Sensitive digital quantification of DNA methylation in clinical samples.

Journal Article (Journal Article)

Analysis of abnormally methylated genes is increasingly important in basic research and in the development of cancer biomarkers. 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 cytometry or next-generation sequencing. We demonstrate enumeration of as few as one methylated molecule in approximately 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.

Full Text

Duke Authors

Cited Authors

  • Li, M; Chen, W-D; Papadopoulos, N; Goodman, SN; Bjerregaard, NC; Laurberg, S; Levin, B; Juhl, H; Arber, N; Moinova, H; Durkee, K; Schmidt, K; He, Y; Diehl, F; Velculescu, VE; Zhou, S; Diaz, LA; Kinzler, KW; Markowitz, SD; Vogelstein, B

Published Date

  • September 2009

Published In

Volume / Issue

  • 27 / 9

Start / End Page

  • 858 - 863

PubMed ID

  • 19684580

Pubmed Central ID

  • PMC2847606

Electronic International Standard Serial Number (EISSN)

  • 1546-1696

Digital Object Identifier (DOI)

  • 10.1038/nbt.1559


  • eng

Conference Location

  • United States