PT - JOURNAL ARTICLE AU - Jonathan Cairns AU - Paula Freire-Pritchett AU - Steven W. Wingett AU - Andrew Dimond AU - Vincent Plagnol AU - Daniel Zerbino AU - Stefan Schoenfelder AU - Biola-Maria Javierre AU - Cameron Osborne AU - Peter Fraser AU - Mikhail Spivakov TI - CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data AID - 10.1101/028068 DP - 2015 Jan 01 TA - bioRxiv PG - 028068 4099 - http://biorxiv.org/content/early/2015/10/05/028068.short 4100 - http://biorxiv.org/content/early/2015/10/05/028068.full AB - 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.