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- Title
Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies.
- Authors
Swanson, Lucas; Robertson, Gordon; Mungall, Karen L.; Butterfield, Yaron S.; Chiu, Readman; Corbett, Richard D.; Roderick Docking, T.; Hogge, Donna; Jackman, Shaun D.; Moore, Richard A.; Mungall, Andrew J.; Nip, Ka Ming; Parker, Jeremy D. K.; Qian, Jenny Qing; Raymond, Anthony; Sung, Sandy; Tam, Angela; Thiessen, Nina; Varhol, Richard; Wang, Sherry
- 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.
- Subjects
CANCER treatment; CHIMERIC proteins; GENE fusion; NUCLEOTIDE sequence; RNA; EUKARYOTES; THERAPEUTICS
- Publication
BMC Genomics, 2013, Vol 14, Issue 1, p1
- ISSN
1471-2164
- Publication type
Article
- DOI
10.1186/1471-2164-14-550