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Using massively-paralleled sequencing to find the cause of inherited conditions that affect the front of the eye

Faculty of Medicine and Health

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Dr M Ali , Prof C Inglehearn Applications accepted all year round Self-Funded PhD Students Only

About the Project

Eye diseases are a common cause of human disability and many of them are inherited. These include congenital as well as adult-onset conditions and diseases of ageing, and may involve abnormalities at the back of the eye or the anterior eye structures. We are currently working on a range of eye diseases that affect the front of the eye including primary glaucoma (eg. Ali et al 2009, Am J Hum Genet 84, 664-671), cataracts (eg. Khan et al 2011, Am J Hum Genet 89, 464-473), corneal dystrophies (eg. Siddiqui et al 2014, Cornea 33:247-51), keratoconus and strabismus. A major strength is our access to patients and patient samples through links with local clinicians. We also benefit from many national and international collaborations, and the group now manages unique cohorts of patients’ DNA and cells. Ultimately it is hoped that genetic analyses of these patients will contribute to the search for cures for both rare and common inherited human eye diseases.

The projects offered involve studying the molecular basis of these potentially blinding conditions in families with multiple affected members. To search for the pathogenic mutation(s), the student will prepare and analyse next-generation sequencing data using the established pipeline. To identify the genes and proteins involved they may also use a combination of autozygosity mapping, genotyping, bioinformatic analysis and Sanger DNA sequencing. Once the mutation has been identified, there will also be the opportunity to perform a range of molecular and cell biological techniques to characterise the mutant protein and determine the function of the normal protein during eye development. These experiments will involve reverse transcription PCR, in situ hybridisation, immunohistochemistry, siRNA (for gene knock-down) and molecular cloning with cell biology (for over-expression studies).

The student will be based in the University of Leeds in the section of Ophthalmology and Neuroscience (OPNE), School of Medicine, University Of Leeds. The appointed student will have the opportunity to learn a broad range of techniques described above. For further details of the Institute’s research visit

This project is available immediately to both Home/EU rate applicants and International applicants who are able to self-fund their studies. Students must be able to provide the appropriate level of fees based on their fee status plus laboratory consumables costs per year. This is in addition to the provision of personal living expenses.

You should hold a first degree equivalent to at least a UK upper second class honours degree in a relevant subject.

Candidate whose first language is not English must provide evidence that their English language is sufficient to meet the specific demands of their study, the Faculty minimum requirements are:

• British Council IELTS - score of 6.5 overall, with no element less than 6.0
• TOEFL iBT - overall score of 92 with the listening and reading element no less than 21, writing element no less than 22 and the speaking element no less than 23.

Applicants with sufficient funding must still undergo formal interview prior to acceptance in order to demonstrate scientific aptitude and English language capability.

How to apply
Applications can be made at any time. To formal apply for this project applicants should complete a Faculty Application form using the link below and send this alongside a full academic CV, degree certificates and transcripts (or marks so far if still studying) to the Faculty Graduate School at [Email Address Removed]

We also require 2 academic references to support your application. Please ask your referees to send these references on your behalf, directly to [Email Address Removed]

Any queries regarding the application process should be directed to [Email Address Removed]
Potential applicants are welcome to contact Informal enquiries to Dr. Manir Ali at [Email Address Removed] with informal enquiries about this research project.

Funding Notes

This project is for self funding applicants only.

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