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Prof D Brewer, Prof C Cooper
No more applications being accepted
Funded PhD Project (European/UK Students Only)
About the Project
Cancer is not a single disease but a collection of diseases arising in a wide range of tissues. Even within a single cancer type such as breast cancer there can be multiple forms. Identifying subtypes will aid individualised treatment for improved survival and benefit the lives of those affected by cancer. Cancer subtypes can be identified by analysing what genes are switched on/upregulated or are turned off/downregulated. Unfortunately, analysis of these data is complex, and has been largely unsuccessful, with the notable exception of breast cancer.
We have previously had success in applying complex clustering methods to data from prostate cancer samples, identifying a subtype called DESNT associated with poor prognosis. In this studentship, you would apply these methods to a dataset from the Cancer Genome Atlas, a large US project that generated comprehensive high-dimensional data mapping key changes in a large number of different cancers (https://cancergenome.nih.gov). Developing an automated pipeline to analyse large and interrogating these results would form a key part of this PhD, with the expectation of discovering and classifying groundbreaking novel cancer subtypes.
This is a bioinformatics/data analysis-based PhD. During the PhD you will gain knowledge on how to deal with BigData, high performance computing, developing pipelines and statistical analyses. You will be part of the Cancer Genetics team at the Norwich Medical School, which is an interdisciplinary team comprising a mixture of bioinformaticians and lab-based scientists. We have a broad interest in translational cancer based molecular studies with the aim of improving patient care. Research includes urine-based biomarker development, whole genome sequencing studies, subtype detection and bacteria in cancer studies.
For more information on the supervisor for this project, please go here: https://www.uea.ac.uk/medicine/people/profile/d-brewer
Type of programme: PhD
Project start date: October 2018
Entry requirements: Acceptable first degree - Computer Science, Physics, Mathematics, Engineering, Biological Sciences, Biochemistry, Biomedical Science.
The standard minimum entry requirement is 2:1.
We have previously had success in applying complex clustering methods to data from prostate cancer samples, identifying a subtype called DESNT associated with poor prognosis. In this studentship, you would apply these methods to a dataset from the Cancer Genome Atlas, a large US project that generated comprehensive high-dimensional data mapping key changes in a large number of different cancers (https://cancergenome.nih.gov). Developing an automated pipeline to analyse large and interrogating these results would form a key part of this PhD, with the expectation of discovering and classifying groundbreaking novel cancer subtypes.
This is a bioinformatics/data analysis-based PhD. During the PhD you will gain knowledge on how to deal with BigData, high performance computing, developing pipelines and statistical analyses. You will be part of the Cancer Genetics team at the Norwich Medical School, which is an interdisciplinary team comprising a mixture of bioinformaticians and lab-based scientists. We have a broad interest in translational cancer based molecular studies with the aim of improving patient care. Research includes urine-based biomarker development, whole genome sequencing studies, subtype detection and bacteria in cancer studies.
For more information on the supervisor for this project, please go here: https://www.uea.ac.uk/medicine/people/profile/d-brewer
Type of programme: PhD
Project start date: October 2018
Entry requirements: Acceptable first degree - Computer Science, Physics, Mathematics, Engineering, Biological Sciences, Biochemistry, Biomedical Science.
The standard minimum entry requirement is 2:1.
Funding Notes
This PhD studentship is funded for three years by the Big C Charity. Funding comprises Home/EU fees, an annual stipend (£14,553 for 2017 entry – this increases each year in line with the GDP deflator) and £1000 per annum to support research training.
References
i) Luca B, Brewer DS, Edwards DR, Edwards S, Whitaker HC, Merson S, et al. DESNT : A Poor Prognosis Category of Human Prostate Cancer. Eur Urol Focus. European Association of Urology; 2017;1–9.
ii) Cooper CS, Eeles R, Wedge DC, Van Loo P, Gundem G, Alexandrov LB, et al. Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nat Genet. 2015 Apr;47(4):367–72.
iii) Rogers S, Girolami M, Campbell C, Breitling R. The latent process decomposition of cDNA microarray data sets. IEEE/ACM Trans Comput Biol Bioinforma. IEEE Computer Society Press; 2005;2(2):143–56.
ii) Cooper CS, Eeles R, Wedge DC, Van Loo P, Gundem G, Alexandrov LB, et al. Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nat Genet. 2015 Apr;47(4):367–72.
iii) Rogers S, Girolami M, Campbell C, Breitling R. The latent process decomposition of cDNA microarray data sets. IEEE/ACM Trans Comput Biol Bioinforma. IEEE Computer Society Press; 2005;2(2):143–56.
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