HiNT: a computational method for detecting copy number variations and translocations from Hi-C data
Open Access
- 23 March 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Genome Biology
- Vol. 21 (1), 1-15
- https://doi.org/10.1186/s13059-020-01986-5
Abstract
The three-dimensional conformation of a genome can be profiled using Hi-C, a technique that combines chromatin conformation capture with high-throughput sequencing. However, structural variations often yield features that can be mistaken for chromosomal interactions. Here, we describe a computational method HiNT (Hi-C for copy Number variation and Translocation detection), which detects copy number variations and interchromosomal translocations within Hi-C data with breakpoints at single base-pair resolution. We demonstrate that HiNT outperforms existing methods on both simulated and real data. We also show that Hi-C can supplement whole-genome sequencing in structure variant detection by locating breakpoints in repetitive regions.Funding Information
- Foundation for the National Institutes of Health (U01CA200059)
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