VIVID: A Web Application for Variant Interpretation and Visualization in Multi-dimensional Analyses. (14th September 2022)

• Record Type: Journal Article
• Authors: Tichkule, Swapnil; Myung, Yoochan; Naung, Myo T; Ansell, Brendan R E; Guy, Andrew J; Srivastava, Namrata; Mehra, Somya; Cacciò, Simone M; Mueller, Ivo; Barry, Alyssa E; van Oosterhout, Cock; Pope, Bernard; Ascher, David B; Jex, Aaron R
• Editors: Teeling, Emma
• Is Part Of: Molecular biology and evolution. Volume 39:Number 9(2022)
• Publication Date: 2022-09-14
• Subjects: protein structure -- variant interpretation -- multi-dimensional analysis -- data visualization -- population genetics -- evolution; Molecular biology -- Periodicals; Molecular evolution -- Periodicals; Evolution, Molecular -- Periodicals; Molecular Biology -- Periodicals; 572.8
• DOI: 10.1093/molbev/msac196
• Languages: English
• ISSNs: 0737-4038

Abstract

Abstract: Large-scale comparative genomics- and population genetic studies generate enormous amounts of polymorphism data in the form of DNA variants. Ultimately, the goal of many of these studies is to associate genetic variants to phenotypes or fitness. We introduce VIVID, an interactive, user-friendly web application that integrates a wide range of approaches for encoding genotypic to phenotypic information in any organism or disease, from an individual or population, in three-dimensional (3D) space. It allows mutation mapping and annotation, calculation of interactions and conservation scores, prediction of harmful effects, analysis of diversity and selection, and 3D visualization of genotypic information encoded in Variant Call Format on AlphaFold2 protein models. VIVID enables the rapid assessment of genes of interest in the study of adaptive evolution and the genetic load, and it helps prioritizing targets for experimental validation. We demonstrate the utility of VIVID by exploring the evolutionary genetics of the parasitic protist Plasmodium falciparum, revealing geographic variation in the signature of balancing selection in potential targets of functional antibodies.