Prostate Cancer Mortality DNA Methylation Analysis

This repository contains code used for the analysis reported in Pidsley, et al. 2022 Clinical and Translational Medicine (https://doi.org/10.1002/ctm2.1030) with contributions from Ruth Pidsley, Dilys Lam, Timothy Peters, Phuc-Loi Luu and Aaron Statham

Please direct correspondence related to this manuscript to Prof Susan Clark ([email protected]) or Dr Ruth Pidsley ([email protected])

Raw and processed Whole Genome Bisulfite Sequencing (WGBS) data

Prostate cancer data, generated in this study, available on the NCBI GEO repository: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE158927

Previously reported LNCaP and PrEC data available on the NCBI GEO repository: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE86832

Targeted Multiplex Bisulphite PCR Sequencing (MBPS) data

Prostate cancer data, generated in this study, available through this GitHub website.
https://github.com/clark-lab/ProstateLethal/tree/main/MBPS/data

Public DNA methylation 450K microarray data

TCGA PRAD data available on the NCI GDC Data portal: https://portal.gdc.cancer.gov

Blood data available on the NCBI GEO repository: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40279

Public RNA-seq data

TCGA PRAD data available on the NCI GDC Data portal: https://portal.gdc.cancer.gov

Metadata

Additional data required for the analysis are available through this GitHub website.
https://github.com/clark-lab/ProstateLethal/tree/main/metadata