Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation
Mark D Robinson, Clare Stirzaker, Aaron L Statham, Marcel W Coolen, Jenny Z Song, Shalima S Nair, Dario Strbenac, Terence P Speed, Susan J Clark
GENOME RESEARCH | COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT | Published : 2010
DNA methylation is an essential epigenetic modification that plays a key role associated with the regulation of gene expression during differentiation, but in disease states such as cancer, the DNA methylation landscape is often deregulated. There are now numerous technologies available to interrogate the DNA methylation status of CpG sites in a targeted or genome-wide fashion, but each method, due to intrinsic biases, potentially interrogates different fractions of the genome. In this study, we compare the affinity-purification of methylated DNA between two popular genome-wide techniques, methylated DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain-based capture (MBDCap), and sh..View full abstract
Awarded by National Health and Medical Research Council (NHMRC)
We thank Kate Patterson for help with preparation of the figures and critical reading of the manuscript and Oleg Mayba for mappability calculation code. This work is supported by National Health and Medical Research Council (NH&MRC) project (427614, 481347) (M.D.R., C.S., D.S.) and Fellowship (S.J.C.), Cancer Institute NSW grants (CINSW: S.J.C., A.L.S.), and NBCF Program Grant (S.J.C.) and ACRF. We also thank the Ramaciotti Centre, University of New South Wales (Sydney, Australia) for array hybridizations and Illumina GAII sequencing of MBDCap DNA.