Sensitive digital quantification of DNA methylation in clinical samples

Meng Li, Wei Dong Chen, Nickolas Papadopoulos, Steven N. Goodman, Niels Christian Bjerregaard, Søren Laurberg, Bernard Levin, Hartmut Juhl, Nadir Arber, Helen Moinova, Kris Durkee, Kerstin Schmidt, Yiping He, Frank Diehl, Victor E. Velculescu, Shibin Zhou, Luis A. Diaz, Kenneth W. Kinzler, Sanford D. Markowitz, Bert Vogelstein

Research output: Contribution to journalArticle

Abstract

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 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.

Original languageEnglish (US)
Pages (from-to)858-863
Number of pages6
JournalNature biotechnology
Volume27
Issue number9
DOIs
StatePublished - Sep 1 2009

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ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering

Cite this

Li, M., Chen, W. D., Papadopoulos, N., Goodman, S. N., Bjerregaard, N. C., Laurberg, S., Levin, B., Juhl, H., Arber, N., Moinova, H., Durkee, K., Schmidt, K., He, Y., Diehl, F., Velculescu, V. E., Zhou, S., Diaz, L. A., Kinzler, K. W., Markowitz, S. D., & Vogelstein, B. (2009). Sensitive digital quantification of DNA methylation in clinical samples. Nature biotechnology, 27(9), 858-863. https://doi.org/10.1038/nbt.1559