Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling [WGBS]

Genome wide DNA methylation profiling of a suite of biological samples for technical evaluation of the HumanMethylationEPIC v2.0 BeadChip. Samples include prostate (LNCaP, PrEC) and breast cancer (MCF7, TAMR) cell lines, as well as primary tumour samples from prostate (SYN*) and breast (FD*). Overall design: To assess the performance of the EPICv2 array we profiled and ran a series of technical analyses on 40 DNA samples from a range of sample types, including: a transformed prostate cancer cell line (LNCaP), primary cell cultures of prostate epithelial cells (PrEC), fresh-frozen human prostate tumour samples (PrCa), transformed breast cancer cell lines (MCF7 and TAMR), and human breast cancer patient derived xenografts (PDX). LNCaP and PrEC were assayed each in triplicate at three different dilutions (500ng, 250ng and 125ng). A subset of the TAMR cells and PDXs had undergone treatment with the hypomethylating drug decitabine. Matched WGBS of prostate tumour samples was used for technical comparisons.