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aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations

MOTIVATION: Copy number variations (CNV) include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH) events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have...

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Autores principales: Renault, Victor, Tost, Jörg, Pichon, Fabien, Wang-Renault, Shu-Fang, Letouzé, Eric, Imbeaud, Sandrine, Zucman-Rossi, Jessica, Deleuze, Jean-François, How-Kit, Alexandre
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736239/
https://www.ncbi.nlm.nih.gov/pubmed/29261730
http://dx.doi.org/10.1371/journal.pone.0189334
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author Renault, Victor
Tost, Jörg
Pichon, Fabien
Wang-Renault, Shu-Fang
Letouzé, Eric
Imbeaud, Sandrine
Zucman-Rossi, Jessica
Deleuze, Jean-François
How-Kit, Alexandre
author_facet Renault, Victor
Tost, Jörg
Pichon, Fabien
Wang-Renault, Shu-Fang
Letouzé, Eric
Imbeaud, Sandrine
Zucman-Rossi, Jessica
Deleuze, Jean-François
How-Kit, Alexandre
author_sort Renault, Victor
collection PubMed
description MOTIVATION: Copy number variations (CNV) include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH) events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH) and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information. RESULTS: To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer), a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs) Affymetrix SNP Array data (Fig 1A). Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test), validated by another cohort of HCCs (p-value of 5.6e-7) (Fig 2B). AVAILABILITY AND IMPLEMENTATION: aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https://hub.docker.com/r/fjdceph/acnviewer/. CONTACT: aCNViewer@cephb.fr
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spelling pubmed-57362392017-12-22 aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations Renault, Victor Tost, Jörg Pichon, Fabien Wang-Renault, Shu-Fang Letouzé, Eric Imbeaud, Sandrine Zucman-Rossi, Jessica Deleuze, Jean-François How-Kit, Alexandre PLoS One Research Article MOTIVATION: Copy number variations (CNV) include net gains or losses of part or whole chromosomal regions. They differ from copy neutral loss of heterozygosity (cn-LOH) events which do not induce any net change in the copy number and are often associated with uniparental disomy. These phenomena have long been reported to be associated with diseases and particularly in cancer. Losses/gains of genomic regions are often correlated with lower/higher gene expression. On the other hand, loss of heterozygosity (LOH) and cn-LOH are common events in cancer and may be associated with the loss of a functional tumor suppressor gene. Therefore, identifying recurrent CNV and cn-LOH events can be important as they may highlight common biological components and give insights into the development or mechanisms of a disease. However, no currently available tools allow a comprehensive whole-genome visualization of recurrent CNVs and cn-LOH in groups of samples providing absolute quantification of the aberrations leading to the loss of potentially important information. RESULTS: To overcome these limitations, we developed aCNViewer (Absolute CNV Viewer), a visualization tool for absolute CNVs and cn-LOH across a group of samples. aCNViewer proposes three graphical representations: dendrograms, bi-dimensional heatmaps showing chromosomal regions sharing similar abnormality patterns, and quantitative stacked histograms facilitating the identification of recurrent absolute CNVs and cn-LOH. We illustrated aCNViewer using publically available hepatocellular carcinomas (HCCs) Affymetrix SNP Array data (Fig 1A). Regions 1q and 8q present a similar percentage of total gains but significantly different copy number gain categories (p-value of 0.0103 with a Fisher exact test), validated by another cohort of HCCs (p-value of 5.6e-7) (Fig 2B). AVAILABILITY AND IMPLEMENTATION: aCNViewer is implemented in python and R and is available with a GNU GPLv3 license on GitHub https://github.com/FJD-CEPH/aCNViewer and Docker https://hub.docker.com/r/fjdceph/acnviewer/. CONTACT: aCNViewer@cephb.fr Public Library of Science 2017-12-19 /pmc/articles/PMC5736239/ /pubmed/29261730 http://dx.doi.org/10.1371/journal.pone.0189334 Text en © 2017 Renault et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Renault, Victor
Tost, Jörg
Pichon, Fabien
Wang-Renault, Shu-Fang
Letouzé, Eric
Imbeaud, Sandrine
Zucman-Rossi, Jessica
Deleuze, Jean-François
How-Kit, Alexandre
aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
title aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
title_full aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
title_fullStr aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
title_full_unstemmed aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
title_short aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
title_sort acnviewer: comprehensive genome-wide visualization of absolute copy number and copy neutral variations
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736239/
https://www.ncbi.nlm.nih.gov/pubmed/29261730
http://dx.doi.org/10.1371/journal.pone.0189334
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