Now showing items 1-10 of 17
Timing the landmark events in the evolution of clear cell renal cell cancer : TRACERx renal
(2018-04-19) - Journal article
Clear cell renal cell carcinoma (ccRCC) is characterized by near-universal loss of the short arm of chromosome 3, deleting several tumor suppressor genes. We analyzed whole genomes from 95 biopsies across 33 patients with ...
A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer
(2015-01) - Journal article
Complex focal chromosomal rearrangements in cancer genomes, also called "firestorms", can be scored from DNA copy number data. The complex arm-wise aberration index (CAAI) is a score that captures DNA copy number alterations ...
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 ...
Mining human prostate cancer datasets : the “camcAPP” shiny app
(2017-03) - Journal item
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 ...
Cholinekinase alpha as an androgen receptor chaperone and prostate cancer therapeutic target
(2016-05-01) - Journal article
Background: The androgen receptor (AR) is a major drug target in prostate cancer (PCa). We profiled the AR-regulated kinome to identify clinically relevant and druggable effectors of AR signaling. Methods: Using genome-wide ...
Decomposition of mutational context signatures using quadratic programming methods
(2016-06-07) - Journal article
Methods for inferring signatures of mutational contexts from large cancer sequencing data sets are invaluable for biological research, but impractical for clinical application where we require tools that decompose the ...
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 ...
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 ...