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Improving genomewide association study strategies for application on environmental bacteria

University of Bath - Biology and Biochemistry

Qualification Type: PhD
Location: Bath
Funding for: UK Students, EU Students
Funding amount: £14,777 UKRI annual stipend (2018/19 rate) + tuition fees + training support grant
Hours: Full Time
Placed On: 22nd October 2018
Closes: 7th January 2019

Lead supervisor: Dr Lauren Cowley, Department of Biology and Biochemistry, University of Bath, email:

This project is one of a number that are in competition for funding from the NERC Great Western Four+ Doctoral Training Partnership (GW4+ DTP). For further details about the programme, please see . 

Full Project Description

Genomewide association studies (GWAS) are a powerful tool in discovering the genetics underlying observed important phenotypes and have been used very successfully in human genetics for several heritable diseases. In bacteria that reproduce asexually, the challenge with GWAS is the high linkage between polymorphisms due to low levels of recombination. A lot of the mutations or genes in bacterial genomes are not acquired independently and it is therefore difficult to differentiate the mutation or gene that is causing the phenotype change from those that are simply hitch hiking with it (linkage disequilibrium). 

Methods developed to achieve bacterial GWAS results of high confidence could be extremely useful in determining the genetic elements associated with phenotypes of environmental importance, such as toxin production, environment survivability, antibiotic resistance or host niche. Previous studies by co-supervisors Professor Sam Sheppard and Dr Ruth Massey (Sheppard et al., 2013, Recker et al., 2017) have shown the capabilities of GWAS in bacteria. 

The aims of the studentship will be: 

  • To develop a novel approach of longitudinal and spatial sampling in big data that offers an opportunity to resolve genuine associations from spurious one’s due to linkage. 
  • This will be tested by using datasets that are deeply sampled longitudinally and testing time periods individually to see if association gene lists change over time and if certain genes remain constant in their assigned significance. In recombining bacteria, sampling over time causes linkage between loci to decline (Arnold and Hanage 2017). 
  • Simulations will be run using the state of the art computational simulation tool Fwdpp (Thornton 2017) to gauge the optimum time period needed to allow enough recombination to happen to decrease spurious linkage enough to make GWAS accurate. The student will aim to estimate the minimum number of required genomes and frequency of sampling when given the recombination rate of the species. 
  • Systematic testing will be performed in a variety of large genomic datasets to develop a robust protocol to provide high confidence results. 
  • To limit the complexity of linkage disequilibrium, highly recombinogenic environmental bacteria such as Legionella pneumophila datasets will be used in initial strategies. 

Candidate - 

  • Essential:
    • A high scoring degree in microbiology, biology or computer science (2.1 or higher)
  • Preferred:
    • A master’s degree in Bioinformatics or computer science
    • Experience of at least one computer programming language


NERC GW4+ DTP funding is for 3.5 years and is open to UK and EU applicants who have been resident in the UK for 3 years or more.

A studentship will provide UK/EU tuition fees, a stipend in line with the UKRI rate (£14,777 per annum for 2018-19) and a generous budget for research expenses and training. For further information please visit:


You may apply for more than one project if you wish but you should submit a separate personal statement relevant to each one. 

Further information on the Department of Biology & Biochemistry may be found here

Anticipated start date: 30 September 2019 

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