VIVID: A Web Application for Variant Interpretation and Visualization in Multi-dimensional Analyses
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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.
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Cites
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764 · see citing works
Genome-wide association studies
Uffelmann, E., Huang, Q. Q., Munung, N. S., de Vries, J., Okada, Y., Martin, A. R., Martin, H. C., Lappalainen, T., & Posthuma, D. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-021-00056-9 · Cited by 1,849 · see citing works
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- Authors
- Tichkule, S., Myung, Y., Naung, M. T., Ansell, B. R. E., Guy, A. J., Srivastava, N., Mehra, S., Cacciò, S. M., Mueller, I., Barry, A. E., van Oosterhout, C., Pope, B., Ascher, D. B., & Jex, A. R.
- Affiliations
- The University of Melbourne (AU)
- Baker Heart and Diabetes Institute (AU)
- Walter and Eliza Hall Institute of Medical Research (AU)
- RMIT University (AU)
- Monash University (AU)
- Burnet Institute (AU)
- Istituto Superiore di Sanità (IT)
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research , Melbourne , Australia
- School of Environmental Sciences, University of East Anglia, Norwich Research Park , Norwich , UK
- The Royal Melbourne Hospital (AU)
- Corresponding author
- Tichkule, Swapnil
- ORCID
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-09-01
- Volume
- 39
- Issue
- 9
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- PMC
- PMC9514033
- OpenAlex
- W4295761272
- Cited by
- 11
- References
- 2
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 1 · 2023: 5 · 2022: 3
- FWCI
- 1.66
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Molecular Biology and Evolution (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- UEA Digital Repository (University of East Anglia) (submittedVersion)
- Figshare (submittedVersion, cc-by-nc)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by-nc)
- Funders
- National Health and Medical Research Council
- Victorian Health and Medical Research Fellowship
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- variant interpretation, variant visualization, web application, DNA variants, mutation mapping, conservation scores, deleterious variant prediction, balancing selection, adaptive evolution, genetic load, Plasmodium falciparum, 3D protein model, AlphaFold2, variant call format, population genetics, comparative genomics
- MeSH terms
- Genotype, Phenotype, Polymorphism, Genetic, Software, Genomics
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