The Application of Genome DNA Sequencing Technologies and Bioinformatics to Understanding Why there are Multiple Areas of Cancer in Prostate Cancer Patients - 2015 Movember Foundation PhD Studentship in Bioinformatics
In recent studies we have observed that in some men with prostate cancer even morphologically normal tissue contain clones of expanding cells. The student will examine using bioinformatics algorithms how this observation relates to the prostate "field effect" that accounts for around 80% of men presenting with multiple areas of cancer. You will become part of a highly successful UK Genome DNA Sequencing (WGS) consortium (ICGC UK Prostate). You will learn to process next-generation sequencing data and call somatic variants. You will also learn methods of post-validation analysis of data including Bayesian Dirichlet analysis and non-negative matrix factorization that have underpinned our recent Nature Genetics and Nature publications. First, the project will involve investigating the relationship between clonal cell expansions in morphologically normal tissue and the presence of prostate cancer in an expanded series of prostates both from patients with prostate cancer and those without. This will allow us to determine the prevalence of clonal expansions, the relationship to age, and the relationship between the clonal expansions and the location of cancer. Secondly, it will involve analysis of Whole Genome and targeted DNA sequencing data from stromal cell and epithelial components to determine in which components the clonal cell expansions arise. Thirdly, it will involve investigating whether the normal prostate contains multiple clones of expanding cells as recently observed for sun-exposed eyelids by examining targeted sequences for numerous small samples. We strongly believe that insights into the nature of the field effect will provide opportunities to prevent or slow cancer progression.
Please note a later start date of October 2016 will also be considered.
Closing Date: 30th March 2016, 5pm
In recent studies we have observed that in some men with prostate cancer even morphologically normal tissue contain clones of expanding cells. The student will examine using bioinformatics algorithms how this observation relates to the prostate "field effect" that accounts for around 80% of men presenting with multiple areas of cancer. You will become part of a highly successful UK Genome DNA Sequencing (WGS) consortium (ICGC UK Prostate). You will learn to process next-generation sequencing data and call somatic variants. You will also learn methods of post-validation analysis of data including Bayesian Dirichlet analysis and non-negative matrix factorization that have underpinned our recent Nature Genetics and Nature publications. First, the project will involve investigating the relationship between clonal cell expansions in morphologically normal tissue and the presence of prostate cancer in an expanded series of prostates both from patients with prostate cancer and those without. This will allow us to determine the prevalence of clonal expansions, the relationship to age, and the relationship between the clonal expansions and the location of cancer. Secondly, it will involve analysis of Whole Genome and targeted DNA sequencing data from stromal cell and epithelial components to determine in which components the clonal cell expansions arise. Thirdly, it will involve investigating whether the normal prostate contains multiple clones of expanding cells as recently observed for sun-exposed eyelids by examining targeted sequences for numerous small samples. We strongly believe that insights into the nature of the field effect will provide opportunities to prevent or slow cancer progression.
Please note a later start date of October 2016 will also be considered.
Closing Date: 30th March 2016, 5pm