Now showing items 1-10 of 11
Crambled : a Shiny application to enable intuitive resolution of conflicting cellularity estimates
(2015-12-07) - Journal article
It is now commonplace to investigate tumour samples using whole-genome sequencing, and some commonly performed tasks are the estimation of cellularity (or sample purity), the genome-wide profiling of copy numbers, and the ...
The importance of DNA methylation in prostate cancer development
(2017-02) - Journal item
After briefly reviewing the nature of DNA methylation, its general role in cancer and the tools available to interrogate it, we consider the literature surrounding DNA methylation as relating to prostate cancer. Specific ...
Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis
(2015-07-10) - Journal article
Background: Mobile elements are active in the human genome, both in the germline and cancers, where they can mutate driver genes. Results: While analysing whole genome paired-end sequencing of oesophageal adenocarcinomas ...
5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer
(2015-04-01) - Journal article
Background : The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is ...
Epigenetic and oncogenic regulation of SLC16A7 (MCT2) results in protein over-expression, impacting on signalling and cellular phenotypes in prostate cancer
(2015-06-02) - Journal article
Monocarboxylate Transporter 2 (MCT2) is a major pyruvate transporter encoded by the SLC16A7 gene. Recent studies pointed to a consistent overexpression of MCT2 in prostate cancer (PCa) suggesting MCT2 as a putative biomarker ...
Authentication and characterisation of a new oesophageal adenocarcinoma cell line : MFD-1
(2016-09-07) - Journal article
New biological tools are required to understand the functional significance of genetic events revealed by whole genome sequencing (WGS) studies in oesophageal adenocarcinoma (OAC). The MFD-1 cell line was isolated from a ...
Telomerecat : a ploidy-agnostic method for estimating telomere length from whole genome sequencing data
(2018-01-22) - Journal article
Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented ...
HES5 silencing is an early and recurrent change in prostate tumourigenesis
(2015-04-01) - Journal article
Prostate cancer is the most common cancer in men, resulting in over 10 000 deaths/year in the UK. Sequencing and copy number analysis of primary tumours has revealed heterogeneity within tumours and an absence of recurrent ...
Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data
(2017-09-25) - Journal article
A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer. Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively ...
Mining human prostate cancer datasets : the “camcAPP” shiny app
(2017-03) - Journal item