Year-end Sale % OFF 
Abstract
BackgroundChimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers.ResultsWe 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.ConclusionsOur 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.
Highlights
Chimeric transcripts, including partial and internal tandem duplications (PTDs, Internal tandem duplication (ITD)) and gene fusions, are important in the detection, prognosis, and treatment of human cancers
Such a transcript can result from genome rearrangement events that occur at the Deoxyribonucleic acid (DNA) level, or transcriptome events that occur at the Ribonucleic acid (RNA) level [1]
We used the Trans-ABySS pipeline for the assemblies and alignments in our experiments below, Barnacle can be applied to the outputs of a variety of combinations of assembly and alignment tools, provided that the outputs can be converted to the accepted formats
Summary
Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers. A chimeric transcript is an RNA molecule that does not have a collinear mapping to a single reference gene model. Such a transcript can result from genome rearrangement events that occur at the DNA level, or transcriptome events that occur at the RNA level [1]. Two types of chimeric transcripts that are important in human cancers are fusions [2]), in which parts of two genes located on the same or on different chromosomes are joined (Figure 1A); and tandem duplications, A1 A2 A3 A1 A2 A2 A1 A2 A2 A3 B1 B2 B3.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
