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CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes

MOTIVATION: DNA copy number (CN) data are a fast-growing source of information used in basic and translational cancer research. Most CN segmentation data are presented without regard to the relationship between chromosomal regions. We offer both a toolkit to help scientists without programming exper...

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Autores principales: Dalgleish, James LT, Wang, Yonghong, Zhu, Jack, Meltzer, Paul S
Formato: Online Artículo Texto
Lenguaje:English
Publicado: SAGE Publications 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6887803/
https://www.ncbi.nlm.nih.gov/pubmed/31832011
http://dx.doi.org/10.1177/1176935119890290
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author Dalgleish, James LT
Wang, Yonghong
Zhu, Jack
Meltzer, Paul S
author_facet Dalgleish, James LT
Wang, Yonghong
Zhu, Jack
Meltzer, Paul S
author_sort Dalgleish, James LT
collection PubMed
description MOTIVATION: DNA copy number (CN) data are a fast-growing source of information used in basic and translational cancer research. Most CN segmentation data are presented without regard to the relationship between chromosomal regions. We offer both a toolkit to help scientists without programming experience visually explore the CN interactome and a package that constructs CN interactomes from publicly available data sets. RESULTS: The CNVScope visualization, based on a publicly available neuroblastoma CN data set, clearly displays a distinct CN interaction in the region of the MYCN, a canonical frequent amplicon target in this cancer. Exploration of the data rapidly identified cis and trans events, including a strong anticorrelation between 11q loss and17q gain with the region of 11q loss bounded by the cell cycle regulator CCND1. AVAILABILITY: The shiny application is readily available for use at http://cnvscope.nci.nih.gov/, and the package can be downloaded from CRAN (https://cran.r-project.org/package=CNVScope), where help pages and vignettes are located. A newer version is available on the GitHub site (https://github.com/jamesdalg/CNVScope/), which features an animated tutorial. The CNVScope package can be locally installed using instructions on the GitHub site for Windows and Macintosh systems. This CN analysis package also runs on a linux high-performance computing cluster, with options for multinode and multiprocessor analysis of CN variant data. The shiny application can be started using a single command (which will automatically install the public data package).
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spelling pubmed-68878032019-12-12 CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes Dalgleish, James LT Wang, Yonghong Zhu, Jack Meltzer, Paul S Cancer Inform Software or Database Review MOTIVATION: DNA copy number (CN) data are a fast-growing source of information used in basic and translational cancer research. Most CN segmentation data are presented without regard to the relationship between chromosomal regions. We offer both a toolkit to help scientists without programming experience visually explore the CN interactome and a package that constructs CN interactomes from publicly available data sets. RESULTS: The CNVScope visualization, based on a publicly available neuroblastoma CN data set, clearly displays a distinct CN interaction in the region of the MYCN, a canonical frequent amplicon target in this cancer. Exploration of the data rapidly identified cis and trans events, including a strong anticorrelation between 11q loss and17q gain with the region of 11q loss bounded by the cell cycle regulator CCND1. AVAILABILITY: The shiny application is readily available for use at http://cnvscope.nci.nih.gov/, and the package can be downloaded from CRAN (https://cran.r-project.org/package=CNVScope), where help pages and vignettes are located. A newer version is available on the GitHub site (https://github.com/jamesdalg/CNVScope/), which features an animated tutorial. The CNVScope package can be locally installed using instructions on the GitHub site for Windows and Macintosh systems. This CN analysis package also runs on a linux high-performance computing cluster, with options for multinode and multiprocessor analysis of CN variant data. The shiny application can be started using a single command (which will automatically install the public data package). SAGE Publications 2019-12-02 /pmc/articles/PMC6887803/ /pubmed/31832011 http://dx.doi.org/10.1177/1176935119890290 Text en © The Author(s) 2019 http://www.creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (http://www.creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage).
spellingShingle Software or Database Review
Dalgleish, James LT
Wang, Yonghong
Zhu, Jack
Meltzer, Paul S
CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes
title CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes
title_full CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes
title_fullStr CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes
title_full_unstemmed CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes
title_short CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes
title_sort cnvscope: visually exploring copy number aberrations in cancer genomes
topic Software or Database Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6887803/
https://www.ncbi.nlm.nih.gov/pubmed/31832011
http://dx.doi.org/10.1177/1176935119890290
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