Visualising errors in animal pedigree genotype data

Graham, Martin; Kennedy, Jessie; Paterson, Trevor; Law, Andy

Abstract

Genetic analysis of a breeding animal population involves determining the inheritance pattern of genotypes for multiple genetic markers across the individuals in the population pedigree structure. However, experimental pedigree genotype data invariably contains errors in both the pedigree structure and in the associated individual genotypes, which introduce inconsistencies into the dataset, rendering them useless for further analysis. The resolution of these errors requires consideration of the genotype inheritance patterns in the context of the pedigree structure. Existing visualisations of pedigree structures are typically more suited to human pedigrees and are less suitable for large complex animal pedigrees which may exhibit cross generational inbreeding. Similarly, current table-based viewers of genotype marker information can highlight where errors become apparent but lack the functionality and interactive visual feedback to enable users to locate the underlying source of errors within the pedigree. In this paper, we detail a design study steered by biologists who work with pedigree data, and describe successive iterations through approaches and prototypes for viewing genotyping errors in the context of a displayed pedigree. We describe how each approach performs with real pedigree genotype data and why eventually we deemed them unsuitable. Finally, a novel prototype visualisation for pedigrees, which we term the ‘sandwich view’, is detailed and we demonstrate how the approach effectively communicates errors in the pedigree context, supporting the biologist in the error identification task.

Citation

Graham, M., Kennedy, J., Paterson, T., & Law, A. (2011). Visualising errors in animal pedigree genotype data. Computer Graphics Forum, 30, 1011-1020. https://doi.org/10.1111/j.1467-8659.2011.01950.x

• Journal Article Type: Article
• Publication Date: 2011
• Deposit Date: Jun 27, 2011
• Publicly Available Date: Dec 31, 2011
• Print ISSN: 0167-7055
• Electronic ISSN: 1467-8659
• Publisher: Wiley
• Peer Reviewed: Peer Reviewed
• Volume: 30
• Pages: 1011-1020
• DOI: https://doi.org/10.1111/j.1467-8659.2011.01950.x
• Keywords: Information visualisation; pedigree; genetic analysis; inheritance pattern; genotype; errors; "sandwich view"
• Public URL: http://researchrepository.napier.ac.uk/id/eprint/4546
• Publisher URL: http://dx.doi.org/10.1111/j.1467-8659.2011.01950.x