sanger sequencing to genotype KRAS, NRAS and BRAF in colorectal cancer patients.

Methods The Ion Torrent panel was first verified on cell lines and on control samples and then prospectively applied to routine specimens (n=114), with Sanger sequencing as reference.

Results The Ion Torrent panel detected mutant alleles at the 5% level on cell lines and correctly classified all control tissues. The Ion Torrent assay was successfully carried out on most (95.6%) routine diagnostic samples. Of these, 12 (11%) harboured mutations in the BRAF gene and 47 (43%) in either of the two RAS genes, in two cases with a low abundance of RAS mutant allele which was missed by Sanger sequencing. The mean TAT, from sample receipt to reporting, was 10.4 (Sanger) and 13.0 (Ion Torrent) working days. The consumable cost for genotyping KRAS, NRAS and BRAF was €196 (Sanger) and €187 (Ion Torrent).

Conclusions Ion Torrent AmpliSeq Colon and Lung Cancer Panel sequencing is as robust as Sanger sequencing in routine diagnostics to select patients for anti-epidermal growth factor receptor (EGFR) therapy for metastatic colorectal cancer.

Keywords
  • colon cancer; KRAS; NRAS
  • BRAF
  • Ion Torrent
  • NGS
  • cetuximab
  • panitumumab

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