CnvCurator: an Interactive Visualization and Editing Tool for Somatic Copy Number Variations

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2015 Oct 17

PMID 26472134

Citations 3

Authors

Lingnan Ma

Maochun Qin

Biao Liu

Qiang Hu

Lei Wei

Jianmin Wang

Song Liu

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

The thorny complexities of visualization research for clinical settings: A case study from genomics.

Stahlbom E, Molin J, Ynnerman A, Lundstrom C Front Bioinform. 2023; 3:1112649.

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Visualization tools for human structural variations identified by whole-genome sequencing.

Yokoyama T, Kasahara M J Hum Genet. 2019; 65(1):49-60.

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iCopyDAV: Integrated platform for copy number variations-Detection, annotation and visualization.

Dharanipragada P, Vogeti S, Parekh N PLoS One. 2018; 13(4):e0195334.

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