Sensitive digital quantification of DNA methylation in clinical samples

被引：257

作者：

Li, Meng ^{[5
,6
]}

Chen, Wei-dong ^{[1
,2
,3
,4
]}

Papadopoulos, Nickolas ^{[5
,6
]}

Goodman, Steven N. ^{[7
]}

Bjerregaard, Niels Christian ^{[8
]}

Laurberg, Soren ^{[8
]}

Levin, Bernard ^{[9
]}

Juhl, Hartmut ^{[10
]}

Arber, Nadir ^{[11
,12
,13
]}

Moinova, Helen ^{[1
,2
,3
,4
]}

Durkee, Kris ^{[14
]}

Schmidt, Kerstin ^{[5
,6
]}

He, Yiping ^{[5
,6
]}

Diehl, Frank ^{[5
,6
]}

Velculescu, Victor E. ^{[5
,6
]}

Zhou, Shibin ^{[5
,6
]}

Diaz, Luis A., Jr. ^{[5
,6
]}

Kinzler, Kenneth W. ^{[5
,6
]}

Markowitz, Sanford D. ^{[1
,2
,3
,4
]}

Vogelstein, Bert ^{[5
,6
]}

机构：

[1] Case Western Reserve Univ, Dept Med, Cleveland, OH 44106 USA

[2] Case Western Reserve Univ, Ireland Canc Ctr, Cleveland, OH 44106 USA

[3] Univ Hosp Cleveland, Case Med Ctr, Cleveland, OH 44106 USA

[4] Howard Hughes Med Inst, Cleveland, OH USA

[5] Johns Hopkins Med Inst, Howard Hughes Med Inst, Ludwig Ctr Canc Genet & Therapeut, Baltimore, MD 21205 USA

[6] Johns Hopkins Med Inst, Sidney Kimmel Canc Ctr, Baltimore, MD 21205 USA

[7] Johns Hopkins Med Inst, Dept Biostat, Baltimore, MD 21205 USA

[8] Aarhus Univ Hosp, Dept Surg P, DK-8000 Aarhus, Denmark

[9] UTMD Anderson Canc Ctr, Houston, TX USA

[10] Israelit Hosp, Ctr Canc Res, Hamburg, Germany

[11] Tel Aviv Univ, Tel Aviv Med Ctr, IL-69978 Tel Aviv, Israel

[12] Tel Aviv Univ, Sackler Sch Med, IL-69978 Tel Aviv, Israel

[13] Tel Aviv Univ, Integrated Canc Prevent Ctr, IL-69978 Tel Aviv, Israel

[14] Exact Sci Corp, Marlborough, MA USA

来源：

NATURE BIOTECHNOLOGY | 2009年 / 27卷 / 09期

基金：

美国国家卫生研究院;

关键词：

COLORECTAL-CANCER; PCR; PLASMA; MUTATIONS; MARKERS; ASSAY;

D O I：

10.1038/nbt.1559

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Analysis of abnormally methylated genes is increasingly important in basic research and in the development of cancer biomarkers(1,2). 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 cytometry(3) or next-generation sequencing. We demonstrate enumeration of as few as one methylated molecule in similar to 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.

引用

页码：858 / U118

页数：8

共 30 条

[1] MS-qFRET: A quantum dot-based method for analysis of DNA methylation [J].

Bailey, Vasudev J. ;

Easwaran, Hariharan ;

Zhang, Yi ;

Griffiths, Elizabeth ;

Belinsky, Steven A. ;

Herman, James G. ;

Baylin, Stephen B. ;

Carraway, Hetty E. ;

Wang, Tza-Huei .

GENOME RESEARCH, 2009, 19 (08) :1455-1461

[2] Detection in fecal DNA of colon cancer-specific methylation of the nonexpressed vimentin gene [J].

Chen, WD ;

Han, ZJ ;

Skoletsky, J ;

Olson, J ;

Sah, J ;

Myeroff, L ;

Platzer, P ;

Lu, SL ;

Dawson, D ;

Willis, J ;

Pretlow, TR ;

Lutterbaugh, J ;

Kasturi, L ;

Willson, JKV ;

Rao, JS ;

Shuber, A ;

Markowitz, SD .

JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE, 2005, 97 (15) :1124-1132

[3] Detection and quantification of mutations in the plasma of patients with colorectal tumors [J].

Diehl, F ;

Li, M ;

Dressman, D ;

He, YP ;

Shen, D ;

Szabo, S ;

Diaz, LA ;

Goodman, SN ;

David, KA ;

Juhl, H ;

Kinzler, KW ;

Vogelstein, B .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (45) :16368-16373

[4] Circulating mutant DNA to assess tumor dynamics [J].

Diehl, Frank ;

Schmidt, Kerstin ;

Choti, Michael A. ;

Romans, Katharine ;

Goodman, Steven ;

Li, Meng ;

Thornton, Katherine ;

Agrawal, Nishant ;

Sokoll, Lori ;

Szabo, Steve A. ;

Kinzler, Kenneth W. ;

Vogelstein, Bert ;

Diaz, Luis A., Jr. .

NATURE MEDICINE, 2008, 14 (09) :985-990

[5] Analysis of mutations in DNA isolated from plasma and stool of colorectal cancer patients [J].

Diehl, Frank ;

Schmidt, Kerstin ;

Durkee, Kristine H. ;

Moore, Kent J. ;

Goodman, Steve N. ;

Shuber, Anthony P. ;

Kinzler, Kenneth W. ;

Vogelstein, Bert .

GASTROENTEROLOGY, 2008, 135 (02) :489-498

[6] BEAMing: single-molecule PCR on microparticles in water-in-oil emulsions [J].

Diehl, Frank ;

Li, Meng ;

He, Yiping ;

Kinzler, Kenneth W. ;

Vogelstein, Bert ;

Dressman, Devin .

NATURE METHODS, 2006, 3 (07) :551-559

[7] Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations [J].

Dressman, D ;

Yan, H ;

Traverso, G ;

Kinzler, KW ;

Vogelstein, B .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (15) :8817-8822

[8] MethyLight: a high-throughput assay to measure DNA methylation [J].

Eads, Cindy A. ;

Danenberg, Kathleen D. ;

Kawakami, Kazuyuki ;

Saltz, Leonard B. ;

Blake, Corey ;

Shibata, Darryl ;

Danenberg, Peter V. ;

Laird, Peter W. .

NUCLEIC ACIDS RESEARCH, 2000, 28 (08) :32

[9] Timeline - The history of cancer epigenetics [J].

Feinberg, AP ;

Tycko, B .

NATURE REVIEWS CANCER, 2004, 4 (02) :143-153

[10] Circulating nucleic acids (CNAs) and cancer - A survey [J].

Fleischhacker, M. ;

Schmidt, B. .

BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER, 2007, 1775 (01) :181-232

← 1 2 3 →