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Fisher KE, Zhang L, Wang J, Smith GH, Newman S, Schneider TM, Pillai RN, Kudchadkar RR, Owonikoko TK, Ramalingam SS, Lawson DH, Delman KA, El-Rayes BF, Wilson MM, Sullivan HC, Morrison AS, Balci S, Adsay NV, Gal AA, Sica GL, Saxe DF, Mann KP, Hill CE, Khuri FR, Rossi MR. Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non-Small Cell Lung, Melanoma, and Gastrointestinal Malignancies. J Mol Diagn 2016; 18:299-315. [PMID: 26801070 DOI: 10.1016/j.jmoldx.2015.11.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 11/05/2015] [Accepted: 11/19/2015] [Indexed: 12/30/2022] Open
Abstract
We tested and clinically validated a targeted next-generation sequencing (NGS) mutation panel using 80 formalin-fixed, paraffin-embedded (FFPE) tumor samples. Forty non-small cell lung carcinoma (NSCLC), 30 melanoma, and 30 gastrointestinal (12 colonic, 10 gastric, and 8 pancreatic adenocarcinoma) FFPE samples were selected from laboratory archives. After appropriate specimen and nucleic acid quality control, 80 NGS libraries were prepared using the Illumina TruSight tumor (TST) kit and sequenced on the Illumina MiSeq. Sequence alignment, variant calling, and sequencing quality control were performed using vendor software and laboratory-developed analysis workflows. TST generated ≥500× coverage for 98.4% of the 13,952 targeted bases. Reproducible and accurate variant calling was achieved at ≥5% variant allele frequency with 8 to 12 multiplexed samples per MiSeq flow cell. TST detected 112 variants overall, and confirmed all known single-nucleotide variants (n = 27), deletions (n = 5), insertions (n = 3), and multinucleotide variants (n = 3). TST detected at least one variant in 85.0% (68/80), and two or more variants in 36.2% (29/80), of samples. TP53 was the most frequently mutated gene in NSCLC (13 variants; 13/32 samples), gastrointestinal malignancies (15 variants; 13/25 samples), and overall (30 variants; 28/80 samples). BRAF mutations were most common in melanoma (nine variants; 9/23 samples). Clinically relevant NGS data can be obtained from routine clinical FFPE solid tumor specimens using TST, benchtop instruments, and vendor-supplied bioinformatics pipelines.
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Affiliation(s)
- Kevin E Fisher
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia; Department of Pathology, Texas Children's Hospital, Houston, Texas; Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas.
| | - Linsheng Zhang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Jason Wang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia; Department of Pathology, University of Texas Southwestern and Children's Medical Center, Dallas, Texas
| | - Geoffrey H Smith
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Scott Newman
- Biostatistics and Bioinformatics Shared Resource, Emory University, Atlanta, Georgia
| | - Thomas M Schneider
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Rathi N Pillai
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, Georgia; Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Ragini R Kudchadkar
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, Georgia; Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Taofeek K Owonikoko
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, Georgia; Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Suresh S Ramalingam
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, Georgia; Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - David H Lawson
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, Georgia; Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Keith A Delman
- Winship Cancer Institute, Emory University, Atlanta, Georgia; Department of Surgery, Emory University School of Medicine, Atlanta, Georgia
| | - Bassel F El-Rayes
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, Georgia; Winship Cancer Institute, Emory University, Atlanta, Georgia
| | | | - H Clifford Sullivan
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Annie S Morrison
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Serdar Balci
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - N Volkan Adsay
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Anthony A Gal
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Gabriel L Sica
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Debra F Saxe
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Karen P Mann
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Charles E Hill
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Fadlo R Khuri
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, Georgia; Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Michael R Rossi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia; Department of Radiation Oncology, Emory University School of Medicine, Atlanta, Georgia
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Fisher KE, Cohen C, Palma JF, Longshore JW. BRAF p.V600E immunohistochemistry in challenging samples: about false-positive and false-negative results--reply. Hum Pathol 2015; 46:1065-6. [PMID: 25971545 DOI: 10.1016/j.humpath.2015.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 03/06/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Kevin E Fisher
- Department of Pathology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX 77030; Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030; Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322.
| | - Cynthia Cohen
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322
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