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BioMed Central, Genome Biology, 1(17)

DOI: 10.1186/s13059-016-0992-2

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

Journal article published in 2015 by Jonathan Cairns, Steven W. Wingett ORCID, Csilla Vรกrnai, Paula Freire-Pritchett, Wingett Sw, Daniel Zerbino, Andrew Dimond, Csilla Várnai ORCID, Vincent Plagnol, Stefan Schoenfelder, Javierre Bm, Biola-Maria Javierre, Cameron Osborne, Peter Fraser ORCID, Mikhail Spivakov ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Abstract 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 ( 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.