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cnvCurator: an interactive visualization and editing tool for somatic copy number variations
BACKGROUND: One of the most important somatic aberrations, copy number variations (CNVs) in tumor genomes is believed to have a high probability of harboring oncotargets. Detection of somatic CNVs is an essential part of cancer genome sequencing analysis, but the accuracy is usually limited due to v...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4608136/ https://www.ncbi.nlm.nih.gov/pubmed/26472134 http://dx.doi.org/10.1186/s12859-015-0766-y |
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author | Ma, Lingnan Qin, Maochun Liu, Biao Hu, Qiang Wei, Lei Wang, Jianmin Liu, Song |
author_facet | Ma, Lingnan Qin, Maochun Liu, Biao Hu, Qiang Wei, Lei Wang, Jianmin Liu, Song |
author_sort | Ma, Lingnan |
collection | PubMed |
description | BACKGROUND: One of the most important somatic aberrations, copy number variations (CNVs) in tumor genomes is believed to have a high probability of harboring oncotargets. Detection of somatic CNVs is an essential part of cancer genome sequencing analysis, but the accuracy is usually limited due to various factors. A post-processing procedure including manual review and refinement of CNV segments is often needed in practice to achieve better accuracy. RESULTS: cnvCurator is a user-friendly tool with functions specifically designed to facilitate the process of interactively visualizing and editing somatic CNV calling results. Different from other general genomics viewers, the index and display of CNV calling results in cnvCurator is segment central. It incorporates multiple CNV-specific information for concurrent, interactive display, as well as a number of relevant features allowing user to examine and curate the CNV calls. CONCLUSIONS: cnvCurator provides important and practical utilities to assist the manual review and edition of results from a chosen somatic CNV caller, such that curated CNV segments will be used for down-stream applications. |
format | Online Article Text |
id | pubmed-4608136 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-46081362015-10-17 cnvCurator: an interactive visualization and editing tool for somatic copy number variations Ma, Lingnan Qin, Maochun Liu, Biao Hu, Qiang Wei, Lei Wang, Jianmin Liu, Song BMC Bioinformatics Software BACKGROUND: One of the most important somatic aberrations, copy number variations (CNVs) in tumor genomes is believed to have a high probability of harboring oncotargets. Detection of somatic CNVs is an essential part of cancer genome sequencing analysis, but the accuracy is usually limited due to various factors. A post-processing procedure including manual review and refinement of CNV segments is often needed in practice to achieve better accuracy. RESULTS: cnvCurator is a user-friendly tool with functions specifically designed to facilitate the process of interactively visualizing and editing somatic CNV calling results. Different from other general genomics viewers, the index and display of CNV calling results in cnvCurator is segment central. It incorporates multiple CNV-specific information for concurrent, interactive display, as well as a number of relevant features allowing user to examine and curate the CNV calls. CONCLUSIONS: cnvCurator provides important and practical utilities to assist the manual review and edition of results from a chosen somatic CNV caller, such that curated CNV segments will be used for down-stream applications. BioMed Central 2015-10-15 /pmc/articles/PMC4608136/ /pubmed/26472134 http://dx.doi.org/10.1186/s12859-015-0766-y Text en © Ma et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Ma, Lingnan Qin, Maochun Liu, Biao Hu, Qiang Wei, Lei Wang, Jianmin Liu, Song cnvCurator: an interactive visualization and editing tool for somatic copy number variations |
title | cnvCurator: an interactive visualization and editing tool for somatic copy number variations |
title_full | cnvCurator: an interactive visualization and editing tool for somatic copy number variations |
title_fullStr | cnvCurator: an interactive visualization and editing tool for somatic copy number variations |
title_full_unstemmed | cnvCurator: an interactive visualization and editing tool for somatic copy number variations |
title_short | cnvCurator: an interactive visualization and editing tool for somatic copy number variations |
title_sort | cnvcurator: an interactive visualization and editing tool for somatic copy number variations |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4608136/ https://www.ncbi.nlm.nih.gov/pubmed/26472134 http://dx.doi.org/10.1186/s12859-015-0766-y |
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