Fusion transcript simulation and application in testing fusion discovery methods
Bruno, Andrew E.
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Gene fusions are the result of chromosomal aberrations and encode chimeric RNA (fusion transcripts) that play an important role in cancer genesis. Recent advances in high throughput transcriptome sequencing have given rise to new computational methods for fusion discovery. The ability to simulate fusion transcripts is essential for testing and improving these tools. To facilitate this need, we developed FUSIM (FUsion SIMulator), a software tool for simulating fusion transcripts. The simulation of events known to create fusion genes and their resulting chimeric proteins is supported, including inter-chromosome translocation, trans-splicing, complex chromosomal rearrangements, and transcriptional read through events. FUSIM provides the ability to assemble a dataset of fusion transcripts useful for testing and benchmarking applications in fusion gene discovery. We demonstrate the capabilities of FUSIM by comparing the accuracy and performance of five existing computational fusion discovery applications. Our analysis provides an example of how FUSIM can be used as an independent simulation program to compare the performance of fusion detection methods and identify areas where these methods can be improved.
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