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

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. We va...

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Bibliographic Details
Published in:PloS one 2015-06, Vol.10 (6), p.e0130219-e0130219
Main Authors: Fujita, Shiro, Masago, Katsuhiro, Takeshita, Jumpei, Okuda, Chiyuki, Otsuka, Kyoko, Hata, Akito, Kaji, Reiko, Katakami, Nobuyuki, Hirata, Yukio
Format: Article
Language:English
Subjects:
Base Sequence
Biomarkers
Biomarkers, Tumor - genetics
Biopsy
Cancer
Cancer genetics
Carcinoma, Non-Small-Cell Lung - genetics
Carcinoma, Non-Small-Cell Lung - therapy
Deoxyribonucleic acid
DNA
DNA - genetics
DNA sequencing
Formaldehyde
Gene mutation
Gene sequencing
Genes
Genetic Markers - genetics
Genomes
Genomics
High-Throughput Nucleotide Sequencing - methods
Humans
Lung cancer
Lung diseases
Lung Neoplasms - genetics
Lung Neoplasms - therapy
Molecular chains
Molecular Sequence Data
Mutation
Mutation - genetics
Non-small cell lung cancer
Non-small cell lung carcinoma
Paraffin
Pathogenesis
Patients
Polymerase Chain Reaction
Proto-Oncogene Proteins p21(ras) - genetics
Receptor, Epidermal Growth Factor - genetics
Sequence Analysis, DNA - methods
Small cell lung carcinoma
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Description
Summary: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. We 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. The 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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0130219