DeAnnCNV: a tool for online detection and annotation of copy number variations from whole-exome sequencing data

Yuanwei Zhang; Zhenhua Yu; Rongjun Ban; Huan Zhang; Furhan Iqbal; Aiwu Zhao; Ao Li; Qinghua Shi

doi:10.1093/nar/gkv556

DeAnnCNV: a tool for online detection and annotation of copy number variations from whole-exome sequencing data

Nucleic Acids Res. 2015 Jul 1;43(W1):W289-94. doi: 10.1093/nar/gkv556. Epub 2015 May 26.

Authors

Yuanwei Zhang¹, Zhenhua Yu², Rongjun Ban², Huan Zhang¹, Furhan Iqbal³, Aiwu Zhao⁴, Ao Li⁵, Qinghua Shi⁶

Affiliations

¹ Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China.
² School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China.
³ Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China Institute of Pure and Applied Biology, Bahauddin Zakariya University Multan, 60800, Pakistan.
⁴ Hefei Institute of Physical Science, China Academy of Science, Hefei 230027, China.
⁵ School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China Research Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China aoli@ustc.edu.cn.
⁶ Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China qshi@ustc.edu.cn.

Abstract

With the decrease in costs, whole-exome sequencing (WES) has become a very popular and powerful tool for the identification of genetic variants underlying human diseases. However, integrated tools to precisely detect and systematically annotate copy number variations (CNVs) from WES data are still in great demand. Here, we present an online tool, DeAnnCNV (Detection and Annotation of Copy Number Variations from WES data), to meet the current demands of WES users. Upon submitting the file generated from WES data by an in-house tool that can be downloaded from our server, DeAnnCNV can detect CNVs in each sample and extract the shared CNVs among multiple samples. DeAnnCNV also provides additional useful supporting information for the detected CNVs and associated genes to help users to find the potential candidates for further experimental study. The web server is implemented in PHP + Perl + MATLAB and is online available to all users for free at http://mcg.ustc.edu.cn/db/cnv/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA Copy Number Variations*
Exome*
High-Throughput Nucleotide Sequencing*
Humans
Infertility, Male / genetics
Internet
Male
Software*