CNViz: An R/Shiny Application for Interactive Copy Number Variant Visualization in Cancer
Copy number variants (CNVs) comprise a class of mutation which includes deletion, duplication, or amplification events that range in size from smaller than a single-gene or exon, to the size of a full chromosome. These changes can affect gene expression levels and are thus implicated in disease, inc...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Journal of Pathology Informatics |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S215335392200089X |
| _version_ | 1797976990430527488 |
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| author | Rebecca G. Ramesh Ashkan Bigdeli Chase Rushton Jason N. Rosenbaum |
| author_facet | Rebecca G. Ramesh Ashkan Bigdeli Chase Rushton Jason N. Rosenbaum |
| author_sort | Rebecca G. Ramesh |
| collection | DOAJ |
| description | Copy number variants (CNVs) comprise a class of mutation which includes deletion, duplication, or amplification events that range in size from smaller than a single-gene or exon, to the size of a full chromosome. These changes can affect gene expression levels and are thus implicated in disease, including cancer. Although a variety of tools and methodologies exist to detect CNVs using data from massively parallel sequencing (also referred to as next-generation sequencing), it can be difficult to appreciate the copy number profile in a list format or as a static image. CNViz is a freely accessible R/Bioconductor package that launches an interactive R/Shiny visualization tool to facilitate review of copy number data. As inputs, it requires genomic locations and corresponding copy number ratios for probe, gene, and/or segment-level data. If supplied, loss of heterozygosity (LOH), focal variant data [single nucleotide variants (SNVs) and small insertions and deletions (indels)], and metadata (e.g., specimen purity and ploidy) can also be incorporated into the visualization. The CNViz R/Bioconductor package is an easy-to-use tool built with the intent of encouraging visualization and exploration of copy number variation. CNViz can be used in a clinical setting as well as for research to study patterns in human cancers more broadly. The intuitive interface allows users to visualize the copy number profile of a specimen, dynamically change resolution to explore gene and probe-level copy number changes, and simultaneously integrate LOH, SNV, and indel findings. CNViz is available for download as an R package via Bioconductor. An example of the application is available at rebeccagreenblatt.shinyapps.io/cnviz_example. |
| first_indexed | 2024-04-11T04:59:50Z |
| format | Article |
| id | doaj.art-56815b941019465ab79bb33470513400 |
| institution | Directory Open Access Journal |
| issn | 2153-3539 |
| language | English |
| last_indexed | 2024-04-11T04:59:50Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Pathology Informatics |
| spelling | doaj.art-56815b941019465ab79bb334705134002022-12-26T04:08:33ZengElsevierJournal of Pathology Informatics2153-35392022-01-0113100089CNViz: An R/Shiny Application for Interactive Copy Number Variant Visualization in CancerRebecca G. Ramesh0Ashkan Bigdeli1Chase Rushton2Jason N. Rosenbaum3Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Corresponding author at: 3020 Market St. Suite 220, Philadelphia, PA 19104, USA.Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, USACenter for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, USACenter for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Pathology, Kaiser Permanente, Oakland, California, USACopy number variants (CNVs) comprise a class of mutation which includes deletion, duplication, or amplification events that range in size from smaller than a single-gene or exon, to the size of a full chromosome. These changes can affect gene expression levels and are thus implicated in disease, including cancer. Although a variety of tools and methodologies exist to detect CNVs using data from massively parallel sequencing (also referred to as next-generation sequencing), it can be difficult to appreciate the copy number profile in a list format or as a static image. CNViz is a freely accessible R/Bioconductor package that launches an interactive R/Shiny visualization tool to facilitate review of copy number data. As inputs, it requires genomic locations and corresponding copy number ratios for probe, gene, and/or segment-level data. If supplied, loss of heterozygosity (LOH), focal variant data [single nucleotide variants (SNVs) and small insertions and deletions (indels)], and metadata (e.g., specimen purity and ploidy) can also be incorporated into the visualization. The CNViz R/Bioconductor package is an easy-to-use tool built with the intent of encouraging visualization and exploration of copy number variation. CNViz can be used in a clinical setting as well as for research to study patterns in human cancers more broadly. The intuitive interface allows users to visualize the copy number profile of a specimen, dynamically change resolution to explore gene and probe-level copy number changes, and simultaneously integrate LOH, SNV, and indel findings. CNViz is available for download as an R package via Bioconductor. An example of the application is available at rebeccagreenblatt.shinyapps.io/cnviz_example.http://www.sciencedirect.com/science/article/pii/S215335392200089X |
| spellingShingle | Rebecca G. Ramesh Ashkan Bigdeli Chase Rushton Jason N. Rosenbaum CNViz: An R/Shiny Application for Interactive Copy Number Variant Visualization in Cancer Journal of Pathology Informatics |
| title | CNViz: An R/Shiny Application for Interactive Copy Number Variant Visualization in Cancer |
| title_full | CNViz: An R/Shiny Application for Interactive Copy Number Variant Visualization in Cancer |
| title_fullStr | CNViz: An R/Shiny Application for Interactive Copy Number Variant Visualization in Cancer |
| title_full_unstemmed | CNViz: An R/Shiny Application for Interactive Copy Number Variant Visualization in Cancer |
| title_short | CNViz: An R/Shiny Application for Interactive Copy Number Variant Visualization in Cancer |
| title_sort | cnviz an r shiny application for interactive copy number variant visualization in cancer |
| url | http://www.sciencedirect.com/science/article/pii/S215335392200089X |
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