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Lin MT, Mosier SL, Thiess M, Beierl KF, Debeljak M, Tseng LH, Chen G, Yegnasubramanian S, Ho H, Cope L, Wheelan SJ, Gocke CD, Eshleman JR. Clinical validation of KRAS, BRAF, and EGFR mutation detection using next-generation sequencing. Am J Clin Pathol 2014; 141:856-66. [PMID: 24838331 DOI: 10.1309/ajcpmwgwgo34egod] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVES To validate next-generation sequencing (NGS) technology for clinical diagnosis and to determine appropriate read depth. METHODS We validated the KRAS, BRAF, and EGFR genes within the Ion AmpliSeq Cancer Hotspot Panel using the Ion Torrent Personal Genome Machine (Life Technologies, Carlsbad, CA). RESULTS We developed a statistical model to determine the read depth needed for a given percent tumor cellularity and number of functional genomes. Bottlenecking can result from too few input genomes. By using 16 formalin-fixed, paraffin-embedded (FFPE) cancer-free specimens and 118 cancer specimens with known mutation status, we validated the six traditional analytic performance characteristics recommended by the Next-Generation Sequencing: Standardization of Clinical Testing Working Group. Baseline noise is consistent with spontaneous and FFPE-induced C:G→T:A deamination mutations. CONCLUSIONS Redundant bioinformatic pipelines are essential, since a single analysis pipeline gave false-negative and false-positive results. NGS is sufficiently robust for the clinical detection of gene mutations, with attention to potential artifacts.
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Affiliation(s)
- Ming-Tseh Lin
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Stacy L. Mosier
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Michele Thiess
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Katie F. Beierl
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Marija Debeljak
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Li-Hui Tseng
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Guoli Chen
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | | | - Hao Ho
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Leslie Cope
- Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Sarah J. Wheelan
- Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christopher D. Gocke
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
- Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - James R. Eshleman
- Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
- Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD
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