CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data

Genome Biol. 2016 Jun 15;17(1):127. doi: 10.1186/s13059-016-0992-2.


Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving targeted regions of interest, such as gene promoters, globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques. We present a background model and algorithms for normalisation and multiple testing that are specifically adapted to CHi-C experiments. We implement these procedures in CHiCAGO ( ), an open-source package for robust interaction detection in CHi-C. We validate CHiCAGO by showing that promoter-interacting regions detected with this method are enriched for regulatory features and disease-associated SNPs.

Keywords: Capture Hi-C; Convolution background model; Gene regulation; Nuclear organisation; P value weighting; Promoter-enhancer interactions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Chromatin / genetics*
  • Chromosomes / genetics
  • Genomics
  • Humans
  • Internet
  • Polymorphism, Single Nucleotide / genetics
  • Software*


  • Chromatin