Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Ma, Lingnan, Qin, Maochun, Liu, Biao, Hu, Qiang, Wei, Lei, Wang, Jianmin, Liu, Song
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
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
_version_ 1782395616445333504
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
work_keys_str_mv AT malingnan cnvcuratoraninteractivevisualizationandeditingtoolforsomaticcopynumbervariations
AT qinmaochun cnvcuratoraninteractivevisualizationandeditingtoolforsomaticcopynumbervariations
AT liubiao cnvcuratoraninteractivevisualizationandeditingtoolforsomaticcopynumbervariations
AT huqiang cnvcuratoraninteractivevisualizationandeditingtoolforsomaticcopynumbervariations
AT weilei cnvcuratoraninteractivevisualizationandeditingtoolforsomaticcopynumbervariations
AT wangjianmin cnvcuratoraninteractivevisualizationandeditingtoolforsomaticcopynumbervariations
AT liusong cnvcuratoraninteractivevisualizationandeditingtoolforsomaticcopynumbervariations