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

Jonathan Cairns; Paula Freire-Pritchett; Steven W. Wingett; Csilla Várnai; Andrew Dimond; Vincent Plagnol; Daniel Zerbino; Stefan Schoenfelder; Biola Maria Javierre; Cameron Osborne; Peter Fraser; Mikhail Spivakov

doi:10.1186/s13059-016-0992-2

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

Jonathan Cairns, Paula Freire-Pritchett, Steven W. Wingett, Csilla Várnai, Andrew Dimond, Vincent Plagnol, Daniel Zerbino, Stefan Schoenfelder, Biola Maria Javierre, Cameron Osborne, Peter Fraser, Mikhail Spivakov^*

^*Corresponding author for this work

Medical & Molecular Genetics

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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.

Original language	English
Article number	127
Journal	Genome Biology
Volume	17
Issue number	1
DOIs	https://doi.org/10.1186/s13059-016-0992-2
Publication status	Published - 15 Jun 2016

Keywords

Capture Hi-C
Convolution background model
Gene regulation
Nuclear organisation
P value weighting
Promoter-enhancer interactions

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10.1186/s13059-016-0992-2Licence: CC BY

CHiCAGO robust detection_CAIRNS_Accepted 25May2016_GOLD VoR
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Cite this

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title = "CHiCAGO: Robust detection of DNA looping interactions in Capture Hi-C data",

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.",

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AU - Cairns, Jonathan

AU - Freire-Pritchett, Paula

AU - Wingett, Steven W.

AU - Várnai, Csilla

AU - Dimond, Andrew

AU - Plagnol, Vincent

AU - Zerbino, Daniel

AU - Schoenfelder, Stefan

AU - Javierre, Biola Maria

AU - Osborne, Cameron

AU - Fraser, Peter

AU - Spivakov, Mikhail

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AB - 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.

KW - Capture Hi-C

KW - Convolution background model

KW - Gene regulation

KW - Nuclear organisation

KW - P value weighting

KW - Promoter-enhancer interactions

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ER -

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

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Keywords

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