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

Research output: Contribution to journalArticlepeer-review


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

Colleges, School and Institutes

External organisations

  • Babraham Institute


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