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Jamshidi F, Pleasance E, Li Y, Shen Y, Kasaian K, Corbett R, Eirew P, Lum A, Pandoh P, Zhao Y, Schein JE, Moore RA, Rassekh R, Huntsman DG, Knowling M, Lim H, Renouf DJ, Jones SJM, Marra MA, Nielsen TO, Laskin J, Yip S. Diagnostic value of next-generation sequencing in an unusual sphenoid tumor. Oncologist 2014; 19:623-30. [PMID: 24807916 DOI: 10.1634/theoncologist.2013-0390] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Extraordinary advancements in sequencing technology have made what was once a decade-long multi-institutional endeavor into a methodology with the potential for practical use in a clinical setting. We therefore set out to examine the clinical value of next-generation sequencing by enrolling patients with incurable or ambiguous tumors into the Personalized OncoGenomics initiative at the British Columbia Cancer Agency whereby whole genome and transcriptome analyses of tumor/normal tissue pairs are completed with the ultimate goal of directing therapeutics. First, we established that the sequencing, analysis, and communication with oncologists could be completed in less than 5 weeks. Second, we found that cancer diagnostics is an area that can greatly benefit from the comprehensiveness of a whole genome analysis. Here, we present a scenario in which a metastasized sphenoid mass, which was initially thought of as an undifferentiated squamous cell carcinoma, was rediagnosed as an SMARCB1-negative rhabdoid tumor based on the newly acquired finding of homozygous SMARCB1 deletion. The new diagnosis led to a change in chemotherapy and a complete nodal response in the patient. This study also provides additional insight into the mutational landscape of an adult SMARCB1-negative tumor that has not been explored at a whole genome and transcriptome level.
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Affiliation(s)
- Farzad Jamshidi
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Erin Pleasance
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yvonne Li
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yaoqing Shen
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Katayoon Kasaian
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard Corbett
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter Eirew
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amy Lum
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pawan Pandoh
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yongjun Zhao
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jacqueline E Schein
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard A Moore
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rod Rassekh
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David G Huntsman
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Meg Knowling
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Howard Lim
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel J Renouf
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Torsten O Nielsen
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen Yip
- Centre for Translational and Applied Genomics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada; Division of Oncology/Hematology/BMT, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada; Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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