Abstract 2196: Genome-wide analysis of DNA methylation patterns in formaldehyde-fixed paraffin-embedded (FFPE) human tumor specimens

Abstract

Abstract Formalin-fixed paraffin-embedded samples (FFPE) are in many case, the only available source of biological materiel available for translational studies. However the quantity and quality of nucleic acid extracted from FFPE samples is very often challenging (small amount and high level of degradation), which makes genomic analysis in general, and epigenomics analysis in particular, difficult to impossible. Here we are showing that we developed a robust, unbiased and cost effective method for genome-wide analysis of DNA methylation of FFPE DNA. Our method, named STAMP for Sequence Tag Analysis of Methylation Patterns, uses a recombinant protein containing a methyl-CpG binding domain (MBD) to precipitate methylated DNA fragments that are then identified by massively parallel sequencing using the SOLiD sequencer (ABI). We generate ∼15-million sequence tags per specimen and utilize an analytical platform comprised of custom-written R-language algorithms to study genomic DNA methylation patterns. We used this technology to compare the methylation patterns of matched fresh frozen (FF) and FFPE tumor specimens. Tissues had been stored for as long as 6 years. Because the STAMP method utilizes fragmented DNA as starting material we hypothesized that this method would be well-suited to the study of FFPE DNA methylation. Using this method, we found the methylation patterns of the FFPE and matched FF specimens were highly correlated. We successfully detected previously known methylated patterns and found hundreds of novel methylated regions. DNA methylation patterns were observed at all scales across the genome: from whole chromosomes to individual genes. We found that densely methylated elements are often highly conserved or closely associated with gene coding regions and promoters. We identified distinct patterns of DNA methylation surrounding the transcription start and termination sites of all genes. Genome-wide analyses of DNA methylation patterns of FFPE samples using the STAMP assay opens up the possibility to analyze large repositories of tumor specimens as well as samples that have been collected during routine clinical work and clinical trials. Large scales studies of DNA methylation using existing FFPE specimens linked to treatment outcomes may be rapidly translated to new epigenetic prognostic measures for cancer patients. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2196.