|
| Status |
Public on Feb 10, 2011 |
| Title |
Large scale screening for known fusion genes in cancer cell lines |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
Genome variation profiling by array
|
| Summary |
We have utilized a version 2.0 of our Fusion gene microarray (version 1.0 described by PMID: 19152679 and GEO, GPL8078) to screen cancer cell lines for known fusion genes
We assembled a comprehensive database of published fusion genes, including those which have been reported only in individual studies and samples, and fusion genes resulting from deep sequencing of cancer genomes and transcriptomes. From the total set of 548 fusion genes, we designed 197,846 unique oligonucleotides, targeting both chimeric transcript junctions as well as sequences internal to each of the fusion gene partners. We investigated the presence of fusion genes in a series of 67 cell lines originating from 15 different cancer types. Data from ten leukaemia cell lines with known fusion gene status were used to evaluate and calibrate an automated scoring algorithm. In five out of ten cell lines the correct fusion gene was the top most scoring hit, and one came second, all six passing a cut-off of 50 percent of theoretical maximum-score. Two additional fusion genes, BCAS4-BCAS3 from the MCF-7 breast cancer cell line and CCDC6-RET from the TPC-1 thyroid cancer cell line were validated as true positive fusion transcripts from the remaining 57 cell lines.
|
| |
|
| Overall design |
A total of 67 cell lines from various cancer types were analysed for presence of known fusion genes
|
| |
|
| Contributor(s) |
Løvf M, Thomassen GS, Bakken AC, Celestino R, Fioertos T, Lind GE, Lothe RA, Skotheim RI |
| Citation(s) |
21305644 |
| |
| Submission date |
Oct 15, 2010 |
| Last update date |
Mar 22, 2012 |
| Contact name |
Gard Olav Thomassen |
| Phone |
+47 93674926
|
| Fax |
+47 22844782
|
| URL |
http://www.rr-research.no/skotheim/
|
| Organization name |
Rikshospitalet
|
| Department |
Institute for Cancer Research
|
| Lab |
Department of Cancer prevention
|
| Street address |
Radiumhospitalet, Rikshospitalet HF
|
| City |
Oslo |
| ZIP/Postal code |
0310 |
| Country |
Norway |
| |
|
| Platforms (1) |
| GPL11054 |
Fusion gene microarray, human, 500k, v.2.0. |
|
| Samples (67)
|
|
| Relations |
| BioProject |
PRJNA132429 |
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