HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics

Handle URI:
http://hdl.handle.net/10754/622727
Title:
HMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristics
Authors:
Ashoor, Haitham ( 0000-0003-2527-0317 ) ; Louis-Brennetot, Caroline; Janoueix-Lerosey, Isabelle; Bajic, Vladimir B. ( 0000-0001-5435-4750 ) ; Boeva, Valentina
Abstract:
Comparing 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.
KAUST Department:
Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Citation:
Ashoor 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.
Publisher:
Oxford University Press (OUP)
Journal:
Nucleic Acids Research
Issue Date:
19-Dec-2016
DOI:
10.1093/nar/gkw1319
Type:
Article
ISSN:
0305-1048; 1362-4962
Sponsors:
KAUST 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.
Additional Links:
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw1319
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorAshoor, Haithamen
dc.contributor.authorLouis-Brennetot, Carolineen
dc.contributor.authorJanoueix-Lerosey, Isabelleen
dc.contributor.authorBajic, Vladimir B.en
dc.contributor.authorBoeva, Valentinaen
dc.date.accessioned2017-01-25T08:57:41Z-
dc.date.available2017-01-25T08:57:41Z-
dc.date.issued2016-12-19en
dc.identifier.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.en
dc.identifier.issn0305-1048en
dc.identifier.issn1362-4962en
dc.identifier.doi10.1093/nar/gkw1319en
dc.identifier.urihttp://hdl.handle.net/10754/622727-
dc.description.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.en
dc.description.sponsorshipKAUST 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.en
dc.publisherOxford University Press (OUP)en
dc.relation.urlhttps://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw1319en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.comen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/en
dc.titleHMCan-diff: a method to detect changes in histone modifications in cells with different genetic characteristicsen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Divisionen
dc.identifier.journalNucleic Acids Researchen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionInstitut Curie, Inserm U830, PSL Research University, F-75005, Paris, France.en
dc.contributor.institutionInstitut Cochin, Inserm U1016, CNRS UMR 8104, Université Paris Descartes UMR-S1016, F-75014 Paris, France.en
kaust.authorAshoor, Haithamen
kaust.authorBajic, Vladimir B.en
All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.