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

Jonathan Cairns, Paula Freire-Pritchett, Steven W Wingett, Csilla Varnai, Andrew Dimond, Vincent Plagnol, Daniel R Zerbino, Stefan Schoenfelder, Biola M Javierre, Cameron S Osborne, Peter Fraser, Mikhail Spivakov

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145 Citations (Scopus)
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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.
Original languageEnglish
Article number127
Number of pages17
JournalGenome Biology
Publication statusPublished - 15 Jun 2016


  • Gene regulation
  • Nuclear organisation
  • Promoter-enhancer interactions
  • Capture Hi-C
  • Convolution background model
  • P value weighting


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