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Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies

Author(s)
Swanson, Lucas; Robertson, Gordon; Mungall, Karen L.; Butterfield, Yaron S.; Chiu, Readman; Corbett, Richard D.; Docking, T. R.; Hogge, Donna; Jackman, Shaun D.; Moore, Richard A.; Mungall, Andrew J.; Nip, Ka Ming; Parker, Jeremy D. K.; Qian, Jenny Q.; Raymond, Anthony; Sung, Sandy; Tam, Angela; Thiessen, Nina; Varhol, Richard; Wang, Sherry; Yorukoglu, Deniz; Zhao, YongJun; Hoodless, Pamela A.; Sahinalp, S. C.; Karsan, Aly; Birol, Inanc; Qian, Jenny; Sahinalp, S.; ... Show more Show less
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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.
Date issued
2013-08
URI
http://hdl.handle.net/1721.1/81361
Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory; Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Journal
BMC Genomics
Publisher
BioMed Central Ltd.
Citation
Swanson, Lucas, Gordon Robertson, Karen L Mungall, et al. 2013. Barnacle: Detecting and Characterizing Tandem Duplications and Fusions in Transcriptome Assemblies. BMC Genomics 14(1): 550.
Version: Final published version
ISSN
1471-2164

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