aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations
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 r...
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| creator | Renault, Victor Tost, Jörg Pichon, Fabien Wang-Renault, Shu-Fang Letouzé, Eric Imbeaud, Sandrine Zucman-Rossi, Jessica Deleuze, Jean-François How-Kit, Alexandre |
| description | 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.
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).
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/.
aCNViewer@cephb.fr. |
| doi_str_mv | 10.1371/journal.pone.0189334 |
| format | Article |
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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).
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/.
aCNViewer@cephb.fr.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0189334</identifier><identifier>PMID: 29261730</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Aberration ; Algorithms ; Biochemistry, Molecular Biology ; Bioinformatics ; Biology and Life Sciences ; Cancer ; Chromosomes ; Computer and Information Sciences ; Copy number ; Copy number variations ; Deoxyribonucleic acid ; DNA ; Epigenetics ; Gene expression ; Genetics ; Genome-wide association studies ; Genomes ; Genomics ; Graphical representations ; Hepatocellular carcinoma ; Heterozygosity ; Histograms ; Identification ; Laboratories ; Life Sciences ; Liver cancer ; Loss of heterozygosity ; Medicine and Health Sciences ; Physical Sciences ; Research and analysis methods ; Single-nucleotide polymorphism ; Tumor suppressor genes ; Tumors ; Uniparental disomy ; Visualization</subject><ispartof>PloS one, 2017-12, Vol.12 (12), p.e0189334-e0189334</ispartof><rights>COPYRIGHT 2017 Public Library of Science</rights><rights>2017 Renault et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><rights>2017 Renault et al 2017 Renault et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c726t-e4a868026d53e8557779439503805c0085ccf309f5bb5139e9c35b17ce2aecc13</citedby><cites>FETCH-LOGICAL-c726t-e4a868026d53e8557779439503805c0085ccf309f5bb5139e9c35b17ce2aecc13</cites><orcidid>0000-0001-8351-7168</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736239/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736239/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29261730$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://cea.hal.science/cea-04516171$$DView record in HAL$$Hfree_for_read</backlink></links><search><contributor>Baudis, Michael</contributor><creatorcontrib>Renault, Victor</creatorcontrib><creatorcontrib>Tost, Jörg</creatorcontrib><creatorcontrib>Pichon, Fabien</creatorcontrib><creatorcontrib>Wang-Renault, Shu-Fang</creatorcontrib><creatorcontrib>Letouzé, Eric</creatorcontrib><creatorcontrib>Imbeaud, Sandrine</creatorcontrib><creatorcontrib>Zucman-Rossi, Jessica</creatorcontrib><creatorcontrib>Deleuze, Jean-François</creatorcontrib><creatorcontrib>How-Kit, Alexandre</creatorcontrib><title>aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>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.
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).
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/.
aCNViewer@cephb.fr.</description><subject>Aberration</subject><subject>Algorithms</subject><subject>Biochemistry, Molecular Biology</subject><subject>Bioinformatics</subject><subject>Biology and Life Sciences</subject><subject>Cancer</subject><subject>Chromosomes</subject><subject>Computer and Information Sciences</subject><subject>Copy number</subject><subject>Copy number variations</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Epigenetics</subject><subject>Gene expression</subject><subject>Genetics</subject><subject>Genome-wide association studies</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Graphical representations</subject><subject>Hepatocellular carcinoma</subject><subject>Heterozygosity</subject><subject>Histograms</subject><subject>Identification</subject><subject>Laboratories</subject><subject>Life Sciences</subject><subject>Liver cancer</subject><subject>Loss of heterozygosity</subject><subject>Medicine and Health Sciences</subject><subject>Physical Sciences</subject><subject>Research and analysis methods</subject><subject>Single-nucleotide polymorphism</subject><subject>Tumor suppressor genes</subject><subject>Tumors</subject><subject>Uniparental 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Comprehensive genome-wide visualization of absolute copy number and copy neutral variations</title><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></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c726t-e4a868026d53e8557779439503805c0085ccf309f5bb5139e9c35b17ce2aecc13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Aberration</topic><topic>Algorithms</topic><topic>Biochemistry, Molecular Biology</topic><topic>Bioinformatics</topic><topic>Biology and Life Sciences</topic><topic>Cancer</topic><topic>Chromosomes</topic><topic>Computer and Information Sciences</topic><topic>Copy number</topic><topic>Copy number variations</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Epigenetics</topic><topic>Gene expression</topic><topic>Genetics</topic><topic>Genome-wide association studies</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Graphical representations</topic><topic>Hepatocellular carcinoma</topic><topic>Heterozygosity</topic><topic>Histograms</topic><topic>Identification</topic><topic>Laboratories</topic><topic>Life Sciences</topic><topic>Liver cancer</topic><topic>Loss of heterozygosity</topic><topic>Medicine and Health Sciences</topic><topic>Physical Sciences</topic><topic>Research and analysis methods</topic><topic>Single-nucleotide polymorphism</topic><topic>Tumor suppressor genes</topic><topic>Tumors</topic><topic>Uniparental disomy</topic><topic>Visualization</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Renault, Victor</creatorcontrib><creatorcontrib>Tost, Jörg</creatorcontrib><creatorcontrib>Pichon, Fabien</creatorcontrib><creatorcontrib>Wang-Renault, Shu-Fang</creatorcontrib><creatorcontrib>Letouzé, 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Fabien</au><au>Wang-Renault, Shu-Fang</au><au>Letouzé, Eric</au><au>Imbeaud, Sandrine</au><au>Zucman-Rossi, Jessica</au><au>Deleuze, Jean-François</au><au>How-Kit, Alexandre</au><au>Baudis, Michael</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2017-12-19</date><risdate>2017</risdate><volume>12</volume><issue>12</issue><spage>e0189334</spage><epage>e0189334</epage><pages>e0189334-e0189334</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>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.
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).
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/.
aCNViewer@cephb.fr.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>29261730</pmid><doi>10.1371/journal.pone.0189334</doi><tpages>e0189334</tpages><orcidid>https://orcid.org/0000-0001-8351-7168</orcidid><oa>free_for_read</oa></addata></record> |
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| issn | 1932-6203 1932-6203 |
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| recordid | cdi_plos_journals_1978703568 |
| source | DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Aberration Algorithms Biochemistry, Molecular Biology Bioinformatics Biology and Life Sciences Cancer Chromosomes Computer and Information Sciences Copy number Copy number variations Deoxyribonucleic acid DNA Epigenetics Gene expression Genetics Genome-wide association studies Genomes Genomics Graphical representations Hepatocellular carcinoma Heterozygosity Histograms Identification Laboratories Life Sciences Liver cancer Loss of heterozygosity Medicine and Health Sciences Physical Sciences Research and analysis methods Single-nucleotide polymorphism Tumor suppressor genes Tumors Uniparental disomy Visualization |
| title | aCNViewer: Comprehensive genome-wide visualization of absolute copy number and copy neutral variations |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-24T18%3A47%3A42IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=aCNViewer:%20Comprehensive%20genome-wide%20visualization%20of%20absolute%20copy%20number%20and%20copy%20neutral%20variations&rft.jtitle=PloS%20one&rft.au=Renault,%20Victor&rft.date=2017-12-19&rft.volume=12&rft.issue=12&rft.spage=e0189334&rft.epage=e0189334&rft.pages=e0189334-e0189334&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0189334&rft_dat=%3Cgale_plos_%3EA519523331%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1978703568&rft_id=info:pmid/29261730&rft_galeid=A519523331&rft_doaj_id=oai_doaj_org_article_87a5d43bfbe34927959c812e20c8d246&rfr_iscdi=true |