Genome-wide DNA methylation analysis of archival formalin-fixed paraffin-embedded tissue using the Illumina Infinium HumanMethylation27 BeadChip

Aberrant DNA methylation of promoter and other genomic regions can lead to changes in gene expression, such as over-expression of oncogenes and the silencing of tumour suppressor genes in the context of cancer. Ability to accurately assess the DNA methylation status is therefore of great importance in health and disease. Recently, various platforms for genome-wide analysis of promoter DNA methylation have been developed, including the Illumina Infinium platform. While some of these platforms can be used with formalin-fixed paraffin-embedded (FFPE) tissue, no protocol has yet been developed for the analysis of FFPE-derived DNA on the Infinium platform using the HumanMethylation27 BeadChip which interrogates 27,578 cytosine-guanine (CpG) dinucleotide sites, selected predominantly from the promoter regions of 14,000 annotated genes. As FFPE preservation has been the method of choice for the archiving of clinical samples, the ability to analyse such samples opens the possibility to study large numbers of clinically well annotated samples which can be expected to lead to more powerful and robust data, particularly for rare cancers. Here, we describe a protocol for the analysis of FFPE samples using the Infinium HumanMethylation27 BeadChip.