Letter abstract
Nature Biotechnology 27, 858 - 863 (2009)
Published online: 16 August 2009 | doi:10.1038/nbt.1559
Sensitive digital quantification of DNA methylation in clinical samples
Meng Li1, Wei-dong Chen2, Nickolas Papadopoulos1, Steven N Goodman3, Niels Christian Bjerregaard4, Søren Laurberg4, Bernard Levin5, Hartmut Juhl6, Nadir Arber7, Helen Moinova2, Kris Durkee8, Kerstin Schmidt1, Yiping He1, Frank Diehl1, Victor E Velculescu1, Shibin Zhou1, Luis A Diaz Jr1, Kenneth W Kinzler1, Sanford D Markowitz2 & Bert Vogelstein1
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.
- The Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute and Sidney Kimmel Cancer Center at the Johns Hopkins Medical Institutions, Baltimore, Maryland, USA.
- Department of Medicine and Ireland Cancer Center, Case Western Reserve University and Case Medical Center of University Hospitals of Cleveland and Howard Hughes Medical Institute, Cleveland, Ohio, USA.
- Department of Biostatistics, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA.
- Department of Surgery P, Aarhus University Hospital, Aarhus, Denmark.
- U.T.M.D. Anderson Cancer Center, Houston, Texas, USA.
- Indivumed, Center for Cancer Research at Israelitic Hospital, Hamburg, Germany.
- Tel Aviv University, Tel Aviv Medical Center and Sackler School of Medicine and Integrated Cancer Prevention Center, Tel Aviv, Israel.
- Exact Sciences Corp., Marlborough, Massachusetts, USA.
Correspondence to: Sanford D Markowitz2 e-mail: sxm10@cwru.edu
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