Our group has a track record of identifying novel colorectal cancer (CRC) predisposition genes and translating these findings into clinical practice (Al-Tassan et al. 2002, Palles et al. 2022). This bioinformatics-based project will analyse Genomics England whole genome sequencing (WGS) data in patients with bowel polyposis (n=170) and CRC (n=3,000) in an attempt to identify further CRC predisposition genes. We will initially study loss of function mutations under different inheritance models and then extend our analyses to include nonsynonymous variants. The student will use online databases (NCBI, Ensembl, GnomAD, 1000 genomes) and in silico tools (CADD, PolyPhen2, SIFT) to analyse variants of interest to determine their likely pathogenicity. Any potential disease causing variants & genes will be validated using in-house exome sequencing data from over 100 unrelated patients with colorectal adenomas and/or CRC. The student will determine the function of CRC-risk variants through in silico analyses. Better understanding of the underlying genomic basis of CRC will be translated to improved diagnostics, including predictive genetic testing to enable cancer prevention through surveillance and intervention.
We seek an enthusiastic candidate that holds (or is predicted to gain) a 1st or 2:1 in a Biological Science with a willingness to learn the required bioinformatics skills to analyse the exome data. Experience in R would be a benefit. This project is primarily computer based and will provide a solid foundation for a future academic career in cancer genetics research. This project has broad scope and allows for creative free thinking.
Further information: Cheadle, Williams & West will oversee the student’s studies. Cheadle has successfully supervised 18 Ph.D. students with a 100% completion record. The student will also be supported by experienced bioinformaticians within our group. Cheadle has a long-standing international reputation in Medical Genetic research and was responsible for the identification of the CRC predisposition gene MUTYH. The group also has substantial expertise in identifying low penetrance CRC-susceptibility alleles, and, germline and somatic alleles that affect prognosis. His laboratory has a strong track record in translating basic research into clinical practice. Our Division holds weekly seminars in which over 20 Ph.D. students attend and the student would be expected to regularly attend these meetings and to present their data via oral presentations on an annual basis. The student will also take part in the annual SoM post-graduate research day and present at the national NCRI Cancer Conference.
References:
Al-Tassan et al. Inherited variants of MYH associated with somatic G:C>T:A mutations in colorectal tumors. Nat Genet. 2002 Feb;30(2):227-32.
Palles et al. Germline MBD4 deficiency causes a multi-tumor predisposition syndrome. Am J Hum Genet. 2022 May 5;109(5):953-960.
For more details on the group see:
https://www.cardiff.ac.uk/people/view/122884-cheadle-jeremy
https://www.cardiff.ac.uk/research/explore/research-units/inherited-tumour-syndromes
Entry Requirements
Applicants should possess a minimum of an upper second class Honours degree, master's degree, or equivalent in a relevant subject.
Applicants whose first language is not English are normally expected to meet the minimum University requirements (e.g. 6.5 IELTS).
How to Apply
This studentship has a start date of October 2023. In order to be considered you must submit a formal application via Cardiff University’s online application service.
There is a box at the top right of the page labelled ‘Apply’, please ensure you select the correct ‘Qualification’ (Doctor of Philosophy), the correct ‘Mode of Study’ (Full Time) and the correct ‘Start Date’ (October 2023). This will take you to the application portal.
In order to be considered candidates must submit the following information:
• Supporting statement
• CV
• Qualification certificates
• References x 2
• Proof of English language (if applicable)
International applicants are welcomed if the difference in fees can be covered.
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