Validation of an Ion Torrent Sequencing Platform for the Detection of Gene Mutations in Biopsy Specimens from Patients with Non-Small-Cell Lung Cancer.

Shiro Fujita,Chiyuki Okuda,Nobuyuki Katakami,Jumpei Takeshita,Kyoko Otsuka,Reiko Kaji,Katsuhiro Masago,Yukio Hirata,Akito Hata,Anthony W.I Lo

doi:10.1371/journal.pone.0130219

Shiro Fujita, Chiyuki Okuda + Show 8 more

Open Access

https://doi.org/10.1371/journal.pone.0130219

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Journal: PloS one	Publication Date: Jun 15, 2015
Citations: 4	License type: CC BY 4.0

Affiliation: Foundation for Biomedical Research and Innovation

Abstract

BackgroundTreatment for patients with advanced non-small cell lung cancer (NSCLC) is often determined by the presence of biomarkers that predict the response to agents targeting specific molecular pathways. Demands for multiplex analysis of the genes involved in the pathogenesis of NSCLC are increasing.MethodsWe validated the Ion Torrent Personal Genome Machine (PGM) system using the Ion AmpliSeq Cancer Hotspot Panel and compared the results with those obtained using the gold standard methods, conventional PCR and Sanger sequencing. The cycleave PCR method was used to verify the results.Results and ConclusionThe Ion Torrent PGM resulted in a similar level of accuracy in identifying multiple genetic mutations in parallel, compared with conventional PCR and Sanger sequencing; however, the Ion Torrent PGM was superior to the other sequencing methods in terms of increased ease of use, even when taking into account the small amount of DNA that was obtained from formalin-fixed paraffin embedded (FFPE) biopsy specimens.

Highlights

BackgroundTreatment for patients with advanced non-small cell lung cancer (NSCLC) is often determined by the presence of biomarkers that predict the response to agents targeting specific molecular pathways
Treatment for patients with advanced non-small cell lung cancer (NSCLC) is often determined, as is the case for other human cancers, by the presence of biomarkers that predict the responsePLOS ONE | DOI:10.1371/journal.pone.0130219 June 15, 2015Validation of an Ion Torrent Sequencing Platform to agents targeting specific molecular pathways in malignant cells
The Ion Torrent Personal Genome Machine (PGM) resulted in a similar level of accuracy in identifying multiple genetic mutations in parallel, compared with conventional PCR and Sanger sequencing; the Ion Torrent PGM was superior to the other sequencing methods in terms of increased ease of use, even when taking into account the small amount of DNA that was obtained from formalin-fixed paraffin embedded (FFPE) biopsy specimens

Summary

Background

Treatment for patients with advanced non-small cell lung cancer (NSCLC) is often determined by the presence of biomarkers that predict the response to agents targeting specific molecular pathways. Demands for multiplex analysis of the genes involved in the pathogenesis of NSCLC are increasing

Methods

Results and Conclusion

Introduction

Results and Discussion