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Improved data visualisation tools for human genome sequence variation.


About This PhD Project

Project Description

Project outline:

Human genome sequence variants should be reported in the literature and in clinical reports using the HGVS sequence variant nomenclature (den Dunnen et al., 2016). This requirement is endorsed by several international organisations which regulate standards-compliance in clinical genetics testing. However, published and anecdotal evidence shows that the quality of reporting is variable with examples of incorrect syntax and/or data being presented in the literature. Such errors certainly lead to confusion, but might also result in inappropriate medical treatment in certain instances. VariantValidator (https://variantvalidator.org/) (Freeman et al., 2017) has been developed as a software tool to provide rigorous checking of sequence variant descriptions with respect to syntax and data inconsistencies.

The general utility of VariantValidator could be improved by harnessing its powerful features via a graphical user interface (GUI), allowing visualisation of sequence variants and integration with variant effect prediction tools. The project will build on the existing successful VariantValidator project to address the needs of human sequence variation in the the era of whole genome sequencing.

Applicant qualifications:

The ideal applicant will have an outstanding understanding of Computer Science or Bioinformatics with a degree at BSc or MSc level (preferably the latter). Applicants with degrees in Biological Sciences are discouraged from applying unless they can demonstrate advanced computing skills including creating relational databases and have the ability to code original applications in languages commonly used in bioinformatics, such as Python, Perl or C/C++. We know from experience that we can teach the necessary genetics skills to academically bright students with little or no prior knowledge of genetics.

References

Freeman PJ, Hart RK, Gretton LJ, Brookes AJ, Dalgleish R (2017) VariantValidator: accurate validation, mapping and formatting of sequence variant descriptions. Human Mutation, 10.1002/humu.23348.

den Dunnen JT, Dalgleish R, Maglott DR, Hart RK, Greenblatt MS, McGowan-Jordan J, Roux A-F, Smith T, Antonarakis SE, Taschner PEM (2016) HGVS recommendations for the description of sequence variants: 2016 update. Human Mutation, 37: 564-569.

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