High-throughput DNA methylation profiling using universal bead arrays

TLDR

The technology promises large‑scale DNA methylation profiling for population studies and could aid classification and diagnosis of diverse cancers and diseases. By adapting the GoldenGate genotyping assay to a BeadArray platform, the authors measured 1536 CpG sites across 371 genes from 200 ng bisulfite‑treated DNA in a single multiplexed reaction, validating the assay in cell lines, normal tissues, and lung cancer biopsies (N = 22) to identify and confirm a panel of highly specific methylation markers. The approach reliably profiles thousands of CpG sites in parallel and successfully identified and validated methylation signatures that distinguish lung adenocarcinomas from normal lung tissue, demonstrating its utility for marker discovery.

Abstract

We have developed a high-throughput method for analyzing the methylation status of hundreds of preselected genes simultaneously and have applied it to the discovery of methylation signatures that distinguish normal from cancer tissue samples. Through an adaptation of the GoldenGate genotyping assay implemented on a BeadArray platform, the methylation state of 1536 specific CpG sites in 371 genes (one to nine CpG sites per gene) was measured in a single reaction by multiplexed genotyping of 200 ng of bisulfite-treated genomic DNA. The assay was used to obtain a quantitative measure of the methylation level at each CpG site. After validating the assay in cell lines and normal tissues, we analyzed a panel of lung cancer biopsy samples ( N = 22) and identified a panel of methylation markers that distinguished lung adenocarcinomas from normal lung tissues with high specificity. These markers were validated in a second sample set ( N = 24). These results demonstrate the effectiveness of the method for reliably profiling many CpG sites in parallel for the discovery of informative methylation markers. The technology should prove useful for DNA methylation analyses in large populations, with potential application to the classification and diagnosis of a broad range of cancers and other diseases.