Academic Journal
In silico validation of RNA-Seq results can identify gene fusions with oncogenic potential in glioblastoma
| Title: | In silico validation of RNA-Seq results can identify gene fusions with oncogenic potential in glioblastoma |
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| Authors: | Ainhoa Hernandez, Ana Maria Muñoz-Mármol, Anna Esteve-Codina, Francesc Alameda, Cristina Carrato, Estela Pineda, Oriol Arpí-Lluciá, Maria Martinez-García, Mar Mallo, Marta Gut, Sonia del Barco, Oscar Gallego, Marc Dabad, Carlos Mesia, Beatriz Bellosillo, Marta Domenech, Noemí Vidal, Iban Aldecoa, Nuria de la Iglesia, Carmen Balana |
| Source: | Scientific Reports, Vol 12, Iss 1, Pp 1-11 (2022) |
| Publisher Information: | Nature Portfolio, 2022. |
| Publication Year: | 2022 |
| Collection: | LCC:Medicine LCC:Science |
| Subject Terms: | Medicine, Science |
| More Details: | Abstract RNA-Sequencing (RNA-Seq) can identify gene fusions in tumors, but not all these fusions have functional consequences. Using multiple data bases, we have performed an in silico analysis of fusions detected by RNA-Seq in tumor samples from 139 newly diagnosed glioblastoma patients to identify in-frame fusions with predictable oncogenic potential. Among 61 samples with fusions, there were 103 different fusions, involving 167 different genes, including 20 known oncogenes or tumor suppressor genes (TSGs), 16 associated with cancer but not oncogenes or TSGs, and 32 not associated with cancer but previously shown to be involved in fusions in gliomas. After selecting in-frame fusions able to produce a protein product and running Oncofuse, we identified 30 fusions with predictable oncogenic potential and classified them into four non-overlapping categories: six previously described in cancer; six involving an oncogene or TSG; four predicted by Oncofuse to have oncogenic potential; and 14 other in-frame fusions. Only 24 patients harbored one or more of these 30 fusions, and only two fusions were present in more than one patient: FGFR3::TACC3 and EGFR::SEPTIN14. This in silico study provides a good starting point for the identification of gene fusions with functional consequences in the pathogenesis or treatment of glioblastoma. |
| Document Type: | article |
| File Description: | electronic resource |
| Language: | English |
| ISSN: | 2045-2322 |
| Relation: | https://doaj.org/toc/2045-2322 |
| DOI: | 10.1038/s41598-022-18608-8 |
| Access URL: | https://doaj.org/article/0b0b63b99c594a57946178f4759c176b |
| Accession Number: | edsdoj.0b0b63b99c594a57946178f4759c176b |
| Database: | Directory of Open Access Journals |
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| ISSN: | 20452322 |
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| DOI: | 10.1038/s41598-022-18608-8 |
| Published in: | Scientific Reports |
| Language: | English |