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CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data

By Jonathan Cairns, Paula Freire-Pritchett, Steven W Wingett, Csilla VĂ¡rnai, Andrew Dimond, Vincent Plagnol, Daniel Zerbino, Stefan Schoenfelder, Biola-Maria Javierre, Cameron Osborne, Peter Fraser, Mikhail spivakov

Posted 01 Oct 2015
bioRxiv DOI: 10.1101/028068 (published DOI: 10.1186/s13059-016-0992-2)

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 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, in which many spatially dispersed regions are captured, such as in Promoter CHi-C. 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 this method are enriched for regulatory features and disease-associated SNPs.

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