CNVannotator: A Comprehensive Annotation Server for Copy Number Variation in the Human Genome

Min Zhao,Zhongming Zhao,Yu Xue

doi:10.1371/journal.pone.0080170

Abstract

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/.

Highlights

All human individuals are different from each other in a postulated 0.1% of genomic DNA sequences [1]
For a list of genes, we provided a batch retrieval interface, through which researchers can search CNVannotator using a list of human gene symbols
The search results in a list of overlapped Copy number variation (CNV) and a hyperlink to access the original references for the reported CNVs

Summary

Introduction

All human individuals are different from each other in a postulated 0.1% of genomic DNA sequences [1]. Copy number variations (CNVs) have been discovered as a major cause of intermediate-scale structural variants in human genomes [3]. These copy number changes often refer to the alterations of DNA fragments and are involved in approximately 12% of the genome in human populations [4]. Common CNVs collectively contribute to some complex diseases, such as HIV [15], malaria [16], chronic obstructive pulmonary disease [17], and Crohn’s disease [17] Due to their impact on human disease, CNVs can be used in both the diagnosis and treatment of diseases [18]

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