| Literature DB >> 34415534 |
Fan Song1,2, Jie Xu1, Jesse Dixon3, Feng Yue4,5.
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.Entities:
Keywords: 3D genome organization; Cancer genomics; Chromatin conformation; Hi-C; Structural variation
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Year: 2022 PMID： 34415534 DOI： 10.1007/978-1-0716-1390-0_7
Source DB: PubMed Journal: Methods Mol Biol ISSN： 1064-3745