title: Vanno: a visualization-aided variant annotation tool.
abstract: Next-generation sequencing (NGS) technologies have revolutionized the field of genetics and are trending toward clinical diagnostics. Exome and targeted sequencing in a disease context represent a major NGS clinical application, considering its utility and cost-effectiveness. With the ongoing discovery of disease-associated genes, various gene panels have been launched for both basic research and diagnostic tests. However, the fundamental inconsistencies among the diverse annotation sources, software packages, and data formats have complicated the subsequent analysis. To manage disease-associated NGS data, we developed Vanno, a Web-based application for in-depth analysis and rapid evaluation of disease-causative genome sequence alterations. Vanno integrates information from biomedical databases, functional predictions from available evaluation models, and mutation landscapes from TCGA cancer types. A highly integrated framework that incorporates filtering, sorting, clustering, and visual analytic modules is provided to facilitate exploration of oncogenomics datasets at different levels, such as gene, variant, protein domain, or three-dimensional structure. Such design is crucial for the extraction of knowledge from sequence alterations and translating biological insights into clinical applications. Taken together, Vanno supports almost all disease-associated gene tests and exome sequencing panels designed for NGS, providing a complete solution for targeted and exome sequencing analysis. Vanno is freely available at http://cgts.cgu.edu.tw/vanno.
authors.affiliation: Bioinformatics Core Laboratory, Chang Gung University, Taoyuan, Taiwan; Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.
authors.forename: Po-Jung
authors.initials: PJ
authors.lastname: Huang
authors.forename: Chi-Ching
authors.initials: CC
authors.lastname: Lee
authors.forename: Bertrand Chin-Ming
authors.initials: BC
authors.lastname: Tan
authors.forename: Yuan-Ming
authors.initials: YM
authors.lastname: Yeh
authors.forename: Kuo-Yang
authors.initials: KY
authors.lastname: Huang
authors.forename: Ruei-Chi
authors.initials: RC
authors.lastname: Gan
authors.forename: Ting-Wen
authors.initials: TW
authors.lastname: Chen
authors.forename: Cheng-Yang
authors.initials: CY
authors.lastname: Lee
authors.forename: Sheng-Ting
authors.initials: ST
authors.lastname: Yang
authors.forename: Chung-Shou
authors.initials: CS
authors.lastname: Liao
authors.forename: Hsuan
authors.initials: H
authors.lastname: Liu
authors.forename: Petrus
authors.initials: P
authors.lastname: Tang
mesh_terms: D066289:Data Curation; D059472:Exome; D015894:Genome, Human; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA; D012984:Software
keywords: NGS; SNV annotation; TCGA; exomes