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

Abstract:

: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.

journal_name

Methods Mol Biol

authors

Song F,Xu J,Dixon J,Yue F

doi

10.1007/978-1-0716-1390-0_7

keywords:

["3D genome organization","Cancer genomics","Chromatin conformation","Hi-C","Structural variation"]

subject

Has Abstract

pub_date

2022-01-01 00:00:00

pages

143-161

eissn

1064-3745

issn

1940-6029

journal_volume

2301

pub_type

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