Evaluating the biopsychosocial impact of whole genome sequencing (WGS) for improved diagnosis of disease

 

Outline, including interdisciplinary dimension

This project combines expertise in genomics, psychology, and bioinformatics to systematically consider complex interactions for health, illness, and healthcare delivery. To help deliver a person-centred WGS service we will focus on appraising the impact of disease and how the burden of disease affects the quality of life and participation of individuals and their families, including social aspects of living with a chronic disease, evaluation of prompt, accurate diagnosis, and accessibility of appropriate genetic disease information. For rare diseases in particular, receiving a prompt, accurate diagnosis through WGS may reduce uncertainty and stress for patients and families, making daily life easier for schools, employment, enhancing quality of life, enabling peer-support, social support, and financial support where often the first question on paperwork and application forms is, “what is your diagnosis?”.

In this studentship we will explore epigenetic features, primarily DNA methylation and microRNAs, associated with stress of delayed diagnosis, living with long-term disease (for patients and carers) and adversity outcomes. Briefly, this project will generate genome-wide methylation and microRNA data for 300 individuals and assess changes in methylation using well-characterised longitudinal cohorts where we have information pre and post exposure to carefully defined stressors. We have rich phenotyping resources, a strong background in epigenetic research, long duration follow-up of multigenerational families, established collaborators for replication, and availability of extensive data linkages within our integrated health and social care system to facilitate high quality outputs from this project.

We will interrogate public resources such as Blood-eQTL browser, GTExPortal, and HaploReg, and also have access to complementary genomic DNA WGS, that will augment epigenetic information to provide functional context to prioritised loci and help identify critical biological pathways mediating stress response(s) and identify opportunities for designing effective therapeutic strategies.

Key words/descriptors

genomic, methylation, whole genome sequencing, epigenetic, SNP, microRNA, assocation

First supervisor

Dr Amy Jayne McKnight - School of Medicine, Dentistry and Biomedical Sciences

Secondary supervisor from a complementary discipline

Dr Teresa Rushe - School of Psychology

Supervisors’ track record of PhD completions, plus excellence and international standing in the project area

The supervisors have an excellent track record of PhD completions with 6 students currently under their direct supervision.  All students have published their research in multiple peer-reviewed journals, all have won awards for their PhD research and all are employed post-PhD. This project complements recent grant awards to the supervisors, Including ESRC (Dr Rushe for adversity and resilience) and MRC (Dr McKnight for WGS and epigenetics) awards. The supervisors have significant international standing in respective fields including organising international meetings, invited plenary talks, grant reviews and participating in government advisory groups.

Intersectoral exposure and/or international mobility

(e.g. secondments to/collaboration with partner organizations)

This project would be run in parallel to the 100,00D genomes project (a UK-wide initiative for whole genome sequencing), which is funded as an NHS transformational project with a strong focus on translational research; this complements similar projects developed by our colleagues in the USA and Europe. There are opportunities for the successful student to work closely with the Public Health Agency, academic and clinical colleagues, liaise with Department of Health, Social Services and Public Safety NI, clinical trials network, UK-wide Genome Medicine Centres, European centres of expertise and major pharmaceutical companies through our established international partnerships; this also ensures a strong research training focus as the student will be part of at least one European network. Funds permitting, the student will spend several months in the USA comparing their data with that of our UK cohorts. Multiple Industrial partners are involved in the scheme as are >30 local charities including the Northern Ireland Rare Disease Partnership.

Describe briefly the international profile of the partner

Several international partners are likely to participate in this project, inducing Dr William Gahl (NHGRI, NIH, instrumental in establishing US undiagnosed disease program), Prof Nine Knoers (Work package leader for EURenOmics; Utrecht), Prof Robert Unwin (www.astrazeneca.co.uk), Dr Robert Holt (www.hologic.com), and Prof Caroline Savage (www.gsk.com).

Training that will be provided through the research project itself

This studentship offers cross-discipline research training evaluating biopsychosocial impacts of stress. The project involves conducting patient interviews, surveys and focus groups, alongside using state-of-the-art equipment such as next generation sequencing and 3D digital quantitative PCR, with complex analytical tools. The student will be encouraged to attend relevant PGT lectures in modules coordinated by Dr Rushe (adversity) and Dr McKnight (genomics). We have an established mentoring scheme for doctoral students and are developing a ‘pitching’ process for early stage researchers to gain expert feedback on planned fellowship applications. We will equip the student with multiple translational research skills and facilitate access to a wide range of expertise.

Examples of additional training in non-research transferable skills

The student will gain skills in project management, critical thinking, leadership, knowledge transfer, writing, public engagement and communication, informed consent, ethics, confidentiality, standardisation of protocols across multiple centres, harmonisation, and awareness of relevant codes of best practice.

Expected dissemination of results: peer-reviewed journals, seminars, workshop and conferences at European/international level

(e.g. public talks, visits to schools, open days, QUB impact showcase)

This project will contribute to important reports to help devise the best strategy policy and practice) for patient engagement in WGS and reporting of results. Results will be disseminated through multiple high quality publications, regular seminars, workshops with project partners and international conferences such as the European and American Society of Human Genetics.

Expected impact activities

(e.g. public talks, visits to schools, open days, QUB impact showcase)

The data generated by this project will add to QUB’s valuable bio-datasets by creating a legacy resource that will continue to be useful well beyond the timeframe of this studentship. Public engagement initiatives will include participation in an exhibition at W5, STEMNET engagement with school visits, NI Science Festival, public lectures and workshops, and information shared through the communication and engagement group within established Centre of Excellence for Public Health NI.