Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias and copy number variation

Abstract: 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 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, affinity-purification of methylated DNA using two popular genome-wide techniques: methylated DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain-based capture (MBDCap) were evaluated, highlighting that each technique operates in a different domain of the CpG density landscape. The effect of whole genome amplification was explored, illustrating that it can reduce sensitivity for detecting DNA methylation in GC-rich regions of the genome. Using MBDCap, microarray- and sequencing-based readouts were compared, highlighting the impact that copy number variation (CNV) can make in differential comparisons of methylomes. These studies reveal that the analysis of DNA methylation data and genome coverage is highly dependent on the method employed and consideration must be made in light of GC content, extent of DNA amplification and copy number. Overall design: Comparison of MeDIP/MBD for DNA methylation profiling, comparison of whole genome amplification techniques, using tiling array for copy number aberration detection and comparisons of tiling array data to sequencing readouts