PanVA: Pangenomic Variant Analysis

• DOI: 10.36227/techrxiv.21572433
• Publication Date: 2022-11-30T06:51:46Z
• Authors: Astrid van den Br...; Eef Jonkheer; Dirk-Jan van Workum; Huub van de Wetering; Sandra Smit; Anna Vilanova
• Keywords: Bioinformatics; Organisms; Visual analytics; DNA; Genomics; comparative genomics; pangenomics; variant analysis; User-Computer Interface; Phenotype; Genetic Variation/genetics; Task analysis; Computer Graphics; design study; Phylogeny; Software; Visualization

<p>Genomics researchers increasingly use multiple reference genomes to comprehensively explore genetic variants underlying differences in detectable characteristics between organisms. Pangenomes allow for an efficient data representation of related and their associated metadata. However, current visual analysis approaches exploring these complex genotype-phenotype relationships are often based on single or lack adequate support interpreting the genomic context with heterogeneous (meta)data. This design study introduces PanVA, a analytics pangenomic variant developed active participation genomics researchers. The uniquely combines tailored representations interactions such as sorting, grouping, aggregation, allowing users navigate different perspectives relations. Through evaluation plants pathogen research, we show that PanVA helps genes generate hypotheses about role phenotypic variation.</p> <p>©2022 IEEE. Personal this material is permitted. Permission from IEEE must be obtained all other uses, any future media, including reprinting/republishing advertising promotional purposes, creating new collective works, resale redistribution servers lists, reuse copyrighted component work works.</p> <p>Citation information: A. van den Brandt, E. M. Jonkheer, D. J. Workum, H. de Wetering, S. Smit Vilanova, "PanVA: Pangenomic Variant Analysis," Transactions Visualization Computer Graphics, doi: 10.1109/TVCG.2023.3282364.</p>