Reanalysis of RNA-Sequencing Data Reveals Several Additional Fusion Genes with Multiple Isoforms

The Institute of Cancer Research, London, United Kingdom
PLoS ONE (Impact Factor: 3.23). 10/2012; 7(10):e48745. DOI: 10.1371/journal.pone.0048745
Source: PubMed


RNA-sequencing and tailored bioinformatic methodologies have paved the way for identification of expressed fusion genes from the chaotic genomes of solid tumors. We have recently successfully exploited RNA-sequencing for the discovery of 24 novel fusion genes in breast cancer. Here, we demonstrate the importance of continuous optimization of the bioinformatic methodology for this purpose, and report the discovery and experimental validation of 13 additional fusion genes from the same samples. Integration of copy number profiling with the RNA-sequencing results revealed that the majority of the gene fusions were promoter-donating events that occurred at copy number transition points or involved high-level DNA-amplifications. Sequencing of genomic fusion break points confirmed that DNA-level rearrangements underlie selected fusion transcripts. Furthermore, a significant portion (>60%) of the fusion genes were alternatively spliced. This illustrates the importance of reanalyzing sequencing data as gene definitions change and bioinformatic methods improve, and highlights the previously unforeseen isoform diversity among fusion transcripts.

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Available from: Sara Kangaspeska
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    • "As the number of junction reads supporting each validated fusion is reported [36,37], and eight of the validated fusions were supported by three or fewer reads, we assessed reducing Barnacle’s read support threshold (Additional file 1: Table S14). While decreasing this threshold increased the number of recovered fusions slightly, it also greatly increased the total number of predictions. "
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