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| Content Provider | Springer Nature : BioMed Central |
|---|---|
| Author | Swanson, Lucas Robertson, Gordon Mungall, Karen L Butterfield, Yaron S Chiu, Readman Corbett, Richard D Docking, T Roderick Hogge, Donna Jackman, Shaun D Moore, Richard A Mungall, Andrew J Nip, Ka Ming Parker, Jeremy DK Qian, Jenny Qing Raymond, Anthony Sung, Sandy Tam, Angela Thiessen, Nina Varhol, Richard Wang, Sherry Yorukoglu, Deniz Zhao, YongJun Hoodless, Pamela A Sahinalp, S Cenk Karsan, Aly Birol, Inanc |
| 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. |
| Related Links | https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-14-550.pdf |
| Ending Page | 19 |
| Page Count | 19 |
| Starting Page | 1 |
| File Format | HTM / HTML |
| ISSN | 14712164 |
| DOI | 10.1186/1471-2164-14-550 |
| Journal | BMC Genomics |
| Issue Number | 1 |
| Volume Number | 14 |
| Language | English |
| Publisher | BioMed Central |
| Publisher Date | 2013-08-14 |
| Access Restriction | Open |
| Subject Keyword | Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Transcriptome assembly Chimeric transcripts Fusion Partial tandem duplication PTD Internal tandem duplication ITD RNA-seq Transcriptome |
| Content Type | Text |
| Resource Type | Article |
| Subject | Biotechnology Genetics |
| Journal Impact Factor | 3.5/2023 |
| 5-Year Journal Impact Factor | 4.1/2023 |
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