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Publication - Dr Tom Gaunt


    a tool for performing automated phenome scans in UK Biobank


    Millard, L, Davies, N, Gaunt, T, Smith, GD & Tilling, K, 2017, ‘PHESANT: a tool for performing automated phenome scans in UK Biobank’. International Journal of Epidemiology.


    Epidemiological cohorts typically contain a diverse set of phenotypes such that automation of phenome scans is non-trivial, because they require highly heterogeneous models. For this reason, phenome scans have to date tended to use a smaller homogeneous set of phenotypes that can be analysed in a consistent fashion. We present PHESANT (PHEnome Scan ANalysis Tool), a software package for performing comprehensive phenome scans in UK Biobank.

    General features
    PHESANT tests the association of a specified trait with all continuous, integer and categorical variables in UK Biobank, or a specified subset. PHESANT uses a novel rule-based algorithm to determine how to appropriately test each trait, then performs the analyses and produces plots and summary tables.

    The PHESANT phenome scan is implemented in R. PHESANT includes a novel Javascript D3.js visualization, and accompanying Java code that converts the phenome scan results to the required JavaScript Object Notation (JSON) format.

    Full details in the University publications repository