Sensitive digital quantification of DNA methylation in clinical samples

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Abstract
Gene-specific changes in DNA methylation are promising biomarkers, but sensitive quantitative detection of these epigenetic marks remains challenging. Li et al. adapt the so-called BEAMing technology to enable high-throughput digital quantification of gene methylation in clinical samples. Analysis of abnormally methylated genes is increasingly important in basic research and in the development of cancer biomarkers1,2. We have developed methyl-BEAMing technology to enable absolute quantification of the number of methylated molecules in a sample. Individual DNA fragments are amplified and analyzed either by flow cytometry3 or next-generation sequencing. We demonstrate enumeration of as few as one methylated molecule in ∼5,000 unmethylated molecules in DNA from plasma or fecal samples. Using methylated vimentin as a biomarker in plasma samples, methyl-BEAMing detected 59% of cancer cases. In early-stage colorectal cancers, this sensitivity was four times more than that obtained by assaying serum-carcinoembryonic antigen (CEA). With stool samples, methyl-BEAMing detected 41% of cancers and 45% of advanced adenomas. In addition to diagnostic and prognostic applications, this digital quantification of rare methylation events should be applicable to preclinical assessment of new epigenetic biomarkers and quantitative analyses in epigenetic research.