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Chromothripsis pp 353-361 | Cite as

Looking for Broken TAD Boundaries and Changes on DNA Interactions: Clinical Guide to 3D Chromatin Change Analysis in Complex Chromosomal Rearrangements and Chromothripsis

  • Kevin Yauy
  • Vincent Gatinois
  • Thomas Guignard
  • Satish Sati
  • Jacques Puechberty
  • Jean Baptiste Gaillard
  • Anouck Schneider
  • Franck Pellestor
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1769)

Abstract

Apparition of next-generation sequencing (NGS) was a breakthrough on knowledge of genome structure. Bioinformatic tools are a key point to analyze this huge amount of data from NGS and characterize the three-dimensional organization of chromosomes. This chapter describes usage of different browsers to explore publicly available online data and to search for possible 3D chromatin changes involved during complex chromosomal rearrangements as chromothripsis. Their pathogenic impact on clinical phenotype and gene misexpression can also be evaluated with annotated databases.

Key words

Topologically associated domains TAD boundaries Enhancers Bioinformatics 3D genome Genome browser Chromothripsis 

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Copyright information

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

Authors and Affiliations

  • Kevin Yauy
    • 1
  • Vincent Gatinois
    • 1
  • Thomas Guignard
    • 1
  • Satish Sati
    • 2
  • Jacques Puechberty
    • 1
  • Jean Baptiste Gaillard
    • 1
  • Anouck Schneider
    • 1
  • Franck Pellestor
    • 1
  1. 1.Unit of Chromosomal Genetics, Department of Medical GeneticsArnaud de Villeneuve Hospital, CHU MontpellierMontpellier Cedex 5France
  2. 2.Chromatin and Cell Biology GroupCNRS—Institute of Human GeneticsMontpellierFrance

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