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BioMed Research International
Volume 2013 (2013), Article ID 340620, 6 pages
http://dx.doi.org/10.1155/2013/340620
Research Article

State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity

1Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126 Torino, Italy
2Department of Computer Science, University of Torino, C.So Svizzera 185, 10149 Torino, Italy
3Unit of Cancer Epidemiology, Department of Biomedical Sciences and Human Oncology, University of Torino, 10126 Torino, Italy

Received 4 October 2012; Revised 11 January 2013; Accepted 15 January 2013

Academic Editor: Tun-Wen Pai

Copyright © 2013 Matteo Carrara et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Background. Gene fusions arising from chromosomal translocations have been implicated in cancer. RNA-seq has the potential to discover such rearrangements generating functional proteins (chimera/fusion). Recently, many methods for chimeras detection have been published. However, specificity and sensitivity of those tools were not extensively investigated in a comparative way. Results. We tested eight fusion-detection tools (FusionHunter, FusionMap, FusionFinder, MapSplice, deFuse, Bellerophontes, ChimeraScan, and TopHat-fusion) to detect fusion events using synthetic and real datasets encompassing chimeras. The comparison analysis run only on synthetic data could generate misleading results since we found no counterpart on real dataset. Furthermore, most tools report a very high number of false positive chimeras. In particular, the most sensitive tool, ChimeraScan, reports a large number of false positives that we were able to significantly reduce by devising and applying two filters to remove fusions not supported by fusion junction-spanning reads or encompassing large intronic regions. Conclusions. The discordant results obtained using synthetic and real datasets suggest that synthetic datasets encompassing fusion events may not fully catch the complexity of RNA-seq experiment. Moreover, fusion detection tools are still limited in sensitivity or specificity; thus, there is space for further improvement in the fusion-finder algorithms.