CNVannotator: A comprehensive annotation server for copy number variation in the human genome

Min Zhao; Z Zhao

doi:10.1371/journal.pone.0080170

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CNVannotator: A comprehensive annotation server for copy number variation in the human genome

Journal article

Open access

Peer reviewed

CNVannotator: A comprehensive annotation server for copy number variation in the human genome

Min Zhao and Z Zhao

PLoS One, Vol.8(11), e80170

2013

DOI: https://doi.org/10.1371/journal.pone.0080170

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Abstract

chromosome fragile sites

databases

genetic

DNA copy number variations

gene dosage

genes

tumor suppressor

genome

human

genome-wide association study

Internet

oncogenes

polymorphism

single nucleotide

regulatory sequences

nucleic acid

Copy number variation (CNV) is one of the most prevalent genetic variations in the genome, leading to an abnormal number of copies of moderate to large genomic regions. High-throughput technologies such as next-generation sequencing often identify thousands of CNVs involved in biological or pathological processes. Despite the growing demand to filter and classify CNVs by factors such as frequency in population, biological features, and function, surprisingly, no online web server for CNV annotations has been made available to the research community. Here, we present CNVannotator, a web server that accepts an input set of human genomic positions in a user-friendly tabular format. CNVannotator can perform genomic overlaps of the input coordinates using various functional features, including a list of the reported 356,817 common CNVs, 181,261 disease CNVs, as well as, 140,342 SNPs from genome-wide association studies. In addition, CNVannotator incorporates 2,211,468 genomic features, including ENCODE regulatory elements, cytoband, segmental duplication, genome fragile site, pseudogene, promoter, enhancer, CpG island, and methylation site. For cancer research community users, CNVannotator can apply various filters to retrieve a subgroup of CNVs pinpointed in hundreds of tumor suppressor genes and oncogenes. In total, 5,277,234 unique genomic coordinates with functional features are available to generate an output in a plain text format that is free to download. In summary, we provide a comprehensive web resource for human CNVs. The annotated results along with the server can be accessed at http://bioinfo.mc.vanderbilt. edu/CNVannotator/. © 2013 Zhao, Zhao.

Details

Title: CNVannotator: A comprehensive annotation server for copy number variation in the human genome
Authors: Min Zhao (Author) - Vanderbilt University School of Medicine, United States
Z Zhao (Author) - Vanderbilt University School of Medicine, United States
Publication details: PLoS One, Vol.8(11), e80170; 8
Publisher: Public Library of Science
Date published: 2013
DOI: 10.1371/journal.pone.0080170
ISSN: 1932-6203
Copyright note: Copyright © 2013 Zhao, Zhao. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Organisation Unit: School of Science and Engineering - Legacy; University of the Sunshine Coast, Queensland; School of Science, Technology and Engineering; Centre for Bioinnovation
Language: English
Record Identifier: 99449086402621
Output Type: Journal article

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