Barnacle: Detecting and characterizing tandem duplications and fusions in transcriptome assemblies
dc.contributor.author | Swanson, L. | |
dc.contributor.author | Robertson, G. | |
dc.contributor.author | Mungall, K. | |
dc.contributor.author | Butterfield, Y. | |
dc.contributor.author | Chiu, R. | |
dc.contributor.author | Corbett, R. | |
dc.contributor.author | Docking, T. | |
dc.contributor.author | Hogge, D. | |
dc.contributor.author | Jackman, S. | |
dc.contributor.author | Moore, R. | |
dc.contributor.author | Mungall, A. | |
dc.contributor.author | Nip, K. | |
dc.contributor.author | Parker, J. | |
dc.contributor.author | Qian, J. | |
dc.contributor.author | Raymond, A. | |
dc.contributor.author | Sung, S. | |
dc.contributor.author | Tam, A. | |
dc.contributor.author | Thiessen, N. | |
dc.contributor.author | Varhol, Richard | |
dc.contributor.author | Wang, S. | |
dc.contributor.author | Yorukoglu, D. | |
dc.contributor.author | Zhao, Y. | |
dc.contributor.author | Hoodless, P. | |
dc.contributor.author | Sahinalp, S. | |
dc.contributor.author | Karsan, A. | |
dc.contributor.author | Birol, I. | |
dc.date.accessioned | 2017-01-30T15:29:06Z | |
dc.date.available | 2017-01-30T15:29:06Z | |
dc.date.created | 2016-02-01T00:47:10Z | |
dc.date.issued | 2013 | |
dc.identifier.citation | Swanson, L. and Robertson, G. and Mungall, K. and Butterfield, Y. and Chiu, R. and Corbett, R. and Docking, T. et al. 2013. Barnacle: Detecting and characterizing tandem duplications and fusions in transcriptome assemblies. BMC Genomics. 14 (550): pp. 2-19. | |
dc.identifier.uri | http://hdl.handle.net/20.500.11937/46752 | |
dc.identifier.doi | 10.1186/1471-2164-14-550 | |
dc.description.abstract |
Background: Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers.Results: We describe Barnacle, a production-grade analysis tool that detects such chimeras in de novo assemblies of RNA-seq data, and supports prioritizing them for review and validation by reporting the relative coverage of co-occurring chimeric and wild-type transcripts. We demonstrate applications in large-scale disease studies, by identifying PTDs in MLL, ITDs in FLT3, and reciprocal fusions between PML and RARA, in two deeply sequenced acute myeloid leukemia (AML) RNA-seq datasets.Conclusions: Our analyses of real and simulated data sets show that, with appropriate filter settings, Barnacle makes highly specific predictions for three types of chimeric transcripts that are important in a range of cancers: PTDs, ITDs, and fusions. High specificity makes manual review and validation efficient, which is necessary in large-scale disease studies. Characterizing an extended range of chimera types will help generate insights into progression, treatment, and outcomes for complex diseases. © 2013 Swanson et al.; licensee BioMed Central Ltd. | |
dc.title | Barnacle: Detecting and characterizing tandem duplications and fusions in transcriptome assemblies | |
dc.type | Journal Article | |
dcterms.source.volume | 14 | |
dcterms.source.number | 1 | |
dcterms.source.title | BMC Genomics | |
curtin.note |
This open access article is distributed under the Creative Commons license | |
curtin.department | Department of Health Policy and Management | |
curtin.accessStatus | Open access |