Chromothripsis pp 133-156 | Cite as

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

  • Anne-Laure Bougé
  • Florence Rufflé
  • Sébastien Riquier
  • Benoit Guibert
  • Jérôme Audoux
  • Thérèse Commes
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1769)

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.

Key words

RNA-Seq Chimeras Genomic rearrangement Chromothripsis Transcription Chimeric RNAs Fusion genes NGS 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Anne-Laure Bougé
    • 1
    • 2
  • Florence Rufflé
    • 1
    • 2
  • Sébastien Riquier
    • 1
    • 2
  • Benoit Guibert
    • 1
    • 2
  • Jérôme Audoux
    • 1
    • 2
  • Thérèse Commes
    • 1
    • 2
  1. 1.Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU MontpellierMontpellierFrance
  2. 2.Institut de Biologie Computationnelle, Université de MontpellierMontpellierFrance

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