Abstract
RNA-Seq approach enables the detection and characterization of fusion or chimeric transcript associated to complex genome rearrangement. Until now, these events are classically identified at DNA level.
Here we describe a complete procedure including a novel way of analyzing reads that combines genomic locations and local coverage to directly infer chimeric junctions with a high sensitivity and specificity, allowing identification of different classes of chimeric RNA events. We also recommend the best practices for the bioinformatics analysis and describe the experimental process for RNA validation using real-time PCR and sequencing.
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Pellestor F, Gatinois V, Puechberty J et al (2014) Chromothripsis, an unexpected novel form of complexity for chromosomal rearrangements. Med Sci (Paris) 30(3):266–273
Wu C, Wyatt AW, McPherson A et al (2012) Poly-gene fusion transcripts and chromothripsis in prostate cancer. Genes Chromosom Cancer 51:1144–1153
Boeva V, Jouannet S, Daveau R et al (2013) Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis. PLoS One 8(8):e72182. https://doi.org/10.1371/journal.pone.0072182
Byron SA, Van Keuren-Jensen KR, Engelthaler DM et al (2016) Translating RNA sequencing into clinical diagnostics: opportunities and challenges. Nat Rev Genet 17(5):257–271
Mertens F, Johansson B, Fioretos T et al (2015) The emerging complexity of gene fusions in cancer. Nat Rev Cancer 15:371–381
Beaumeunier S, Audoux J, Boureux A et al (2016) On the evaluation of the fidelity of supervised classifiers in the prediction of chimeric RNAs. BioData Min 9:34
Philippe N, Salson M, Commes T et al (2013) CRAC: an integrated approach to the analysis of RNA-seq reads. Genome Biol 14:R30. https://doi.org/10.1186/gb-2013-14-3-r30
Rufflé F, Audoux J, Boureux A et al (2017) New chimeric RNAs in acute myeloid leukemia. F1000Res 6:1302
Philippe N, Bou Samra E, Boureux A et al (2014) Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome. Nucleic Acids Res 42(5):2820–2832
Krzywinski MI, Schein JE, Birol I et al (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19(9):1639–1645
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Bougé, AL., Rufflé, F., Riquier, S., Guibert, B., Audoux, J., Commes, T. (2018). RNA-Seq Analysis to Detect Abnormal Fusion Transcripts Linked to Chromothripsis. In: Pellestor, F. (eds) Chromothripsis. Methods in Molecular Biology, vol 1769. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7780-2_9
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DOI: https://doi.org/10.1007/978-1-4939-7780-2_9
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Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7779-6
Online ISBN: 978-1-4939-7780-2
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