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Chapitre D'ouvrage Année : 2018

RNA-Seq Analysis to Detect Abnormal Fusion Transcripts Linked to Chromothripsis

Résumé

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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Dates et versions

hal-02503709 , version 1 (10-03-2020)

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Anne-Laure Bouge, Florence Ruffle, Sébastien Riquier, Benoît Guibert, Jérôme Audoux, et al.. RNA-Seq Analysis to Detect Abnormal Fusion Transcripts Linked to Chromothripsis. Franck Pellestor. Chromothripsis-Methods and Protocols, Humana Press, New York, NY -, pp.133-156, 2018, Hardcover ISBN 978-1-4939-7779-6 ; Softcover ISBN 978-1-4939-9283-6 ; eBook ISBN 978-1-4939-7780-2. ⟨10.1007/978-1-4939-7780-2_9⟩. ⟨hal-02503709⟩
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