Variant View: Visualizing Sequence Variants in their Gene Context

You are here

TitleVariant View: Visualizing Sequence Variants in their Gene Context
Publication TypeJournal Article
Year of Publication2013
AuthorsFerstay, JA, Nielsen, CB, Munzner, T
JournalIEEE Transactions on Visualization and Computer Graphics
Pagination2546 - 2555
Date PublishedJan-12-2013
KeywordsGenome, perceptual, variant

Scientists use DNA sequence differences between an individual's genome and a standard reference genome to study the genetic basis of disease. Such differences are called sequence variants, and determining their impact in the cell is difficult because it requires reasoning about both the type and location of the variant across several levels of biological context. In this design study, we worked with 4 analysts to design a visualization tool supporting variant impact assessment for 3 different tasks. We contribute data and task abstractions for the problem of variant impact assessment, and the carefully justified design and implementation of the Variant View tool. Variant View features an information-dense visual encoding that provides maximal information at the overview level, in contrast to the extensive navigation required by currently-prevalent genome browsers. We provide initial evidence that the tool simplified and accelerated workflows for these three tasks through four case studies. Finally, we reflect on the lessons learned in creating and refining data and task abstractions that allow for concise overviews of sprawling information spaces that can reduce or remove the need for the memory-intensive use of navigation.

Short TitleIEEE Trans. Visual. Comput. Graphics
Refereed DesignationDoes Not Apply