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dc.contributor.authorEdgren, Henrik
dc.contributor.authorMurumagi, Astrid
dc.contributor.authorKangaspeska, Sara
dc.contributor.authorNicorici, Daniel
dc.contributor.authorHongisto, Vesa
dc.contributor.authorKleivi, Kristine
dc.contributor.authorRye, Inga H
dc.contributor.authorNyberg, Sandra
dc.contributor.authorWolf, Maija
dc.contributor.authorBorresen-Dale, Anne-Lise
dc.contributor.authorKallioniemi, Olli
dc.date.accessioned2015-10-09T02:15:02Z
dc.date.available2015-10-09T02:15:02Z
dc.date.issued2011
dc.identifier.citationGenome Biology. 2011 Jan 19;12(1):R6
dc.identifier.urihttp://hdl.handle.net/10852/46857
dc.description.abstractBackground Until recently, chromosomal translocations and fusion genes have been an underappreciated class of mutations in solid tumors. Next-generation sequencing technologies provide an opportunity for systematic characterization of cancer cell transcriptomes, including the discovery of expressed fusion genes resulting from underlying genomic rearrangements. Results We applied paired-end RNA-seq to identify 24 novel and 3 previously known fusion genes in breast cancer cells. Supported by an improved bioinformatic approach, we had a 95% success rate of validating gene fusions initially detected by RNA-seq. Fusion partner genes were found to contribute promoters (5' UTR), coding sequences and 3' UTRs. Most fusion genes were associated with copy number transitions and were particularly common in high-level DNA amplifications. This suggests that fusion events may contribute to the selective advantage provided by DNA amplifications and deletions. Some of the fusion partner genes, such as GSDMB in the TATDN1-GSDMB fusion and IKZF3 in the VAPB-IKZF3 fusion, were only detected as a fusion transcript, indicating activation of a dormant gene by the fusion event. A number of fusion gene partners have either been previously observed in oncogenic gene fusions, mostly in leukemias, or otherwise reported to be oncogenic. RNA interference-mediated knock-down of the VAPB-IKZF3 fusion gene indicated that it may be necessary for cancer cell growth and survival. Conclusions In summary, using RNA-sequencing and improved bioinformatic stratification, we have discovered a number of novel fusion genes in breast cancer, and identified VAPB-IKZF3 as a potential fusion gene with importance for the growth and survival of breast cancer cells.
dc.language.isoeng
dc.rightsEdgren et al.; licensee BioMed Central Ltd.
dc.rightsAttribution 2.0 Generic
dc.rights.urihttp://creativecommons.org/licenses/by/2.0/
dc.titleIdentification of fusion genes in breast cancer by paired-end RNA-sequencing
dc.typeJournal article
dc.date.updated2015-10-09T02:15:02Z
dc.creator.authorEdgren, Henrik
dc.creator.authorMurumagi, Astrid
dc.creator.authorKangaspeska, Sara
dc.creator.authorNicorici, Daniel
dc.creator.authorHongisto, Vesa
dc.creator.authorKleivi, Kristine
dc.creator.authorRye, Inga H
dc.creator.authorNyberg, Sandra
dc.creator.authorWolf, Maija
dc.creator.authorBorresen-Dale, Anne-Lise
dc.creator.authorKallioniemi, Olli
dc.identifier.doihttp://dx.doi.org/10.1186/gb-2011-12-1-r6
dc.identifier.urnURN:NBN:no-51037
dc.type.documentTidsskriftartikkel
dc.type.peerreviewedPeer reviewed
dc.identifier.fulltextFulltext https://www.duo.uio.no/bitstream/handle/10852/46857/1/13059_2010_Article_2471.pdf
dc.type.versionPublishedVersion
cristin.articleidR6


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