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bioRxiv · 10.1101/657080

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

Wang, S.·Lee, S.·Chu, C.·Jain, D.·Nelson, G.·Walsh, J. M.·Alver, B. H.·Park, P. J.
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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 (SV) 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 inter-chromosomal 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 SV detection by locating breakpoints in repetitive regions.

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Wang, S., Lee, S., Chu, C., Jain, D., Nelson, G., Walsh, J. M., Alver, B. H., Park, P. J.. 2019-06-03. HiNT: a computational method for detecting copy number variations and translocations from Hi-C data. https://doi.org/10.1101/657080

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