HiNT: a computational method for detecting copy number variations and translocations from Hi-C data

Autor: Su Wang, Soohyun Lee, Chong Chu, Dhawal Jain, Peter Kerpedjiev, Geoffrey M. Nelson, Jennifer M. Walsh, Burak H. Alver, Peter J. Park
Jazyk: angličtina
Rok vydání: 2020
Předmět:
Zdroj: Genome Biology, Vol 21, Iss 1, Pp 1-15 (2020)
Druh dokumentu: article
ISSN: 1474-760X
DOI: 10.1186/s13059-020-01986-5
Popis: 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.
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