Capture Hi-C (CHi-C) is a state-of-the art 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 with other Hi-C-like techniques. We present a noise model and algorithms for background correction and multiple testing that are specifically adapted to CHi-C data. We implement these procedures in CHiCAGO (http://regulatorygenomicsgroup.org/chicago), an open-source package for robust interaction detection in CHi-C. We validate CHiCAGO by showing that promoter-interacting regions detected with it are enriched for regulatory features and disease-associated SNPs.
Cairns, J., Freire-Pritchett, P., Wingett, S. W., Várnai, C., Dimond, A., Plagnol, V., … Spivakov, M. (2016). CHiCAGO: Robust detection of DNA looping interactions in Capture Hi-C data. Genome Biology, 17(1). https://doi.org/10.1186/s13059-016-0992-2