Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis

Next Generation Sequencing (NGS) has the potential of becoming an important tool in clinical diagnosis and therapeutic decision-making in oncology owing to its enhanced sensitivity in DNA mutation detection, fast-turnaround of samples in comparison to current gold standard methods and the potential...

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Bibliographic Details
Published in:PloS one 2013-07, Vol.8 (7), p.e69604-e69604
Main Authors: McCourt, Clare M, McArt, Darragh G, Mills, Ken, Catherwood, Mark A, Maxwell, Perry, Waugh, David J, Hamilton, Peter, O'Sullivan, Joe M, Salto-Tellez, Manuel
Format: Article
Language:English
Subjects:
Bioinformatics
Biology
Cancer
Clinical decision making
Colon
Colorectal cancer
Decision making
Deoxyribonucleic acid
Diagnostic systems
DNA
DNA Mutational Analysis
Epidermal growth factor
Epidermal growth factor receptors
Genes
Genomes
Hematology
Humans
K-Ras protein
Kinases
Lead
Lung cancer
Lung carcinoma
Medical diagnosis
Medical research
Medicine
Melanoma
Molecular Diagnostic Techniques - methods
Molecular Diagnostic Techniques - standards
Mutation
Mutation - genetics
Neoplasms - diagnosis
Neoplasms - genetics
Pathology
Platforms
Prostate cancer
Proto-Oncogene Proteins - genetics
Proto-Oncogene Proteins B-raf - genetics
Proto-Oncogene Proteins p21(ras)
Quality standards
ras Proteins - genetics
Receptor, Epidermal Growth Factor - genetics
Reference Standards
Reliability analysis
Reproducibility of Results
Sensitivity enhancement
Skin cancer
Technology
Technology assessment
Tumorigenesis
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Summary:Next Generation Sequencing (NGS) has the potential of becoming an important tool in clinical diagnosis and therapeutic decision-making in oncology owing to its enhanced sensitivity in DNA mutation detection, fast-turnaround of samples in comparison to current gold standard methods and the potential to sequence a large number of cancer-driving genes at the one time. We aim to test the diagnostic accuracy of current NGS technology in the analysis of mutations that represent current standard-of-care, and its reliability to generate concomitant information on other key genes in human oncogenesis. Thirteen clinical samples (8 lung adenocarcinomas, 3 colon carcinomas and 2 malignant melanomas) already genotyped for EGFR, KRAS and BRAF mutations by current standard-of-care methods (Sanger Sequencing and q-PCR), were analysed for detection of mutations in the same three genes using two NGS platforms and an additional 43 genes with one of these platforms. The results were analysed using closed platform-specific proprietary bioinformatics software as well as open third party applications. Our results indicate that the existing format of the NGS technology performed well in detecting the clinically relevant mutations stated above but may not be reliable for a broader unsupervised analysis of the wider genome in its current design. Our study represents a diagnostically lead validation of the major strengths and weaknesses of this technology before consideration for diagnostic use.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0069604