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Visualising errors in animal pedigree genotype data.

Graham, Martin, Kennedy, Jessie, Paterson, Trevor and Law, Andy (2011) Visualising errors in animal pedigree genotype data. Computer Graphics Forum , 30 (3). pp. 1011-1020. ISSN 0167-7055

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    Abstract/Description

    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.

    Item Type: Article
    Print ISSN: 0167-7055
    Electronic ISSN: 1467-8659
    Uncontrolled Keywords: Information visualisation; pedigree; genetic analysis; inheritance pattern; genotype; errors; "sandwich view";
    University Divisions/Research Centres: Edinburgh Napier University, Institute for Informatics and Digital Innovation
    Dewey Decimal Subjects: 000 Computer science, information & general works > 000 Computer science, knowledge & systems > 006 Special Computer Methods > 006.3 Artificial intelligence
    Library of Congress Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
    Item ID: 4546
    Depositing User: Computing Research
    Date Deposited: 27 Jun 2011 12:04
    Last Modified: 29 Nov 2012 14:41
    URI: http://researchrepository.napier.ac.uk/id/eprint/4546

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