Sensitive digital quantification of DNA methylation in clinical samples.
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.
Li
Meng
M
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.
Chen
Wei-Dong
WD
Papadopoulos
Nickolas
N
Goodman
Steven N
SN
Bjerregaard
Niels Christian
NC
Laurberg
Søren
S
Levin
Bernard
B
Juhl
Hartmut
H
Arber
Nadir
N
Moinova
Helen
H
Durkee
Kris
K
Schmidt
Kerstin
K
He
Yiping
Y
Diehl
Frank
F
Velculescu
Victor E
VE
Zhou
Shibin
S
Diaz
Luis A
LA
Kinzler
Kenneth W
KW
Markowitz
Sanford D
SD
Vogelstein
Bert
B
D014408:Biomarkers, Tumor / Q000097:blood / Q000235:genetics*; D015179:Colorectal Neoplasms / Q000235:genetics; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000097:blood / Q000737:chemistry / Q000235:genetics*; D005243:Feces / Q000737:chemistry; D005821:Genetic Techniques; D006801:Humans; D012680:Sensitivity and Specificity; D014746:Vimentin / Q000737:chemistry
D014408:Biomarkers, Tumor; D004273:DNA, Neoplasm; D014746:Vimentin
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