TY - JOUR
T1 - Sensitive digital quantification of DNA methylation in clinical samples
AU - Li, Meng
AU - Chen, Wei Dong
AU - Papadopoulos, Nickolas
AU - Goodman, Steven N.
AU - Bjerregaard, Niels Christian
AU - Laurberg, Søren
AU - Levin, Bernard
AU - Juhl, Hartmut
AU - Arber, Nadir
AU - Moinova, Helen
AU - Durkee, Kris
AU - Schmidt, Kerstin
AU - He, Yiping
AU - Diehl, Frank
AU - Velculescu, Victor E.
AU - Zhou, Shibin
AU - Diaz, Luis A.
AU - Kinzler, Kenneth W.
AU - Markowitz, Sanford D.
AU - Vogelstein, Bert
N1 - Funding Information:
We thank B. Berger for helpful discussions; D. Edelstein for the help with plasma collection; and M. Whalen and L. Kasturi for expert technical assistance. This work was supported by the Virginia and D.K. Ludwig Fund for Cancer Research; the Miracle Foundation; the Edelstein Fund; the US National Colorectal Cancer Research Alliance; The US National Institutes of Health grants CA43460,CA62924 and CA120237; The Danish Cancer Society; The Danish Research Council; and The Institute of Experimental Clinical Research, Aarhus University.
PY - 2009/9
Y1 - 2009/9
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=70249147655&partnerID=8YFLogxK
U2 - 10.1038/nbt.1559
DO - 10.1038/nbt.1559
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C2 - 19684580
AN - SCOPUS:70249147655
SN - 1087-0156
VL - 27
SP - 858
EP - 863
JO - Nature Biotechnology
JF - Nature Biotechnology
IS - 9
ER -