About the Project
We have successfully modelled Joubert syndrome [Hynes et al. PNAS (2014) 111:9893-8 (PMCID: PMC4103340)] leading to the identification of treatments that ameliorate disease in patient cells [Srivastava et al. Hum Mol Gen (2017) 26:4657-67 (PMCID: PMC5886250)] and mouse models [Ramsbottom et al. PNAS (2018) 115:12489-94 (PMCID: PMC6298104)]. However, limiting patient numbers and extensive genotype/phenotype heterogeneity complicates efforts to understand these conditions and precludes most conventional genomic association-based approaches. Consequently, there is an urgent need to develop bespoke in silico genomic tools for rare diseases such as ciliopathies.
We have recently demonstrated the power of integrating a priori knowledge, gained from ciliopathy models, to dissect complex genetic mechanisms underlying rare disease [Ramsbottom et al. PNAS (2020) 117:1113-8 (PMCID: PMC6969532)]. This serves as the proof of principle that underpins this PhD project, the aim of which is to develop methodologies that will a) identify novel genetic causes for the ~40% of ciliopathy patients currently lacking a genetic diagnosis and b) refine existing genetic diagnoses.
Based in the Newcastle University laboratories of Prof Sayer (https://www.ncl.ac.uk/medical-sciences/people/profile/johnsayer.html) and Dr Miles (https://www.ncl.ac.uk/medical-sciences/people/profile/colinmiles.html), this PhD benefits from a cross-faculty, multi-centred, multi-disciplinary supervisory team including Prof Heather Cordell (https://www.ncl.ac.uk/medical-sciences/people/profile/heathercordell.html), Prof David Westhead (https://www.turing.ac.uk/people/researchers/david-westhead), Dr Phillip Lord (https://www.ncl.ac.uk/sage/staff/profile/philliplord.html#background) providing state-of-the-art genetics and genomics training in bioinformatics, statistical genetics and computational biology, in the context of rare disease.
As well as working closely with patients from our clinics, for example: (https://www.chroniclelive.co.uk/news/health/newcastle-university-kidney-research-sayer-15431046) (https://www.chroniclelive.co.uk/news/north-east-news/siblings-who-developed-kidney-failure-17535415), we have assembled one of the largest cohorts of ciliopathy patients available (through the UK National Registry of Rare Kidney Diseases, Genomics England 100,000 Genomes Project, and collaborators across UK, Europe, USA and the Middle East). This will enable patient stratification for association studies to be conducted with unprecedented precision and provide a solid foundation for subsequent enhanced genetic association studies complemented by a priori knowledge broadly falling within three categories: 1. Assessment of allele burden in ~300 unsolved renal ciliopathy patients, 2. Identification of genetic modifiers using the power of mouse genetics, 3. Identification of novel causative genes and modifiers by integration of transcriptomic datasets derived from mouse models and primary patient-derived renal cells.
This PhD project will contribute towards the MRC and UK Government’s burgeoning genomic/precision medicine initiative as highlighted by the UK Government’s recent announcement (https://www.gov.uk/government/news/landmark-strategy-launched-to-cement-uks-position-as-global-leader-in-genomics) and provide training that truly reflects “the skills of tomorrow” whilst also providing an opportunity to improve patient diagnosis today (https://www.youtube.com/watch?v=Who-HL2GVv4)
Please note that this is a computational biology project, conducted entirely in silico. Further, informal enquiries are encouraged and should be directed to Prof Sayer and Dr Miles.
Benefits of being in the DiMeN DTP:
This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.
We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.
Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here: http://www.dimen.org.uk/overview/student-profiles/flexible-supplement-awards
Further information on the programme and how to apply can be found on our website:
Studentships commence: 1st October 2021
Devlin & Sayer. Curr Opin Genet Dev. 2019. 56:49-60. DOI: 10.1016/j.gde.2019.07.005
Bachmann-Gagescu et al. Am J Med Genet A. 2020. 182(1):229-249. DOI: 10.1002/ajmg.a.61399
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