UCL Department: Institute of Ophthalmology
PhD Duration: 3 years
PhD Title: Elucidating novel genetic origins and molecular mechanisms underlying inherited corneal disease
Supervisors: Associate Professor Alice Davidson and Dr Nikolas Pontikos
Project Background: Inherited corneal diseases (ICDs) are a group of phenotypically and genetically heterogeneous disorders that affect the cornea. They can cause severe visual impairment and blindness that has a major impact on patients' vision and quality of life. Over the past decade, the diagnosis of ICD has been revolutionised by advances in next generation sequencing and it is now possible to identify the genetic cause of disease in approximately 75% of individuals. However, the cause for disease in the remaining 25% remains unsolved. Determining this ‘missing heritability’ is a major challenge, despite the unprecedented amount of genomic, transcriptomic and proteomic data that is available. This is largely due to the difficulty in predicting the functional impact of variants that affect non-coding genomic regions, which we hypothesise underlie disease in many unsolved ICD cases.
Studentship Objectives: We are offering a funded PhD studentship to tackle this challenge by utilising our genetically refined ICD discovery cohort of cases that are unsolved, despite extensive screening of associated genes/transcripts. Development of informatic pipelines to analyse in-house genomic and transcriptomic datasets from this powerful discovery cohort, in combination with the growing body of publicly available heterogeneous and complementary corneal-specific datasets, offers the student a timely opportunity to understand the regulatory landscape of the cornea and how mutations affecting such genomic regions cause ICDs. The student will also determine the biological relevance of candidate variants using a range of functional approaches in cornea-specific cellular systems. The discoveries we generate are anticipated to have far-reaching translational relevance for the ICD patient population and beyond.
Environment: A wide range of expertise will be readily available to support the student across all aspects of the study. The position is based at UCL Institute of Ophthalmology (IoO). UCL IoO and Moorfields Eye Hospital (MEH) environment provides an unparalleled location is support ophthalmic research. It is exceptionally well equipped with laboratories and core facilities. The joint site and close association of IoO with MEH means day to day contact with clinical colleagues and access to the most extensive clinical ophthalmic resource in the UK. The student will become embedded within the inherited corneal disease lab, led by Associate Professor Alice Davidson (https://www.ucl.ac.uk/ioo/inherited-corneal-disease-lab) and the healthcare informatics group, led by Dr Nikolas Pontikos (https://www.ucl.ac.uk/ioo/pontikos-lab).
Skills, training and methodology: We are seeking a candidate who either has strong bioinformatics and/or human genetics skills or that is eager to learn. They will be supported to develop bioinformatics. methodology and pipelines to facilitate genomic discoveries, integrating publicly available and in-house generated corneal multi-omics datasets. Furthermore, they will also get the opportunity to work in a wet lab environment to validate the biological relevance of candidate variants using a range of functional approaches in cornea-specific cellular systems.
The student will benefit from Associate Professor Davidson’s genomic discovery expertise and broader program of translational corneal dystrophy research and Dr Pontikos’ computational research team that have extensive experience developing bespoke bioinformatic analytical pipelines and databases, as well as integrating standardised phenotypic information for genomics discovery in rare eye disease.
This studentship has also been designed to equip the prospective student with relevant knowledge, a multidisciplinary skill set, and an overall grounding to develop as a potential leader in their chosen area of interest, whether that vision science, computational biology and/or functional genomics.
Duties and Responsibilities
The successful candidate is expected to:
• Conduct bioinformatic analysis of next generation sequencing data (whole exome sequencing, whole genome sequencing and RNA-Seq)
• Undertake appropriate molecular/cellular experimental approaches to validate the functional significance of disease-associated variants.
• Work in collaboration with other researchers, clinicians and allied healthcare workers
• Prepare presentations for delivery by self and others.
• Travel for collaboration and other meetings or conferences.
• Prepare reports, and manuscripts for submission to peer-reviewed journals.
• Contribute to the overall activities of the research team, department and be aware of UCL policies.
• Hold, or expect to receive, a minimum upper-second degree or equivalent in an associated subject such as biology, genetics, or life sciences with a computational or statistical background. A Master’s degree or previous lab-based research experience is desirable.
• Interested in bioinformatics, genetics, cell biology and human diseases as well as translational research
• Experience with statistical methods and software packages (e.g. in R or Python)
• Experience in bioinformatics or computational biology
• Experimental skills in human genetics, molecular and cellular biology
• High proficiency in written and spoken English is required
• Very strong work ethic, with the ability to think creatively and work both independently and within a team
Informal project enquiries should be made to Associate Professor Alice Davidson (firstname.lastname@example.org) or Dr Nikolas Pontikos (email@example.com)
How to apply
Applicants should submit an application to the Research Degrees Manager firstname.lastname@example.org. You will be required to submit a CV, a covering letter outlining motivation, interest, and suitability for this project, and contact details for two academic referees.
Enquiries on the application process should be sent to the Research Degrees Manager (email@example.com).
Shortlisted candidates will be contacted directly for interview.
The successful candidate will ideally start on 26 September 2022, but flexibility with respect to the start date is possible.
This studentship is funded for 3 years by Fight For Sight and includes UK UCL PhD tuition fees (currently £5,525 per year), laboratory costs and an annual salary stipend starting at £20,000 to be used for accommodation and living expenses.
The full studentship is eligible to all UK nationals and some EU nationals depending on their settlement status.
Applicants who will incur international fees are welcome to apply and must show that they can supplement the difference between UK and international fees (currently £26,680 per year) in their application.
1 July 2022 11:59pm (extended from 17 June 2022)
Proposed interview date
Week beginning 18 July 2022