Validation of a Next-Generation Sequencing Assay Targeting RNA for the Multiplexed Detection of Fusion Transcripts and Oncogenic Isoforms.
Context.--Next-generation sequencing is a high-throughput method for detecting genetic abnormalities and providing prognostic and therapeutic information for patients with cancer. Oncogenic fusion transcripts are among the various classifications of genetic abnormalities present in tumors and are ty...
| Publicado en: | Archives of Pathology & Laboratory Medicine Vol. 144; no. 1; pp. 90 - 99 |
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| Autores principales: | , , , , , |
| Formato: | research tables/charts Journal Article |
| Publicado: |
College of American Pathologists
Jan2020
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=140960449&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 140960449 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 00039985 1FS jtl: Archives of Pathology & Laboratory Medicine issn: 00039985 maglogo: N pubinfo: dt: Jan2020 vid: 144 iid: 1 pid: 2550 pub: College of American Pathologists place: Northfield, Illinois artinfo: ui: 140960449 140960449 140960449 10.5858/arpa.2018-0441-OA 140960449 ppf: 90 ppct: 9 formats: fmt: @attributes: type: P tig: atl: Validation of a Next-Generation Sequencing Assay Targeting RNA for the Multiplexed Detection of Fusion Transcripts and Oncogenic Isoforms. aug: au: Sussman, Robyn T. Oran, Amanda R. Paolillo, Carmela Lieberman, David Morrissette, Jennifer J. D. Rosenbaum, Jason N. affil: Center for Personalized Diagnostics, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia sug: subj: Sequence Analysis Methods Polymerase Chain Reaction Methods Genes Oncogenes Clinical Laboratories Human Nucleic Acids Blood Paraffin Embedding In Situ Hybridization, Fluorescence Sensitivity and Specificity Lung Neoplasms Glioma ab: Context.--Next-generation sequencing is a high-throughput method for detecting genetic abnormalities and providing prognostic and therapeutic information for patients with cancer. Oncogenic fusion transcripts are among the various classifications of genetic abnormalities present in tumors and are typically detected clinically with fluorescence in situ hybridization (FISH). However, FISH probes only exist for a limited number of targets, do not provide any information about fusion partners, cannot be multiplex, and have been shown to be limited in specificity for common targets such as ALK. Objective.--To validate an anchored multiplex polymerase chain reaction--based panel for the detection of fusion transcripts in a university hospital--based clinical molecular diagnostics laboratory. Design.--We used 109 unique clinical specimens to validate a custom panel targeting 104 exon boundaries from 17 genes involved in fusions in solid tumors. The panel can accept as little as 100 ng of total nucleic acid from PreservCyt-fixed tissue, and formalin-fixed, paraffin-embedded specimens with as little as 10% tumor nuclei. Results.--Using FISH as the gold standard, this assay has a sensitivity of 88.46% and a specificity of 95.83% for the detection of fusion transcripts involving ALK, RET, and ROS1 in lung adenocarcinomas. Using a validated next-generation sequencing assay as the orthogonal gold standard for the detection of EGFR variant III (EGFRvIII) in glioblastomas, the assay is 92.31% sensitive and 100% specific. Conclusions.--This multiplexed assay is tumor and fusion partner agnostic and will provide clinical utility in therapy selection for patients with solid tumors. pubtype: Academic Journal doctype: research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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