Graduate position: Geographic Information Science (GISc) for human genetics

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Funded PhD position in Geographic Information Science (GISc) as a tool for the analysis of human genetic and genomic data

University of Leicester, UK

Supervisors: Prof Mark A Jobling (Genetics), Dr Nick Tate (Geography)

Background: Genetic data on human populations are expanding exponentially through the activities of medical genetic consortia, individual research groups, and thousands of private individuals purchasing genomic predictive health testing and genetic genealogy services. All these data share a geographical (spatial) element: sampling locations, birthplaces of DNA donors, or ancestral locations based on grandparental birthplaces. There are other relevant geographically restricted variables, too: in complex disease epidemiology, these are interacting environmental factors, while for genetic ancestry, they are factors affecting population structure, such as indicators of past migrations in surnames, place-names, or archaeological evidence. So far, these geographical relationships have been assessed by a mix of ad hoc methods, with limited power to understand correlations and their explanations. There is a need to study geographical patterns of genetic diversity in a more sophistica
ted way, and an ideal and unexploited tool exists to do this: Geographic Information Systems (GIS), the scientific marriage of cartography, statistical analysis, and database technology.

Aims: The project lies at the interface between Genetics and Geographical Information Science (GISc) and will provide you with a unique opportunity to be trained in and work across these two disciplines. It aims to: (i) Explore and develop the use of GIS to represent and analyse existing genetic datasets, including data based on binary SNPs (single nucleotide polymorphisms) and multiallelic short tandem repeats; (ii) Develop methods to co-analyse existing and forthcoming genetic and non-genetic data taking into account different levels of spatial granularity and scale; (iii) Address a specific genetical and geographic research question that will be defined within the first year. The novel nature of the project makes it inappropriate to specify the research question beforehand, but an example might be an analysis of the distribution of rare variants that may contribute to disease phenotype heritability, within the context of other data relevant to both disease aetiology and po
pulation structure.

Methodology: Genetic datasets that can be considered include: available Y-chromosomal data; available whole-genome SNP data from the Wellcome Trust Case Control Consortium; forthcoming TwinsUK whole genome SNP data; whole-genome SNP data from the ‘People of the British Isles' project. Possible spatial analytical tools and techniques from GISc for use with these datasets include Kernel Density Estimation and Geographically Weighted Regression.

Supervision and support: You will be cosupervised by Prof Mark Jobling (Genetics) and Dr Nick Tate (Geography), who have worked together on the HALOGEN project (History, Archaeology, Linguistics, Onomastics, GENetics: throwing light on the past through cross-disciplinary databasing http://www2.le.ac.uk/offices/itservices/resources/cs/pso/project-websites/halogen). You will gain dynamic interdisciplinary support through membership of the Impact of Diasporas (http://www2.le.ac.uk/projects/impact-of-diasporas) group, which includes historians, linguists, archaeologists, geneticists and mathematical modellers. Training will take place in both Genetics and Geography Departments. Please contact either Mark (maj4@le.ac.uk) or Nick (njt9@le.ac.uk) for further details.

Funding: Applicants should have or expect to obtain a first-class or upper second-class degree in Geography (ideally with experience of GIS) or Genetics. This studentship is fully funded at UK/EU rates by the University of Leicester. International students are welcome to apply but would need to pay the difference between the UK/EU rate and the international fee rate and must provide evidence of additional funding.


References:

Bowden GR, et al. (2008) Excavating past population structures by surname-based sampling: the genetic legacy of the Vikings in northwest England. Mol Biol Evol, 25:301-309. Paper from the Jobling group using geographically restricted surnames to select males for population genetic sampling.

Balaresque P, et al. (2010). A predominantly Neolithic origin for European paternal lineages. PLoS Biol, 8:e1000285. Paper from the Jobling group containing examples of spatial approaches to archaeological and genetic data.

Longley PA, Cheshire JA, Mateos P (2011). Creating a regional geography of Britain through the spatial analysis of surnames. Geoforum, 42:506-516. An example of the quantitative analysis of spatial distributions of surnames.

To Apply:

Visit: http://www.findaphd.com/search/ProjectDetails.aspx?PJID=3D1164&LID=3D775

Prof Mark A. Jobling
Wellcome Trust Senior Research Fellow in Basic Biomedical Science
Department of Genetics
Room G5, Adrian Building
University of Leicester
University Road
Leicester
LE1 7RH UK

tel.: +44 (0)116 252 3427
mob.: +44 (0)7955 882334
fax: +44 (0)116 252 3378
email: maj4@le.ac.uk
web: http://www2.le.ac.uk/departments/genetics/people/jobling


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Funded PhD position in Geographic Information Science (GISc) as a tool for the analysis of human genetic and genomic data

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