Chapter title |
RNA-Seq Analysis to Detect Abnormal Fusion Transcripts Linked to Chromothripsis
|
---|---|
Chapter number | 9 |
Book title |
Chromothripsis
|
Published in |
Methods in molecular biology, January 2018
|
DOI | 10.1007/978-1-4939-7780-2_9 |
Pubmed ID | |
Book ISBNs |
978-1-4939-7779-6, 978-1-4939-7780-2
|
Authors |
Anne-Laure Bougé, Florence Rufflé, Sébastien Riquier, Benoit Guibert, Jérôme Audoux, Thérèse Commes |
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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