inCNV: An Integrated Analysis Tool for Copy Number Variation on Whole Exome Sequencing.

Evol Bioinform Online 2020 24;16:1176934320956577. Epub 2020 Sep 24.

Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand.

The detection of copy number variations (CNVs) on whole-exome sequencing (WES) represents a cost-effective technique for the study of genetic variants. This approach, however, has encountered an obstacle with high false-positive rates due to biases from exome sequencing capture kits and GC contents. Although plenty of CNV detection tools have been developed, they do not perform well with all types of CNVs. In addition, most tools lack features of genetic annotation, CNV visualization, and flexible installation, requiring users to put much effort into CNV interpretation. Here, we present "inCNV," a web-based application that can accept multiple CNV-tool results, then integrate and prioritize them with user-friendly interfaces. This application helps users analyze the importance of called CNVs by generating CNV annotations from Ensembl, Database of Genomic Variants (DGV), ClinVar, and Online Mendelian Inheritance in Man (OMIM). Moreover, users can select and export CNVs of interest including their flanking sequences for primer design and experimental verification. We demonstrated how inCNV could help users filter and narrow down the called CNVs to a potentially novel CNV, a common CNV within a group of samples of the same disease, or a CNV of a sample within the same family. Besides, we have provided in CNV as a docker image for ease of installation (https://github.com/saowwapark/inCNV).

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Source
http://dx.doi.org/10.1177/1176934320956577DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7520931PMC
September 2020

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