3-Year Moorfields Eye Charity PhD Studentship: Comprehensive human genomic analysis using single molecular sequencing: elucidating the molecular pathology of rare disease.

Institute of Ophthalmology 3-Year Moorfields Eye Charity PhD Studentship

UCL Department / Division: UCL Institute of Ophthalmology

Duration of Studentship: 3 years, available to start from 2 May 2023.

PhD Title: Comprehensive human genomic analysis using single molecular sequencing: elucidating the molecular pathology of rare disease.

Supervisors: Dr Gavin Arno and Prof Andrew Webster

Key Collaborators: Matthew Loose (University of Nottingham), Greg Elgar (Genomics England

We are offering a fulltime, 3-year PhD studentship to investigate the efficacy of Oxford Nanopore Technologies single molecule sequencing (ONT-SMS) in the diagnosis of inherited disease using eye disease as a paradigm.

Next generation sequencing (NGS) technology has revolutionized our ability to detect genetic variation and whole genome sequencing (WGS) improves coverage, enables better characterization of genomic rearrangements and unlocks our ability to interrogate the non-coding genome, widely ignored and poorly understood to date. In the UK, WGS is now available as a clinical diagnostic test for many rare diseases following the completion of the 100,000 genomes project. Numerous factors contribute to missing or incomplete molecular diagnoses: variants of uncertain significance (VUS) without adequate evidence of pathogenicity, non-coding or structural variants undetected by current pipelines, failure of NGS to sequence intractable genomic regions, novel genes, etc. This project investigates the use of ONT-SMS to characterise both RNA and DNA sequences in rare disease patients.

Inherited Eye Disease (IED) is the major cause of blindness in working age people in the United Kingdom. Over 300 genes and loci have been implicated in IED (www.RetNet.org), many of which are highly amenable to gene therapies. At Moorfields Eye Hospital (MEH)/UCL Institute of Ophthalmology (UCL-IoO), we are leaders in the field of IED genomics; patients and families from MEH form significant portions of two of the largest WGS studies undertaken to date – National Institute for Health Research-Rare Disease (NIHR-RD, 753 MEH IED patients) and the UK’s 100,000 genomes project (100KGP with over 2000 MEH patients and families sequenced), however up to 50% of patients remain unsolved following WGS.

This exciting project aims to investigate the unsolved patient cohort with a variety of cutting-edge methods and technologies including:

·      Bioinformatic analysis and novel pipeline development for WGS variant data in the 100,000 genomes project research embassy to identify and characterise candidate pathogenic genotypes for molecular investigations.

·      Molecular characterisation of variants of uncertain significance (VUS) and non-coding variants for their potential effect on transcripts using ONT-SMS targeted mRNA transcript analysis.

·      Develop novel methods to sequence intractable genes/genomic regions using targeted ultra-long read sequencing. Focusing on the OPN1LW/OPN1MW gene array, the candidate will use Cas9 targeted ultra-long read sequencing to enable mutation detection and gene array characterisation of this NGS intractable genomic region.

·      Investigate the use of adaptive sampling and whole genome long-read sequencing for IRD genetic analysis. With huge potential for genomic analysis, targeted ONT-SMS using adaptive sampling (ReadFish, Matt Loose Lab, Nottingham) or whole genome long read sequencing (Greg Elgar, Genomics England) represent an exciting new area for rare disease genetic research. The project will investigate these methods using the MEH patient cohort in a pilot study.

Applicants should hold, or expect to receive, a minimum upper-second degree or equivalent in an associated subject such as Biology, Molecular Biology, Genetics or related life science. A Master’s degree or previous lab-based/bioinformatics research experience is desirable.

Duties and Responsibilities

The successful candidate is expected to:

• Perform variant filtering and interrogation on WGS datasets

• Perform molecular investigations of various classes of candidate mutations (splicing, regulatory, structural) using RT-PCR, ONT-SMS, cloning and expression studies, Luciferase assays etc

• Develop new methods for Cas9 targeted ultra-long read sequencing using the SageHLS platform and ONT sequencing

• Analyse ONT-SMS datasets, including bioinformatics and pipeline development of read data, variant analysis etc

• Work in collaboration with other researchers and clinician in the MEH/IoO team and the collaborative group across several institutions

• Prepare progress reports

• Prepare presentations for institutional, local, national and international meetings

• Travel for collaboration and other meetings or conferences

• Prepare manuscripts for submission to international peer-reviewed journals

• Contribute to the overall activities of the research team, department and be aware of UCL policies

Person Specification

• A good degree (2.1 or above; or equivalent EU/overseas degree) and/or MSc in a relevant subject area

• Demonstrable interest in genetics/genomics of rare disease

• Experience with molecular biology methods

• Experience of bioinformatics/computational biology

• Excellent methodological skills, particularly in project planning

• High proficiency in written and spoken English is required

• Very strong work ethic, with the ability to think creatively and work both individually and within a team

Informal enquiries should be made to Dr Gavin Arno ([Email Address Removed])

How to apply

Applicants should submit an application to the Research Degrees Manager [Email Address Removed]. 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 relating to the application process should be sent to the Research Degrees Manager [Email Address Removed].

Shortlisted candidates will be contacted directly for interview.

The successful candidate is expected to start 2 May 2023, but flexibility with respect to the start date is possible.

 Funding Notes

This studentship is funded for 3 years by the Moorfields Eye Charity and includes UK UCL PhD tuition fees, laboratory costs and an annual salary stipend of £22,000 in year 1, £23,000 year 2 and £24,000 in year 3.

Eligibility

The full studentship (tuition fees and salary stipend) 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, but they must show that they can supplement the difference between UK and international fees (for the current 2022-2023 academic year International fees are £27, 480; for 2023-2024 £32, 100. The fees will be subject to further annual increases).

Application deadline: Friday 24 February 2023

Proposed interview date: Monday 3 April 2023