Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies
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1471-2164-14-550.pdf
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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.
Date Issued
August 2013
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
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.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
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DOI of Published Version
https://doi.org/10.1186/1471-2164-14-550
