Analysis of Hi-C Data for Discovery of Structural Variations in Cancer

Fan Song, Jie Xu, Jesse Dixon, Feng Yue*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapter


Structural variations (SVs) are large genomic rearrangements that can be challenging to identify with current short read sequencing technology due to various confounding factors such as existence of genomic repeats and complex SV structures. Hi-C breakfinder is the first computational tool that utilizes the technology of high-throughput chromatin conformation capture assay (Hi-C) to systematically identify SVs, without being interfered by regular confounding factors. SVs change the spatial distance of genomic regions and cause discontinuous signals in Hi-C, which are difficult to analyze by routine informatics practice. Here we provide step-by-step guidance for how to identify SVs using Hi-C data and how to reconstruct Hi-C maps in the presence of SVs.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages19
StatePublished - 2022

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • 3D genome organization
  • Cancer genomics
  • Chromatin conformation
  • Hi-C
  • Structural variation

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology


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