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Neill SG, Saxe DF, Rossi MR, Schniederjan MJ, Brat DJ. Genomic Analysis in the Practice of Surgical Neuropathology: The Emory Experience. Arch Pathol Lab Med 2017; 141:355-365. [DOI: 10.5858/arpa.2016-0276-sai] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The evaluation of central nervous system tumors increasingly relies on molecular genetic methods to aid in classification, offer prognostic information, and predict response to therapy. Available assays make it possible to assess genetic losses, amplifications, translocations, mutations, or the expression levels of specific gene transcripts or proteins. Current molecular diagnostics frequently use a panel-based approach and whole genome analysis, and generally rely either on DNA sequencing or on hybridization-based methodologies, such as those used in cytogenomic microarrays. In some cases, immunohistochemistry can be used as a surrogate for genetic analysis when the mutation of interest consistently results in overexpression or underexpression of a known protein product. In surgical neuropathology practice, the diagnostic workup of diffuse gliomas, medulloblastomas, low-grade circumscribed gliomas, as well as other diseases, now routinely incorporates the results of genomic studies. Here we summarize our institution's current approach to diagnostic surgical neuropathology, using these contemporary molecular diagnostic applications.
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Affiliation(s)
| | | | | | | | - Daniel J. Brat
- From the Departments of Pathology and Laboratory Medicine (Drs Neill, Saxe, Rossi, Schniederjan, and Brat) and Radiation Oncology (Dr Rossi), Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia; and the Department of Pathology, Children's Healthcare of Atlanta, Atlanta, Georgia (Dr Schniederjan)
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McGowan ML, Ponsaran RS, Silverman P, Harris LN, Marshall PA. "A rising tide lifts all boats": establishing a multidisciplinary genomic tumor board for breast cancer patients with advanced disease. BMC Med Genomics 2016; 9:71. [PMID: 27871291 PMCID: PMC5117517 DOI: 10.1186/s12920-016-0234-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 11/14/2016] [Indexed: 12/02/2022] Open
Abstract
Background Research suggests that multidisciplinary genomic tumor boards (MGTB) can inform cancer patient care, though little is known about factors influencing how MGTBs interpret genomic test results, make recommendations, and perceive the utility of this approach. This study’s objective was to observe, describe, and assess the establishment of the Breast Multidisciplinary Genomic Tumor Board, the first MGTB focused on interpreting genomic test results for breast cancer patients with advanced disease. Methods We conducted a qualitative case study involving participant observation at monthly MGTB meetings from October 2013 through November 2014 and interviews with 12 MGTB members. We analyzed social dynamics and interactions within the MGTB regarding interpretation of genomic findings and participants’ views on effectiveness of the MGTB in using genomics to inform patient care. Results Twenty-two physicians, physician-scientists, basic scientists, bioethicists, and allied care professionals comprised the MGTB. The MGTB reviewed FoundationOne™ results for 40 metastatic breast cancer patients. Based on findings, the board mostly recommended referring patients to clinical trials (34) and medical genetics (15), and Food and Drug Administration-approved (FDA) breast cancer therapies (13). Though multidisciplinary, recommendations were driven by medical oncologists. Interviewees described providing more precise care recommendations and professional development as advantages and the limited actionability of genomic test results as a challenge for the MGTB. Conclusions Findings suggest both feasibility and desirability of pooling professional expertise in genomically-guided breast cancer care and challenges to institutionalizing a Breast MGTB, specifically in promoting interdisciplinary contributions and managing limited actionability of genomic test results for patients with advanced disease.
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Affiliation(s)
- Michelle L McGowan
- Ethics Center, Division of General and Community Pediatrics, Cincinnati Children's Hospital Medical Center, Departments of Pediatrics and Women's, Gender, and Sexuality Studies, University of Cincinnati, 3333 Burnet Avenue, MLC 15006, Cincinnati, OH, 45229, USA.
| | | | - Paula Silverman
- Case Western Reserve University School of Medicine, University Hospitals Seidman Cancer Center, Cleveland, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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