HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics
Bajic, Vladimir B.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
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AbstractComparing histone modification profiles between cancer and normal states, or across different tumor samples, can provide insights into understanding cancer initiation, progression and response to therapy. ChIP-seq histone modification data of cancer samples are distorted by copy number variation innate to any cancer cell. We present HMCan-diff, the first method designed to analyze ChIP-seq data to detect changes in histone modifications between two cancer samples of different genetic backgrounds, or between a cancer sample and a normal control. HMCan-diff explicitly corrects for copy number bias, and for other biases in the ChIP-seq data, which significantly improves prediction accuracy compared to methods that do not consider such corrections. On in silico simulated ChIP-seq data generated using genomes with differences in copy number profiles, HMCan-diff shows a much better performance compared to other methods that have no correction for copy number bias. Additionally, we benchmarked HMCan-diff on four experimental datasets, characterizing two histone marks in two different scenarios. We correlated changes in histone modifications between a cancer and a normal control sample with changes in gene expression. On all experimental datasets, HMCan-diff demonstrated better performance compared to the other methods.
CitationAshoor H, Louis-Brennetot C, Janoueix-Lerosey I, Bajic VB, Boeva V (2017) HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics. Nucleic Acids Research: gkw1319. Available: http://dx.doi.org/10.1093/nar/gkw1319.
SponsorsKAUST Base Research Funds (to V.B.B. and H.A.); French program ‘Investissement d'Avenir’, action bioinformatique (ABS4NGS project) (to V.B.); ATIP-Avenir program. Funding for open access charge: ATIP-Avenir program.
PublisherOxford University Press (OUP)
JournalNucleic Acids Research
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