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Identification of variants contributing to schizophrenia using high-throughput genomics

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  • Full or part time
    Dr L Crooks
    Dr C F Dalton
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (European/UK Students Only)
    Funded PhD Project (European/UK Students Only)

Project Description

Next generation sequencing methods have allowed us to progress from studying single genes to the full complement of an individual’s DNA, which is called genomics. My interest is in understanding genetic factors that contribute to disease. Genomics offers tremendous opportunities to make advances in this area. We can now measure nearly all the hundreds of thousands of genetic variants an individual carries. However, the difficulty is how to filter through all this information to identify the variants that cause a specific disease. To fully utilise the extremely large datasets, computational methods are needed.

The aim of this project is to identify genetic variants that may increase the risk of developing schizophrenia from exome-sequence data. Schizophrenia is a chronic brain disorder that can affect cognition, emotions and behaviour. The lifetime prevalence is 0.5-1% and it is ranked as the twelfth highest worldwide cause of disability. A few rare copy number variants are known to convey a high risk of schizophrenia. About 100 single nucleotide polymorphisms have also been implicated in schizophrenia by genome-wide association but these only explain about 3% of schizophrenia risk. This project will look for schizophrenia predisposing variants by detailed consideration of the variants in each patient. Biological information from multiple sources will be combined to generate a short list of variants per patient. Using gene expression data from public transcriptome datasets to identify differential expression in the brain or specific brain regions will particularly be explored. The sets of prioritised variants will then be investigated for shared biological pathways.

This project is primarily a data analysis project as opposed to ‘wet-lab’. The skills you will learn are increasingly in demand both in academia and industry. It is an advantage if you can demonstrate experience working on the Linux command line and/or programming in a language such as Perl. However, you can also learn these during the studentship. It is essential that you have a logical mind, can break down problems into simpler steps, and are able to troubleshoot. This will be tested at interview. You should consider this position if you are strong at maths or physics.

You would become a member of the Sheffield Bioinformatics Hub, which is a group of Sheffield-based researchers including several from the University of Sheffield and their PhD students. It offers a network of support, advice and expertise in bioinformatics.

Sheffield is a lovely city to live in, with a reasonable cost of living. It has many parks and green spaces and you can quickly leave the city to enjoy the outdoors in the Peak District. Sheffield has a high retention rate of students who remain here after their studies finish.

Applicant Profile
As a minimum, applicants should possess a 1st or 2.1 Honours degree in either a biological subject with a maths or statistics component, physics or computer science.

Where English is not your first language, you must show evidence of English language ability to the following minimum level of proficiency: an overall IELTS score of 7 or above, with at least 6.5 in each component or an accepted equivalent. Please note that your test score must be current, i.e. within the last two years.

Application Process
Students should apply to Sheffield Hallam University via the University’s application form, including a statement in section 9 identifying how your background suits that particular area. It would be useful to include your laboratory expertise if it is relevant to this area. Please send applications forms and supporting documentation to [email protected]

You can access an application form at: https://www.shu.ac.uk/study-here/how-to-apply/postgraduate/application-form

For informal enquiries about the project please contact Dr Lucy Crooks (email: [email protected]).
For more information on the application process please contact: [email protected]

Funding Notes

This is a 3 year fully funded PhD studentship. The studentship covers the tuition fees and a stipend equivalent to full UK Research Council rate.
The stipend is approximately £14,553 in year 1, with cost of living increases in years 2 and 3.

International applicants will need to fund the shortfall of tuition fees (approx. £8000 per year) and bench fees (approx. £12,000 per year).

Key Dates:
•Deadline for applications Friday 30 June 2017
•Interviews will be held in July 2017
•Studentship begins 02 October 2017

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