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

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 computationa...

Full description

Saved in:
Bibliographic Details
Published in:Genome Biology 2020-03, Vol.21 (1), p.73-15, Article 73
Main Authors: Wang, Su, Lee, Soohyun, Chu, Chong, Jain, Dhawal, Kerpedjiev, Peter, Nelson, Geoffrey M, Walsh, Jennifer M, Alver, Burak H, Park, Peter J
Format: Article
Language:English
Subjects:
Breakpoints
Cancer
Cell cycle
Chromatin
Chromosomal interactions
Chromosome Breakpoints
Chromosome translocations
Computer applications
Conformation
Copy number
DNA Copy Number Variations
Gene loci
Genomes
Genomics - methods
High-Throughput Nucleotide Sequencing
Method
Next-generation sequencing
Repetitive region
Repetitive Sequences, Nucleic Acid
Sequence Analysis, DNA
Structural variation
Translocation, Genetic
Variation
Whole Genome Sequencing
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-020-01986-5