Abstract 149: DNA methylation biomarker discovery using the Methyl-Profiler PCR Array System

Histone modifications and DNA methylation are epigenetic events that can modulate gene expression patterns associated with normal development and disease pathology. Epigenetic alterations are clearly involved in breast cancer initiation and progression, as they silence tumor suppressor genes and activate proto-oncogenes. As a result, the profiling of gene promoter DNA methylation status can lead to the identification of novel biomarkers which can aid in the development and improvement of diagnostic, prognostic, and therapeutic treatments. The Methyl-Profiler PCR Array System proves to be quite useful for these purposes. The Methyl-Profiler DNA Methylation technology method is designed for semi high-throughput gene/target-specific DNA methylation profiling. The method involves the selective digestion of sample DNA with methylation-specific restriction enzymes, followed by precise quantization of intact remaining target DNA by real-time PCR using assays specially designed and validated for high G/C content amplicons. Attesting to the power of this method, as little as one µg of genomic DNA can be used to profile the methylation status of up to 96 gene/target assays, and as low as five % hyper-methylated DNA copies can be reliably detected in a heterogeneous sample. In short, this technology yields quantitative data comparable to bisulfite sequencing, but without the need for bisulfite conversion. Using the Methyl-Profiler assay, the methylation status of highly relevant methylation targets in breast cancer cell lines was profiled in an effort to discover novel DNA methylation biomarkers. Several putative markers were identified and compared with results as generated by Illumina® Infinium® Methylation Assay platform, demonstrating the viability of the Methyl-Profiler method in discovering DNA methylation biomarkers. In three short procedural steps, the Methyl-Profiler PCR System can efficiently and reproducible identify novel methylation-related targets that may prove to be valuable in developing breast cancer preventative and therapeutic strategies. 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 149.