High-throughput methylation profiling by MCA coupled to CpG island microarray

被引:102
作者
Estecio, Marcos R. H. [1 ]
Yan, Pearlly S.
Ibrahim, Ashraf E. K.
Tellez, Carmen S.
Shen, Lanlan
Huang, Tim H-M
Issa, Jean-Pierre J.
机构
[1] Univ Texas, MD Anderson Canc Ctr, Dept Leukemia, Houston, TX 77030 USA
[2] Ohio State Univ, Ctr Comprehens Canc, Human Canc Genet Program, Columbus, OH 43210 USA
[3] Univ Cambridge, Dept Pathol, Cambridge CB2 1TN, England
关键词
D O I
10.1101/gr.6417007
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
An abnormal pattern of DNA methylation occurs at specific genes in almost all neoplasms. The lack of high- throughput methods with high specificity and sensitivity to detect changes in DNA methylation has limited its application for clinical profiling. Here we overcome this limitation and present an improved method to identify methylated genes genome- wide by hybridizing a CpG island microarray with amplicons obtained by the methylated CpG island amplification technique ( MCAM). We validated this method in three cancer cell lines and 15 primary colorectal tumors, resulting in the discovery of hundreds of new methylated genes in cancer. The sensitivity and specificity of the method to detect hypermethylated loci were 88% and 96%, respectively, according to validation by bisulfite- PCR. Unsupervised hierarchical clustering segregated the tumors into the expected subgroups based on CpG island methylator phenotype classification. In summary, MCAM is a suitable technique to discover methylated genes and to profile methylation changes in clinical samples in a high- throughput fashion.
引用
收藏
页码:1529 / 1536
页数:8
相关论文
共 31 条
[1]   Aberrant CpG-island methylation has non-random and tumour-type-specific patterns [J].
Costello, JF ;
Frühwald, MC ;
Smiraglia, DJ ;
Rush, LJ ;
Robertson, GP ;
Gao, X ;
Wright, FA ;
Feramisco, JD ;
Peltomäki, P ;
Lang, JC ;
Schuller, DE ;
Yu, L ;
Bloomfield, CD ;
Caligiuri, MA ;
Yates, A ;
Nishikawa, R ;
Huang, HJS ;
Petrelli, NJ ;
Zhang, XL ;
O'Dorisio, MS ;
Held, WA ;
Cavenee, WK ;
Plass, C .
NATURE GENETICS, 2000, 24 (02) :132-138
[2]   PURIFICATION OF CPG ISLANDS USING A METHYLATED DNA-BINDING COLUMN [J].
CROSS, SH ;
CHARLTON, JA ;
NAN, XS ;
BIRD, AP .
NATURE GENETICS, 1994, 6 (03) :236-244
[3]  
DeRisi J, 1996, NAT GENET, V14, P457
[4]   LHX6 is a sensitive methylation marker in head and neck carcinomas [J].
Estecio, M. R. H. ;
Youssef, E. M. ;
Rahal, P. ;
Fukuyama, E. E. ;
Gois-Filho, J. F. ;
Maniglia, J. V. ;
Goloni-Bertollo, E. M. ;
Issa, J-P J. ;
Tajara, E. H. .
ONCOGENE, 2006, 25 (36) :5018-5026
[5]   Optimal bridge maintenance planning using improved multi-objective genetic algorithm [J].
Furuta, Hitoshi ;
Kameda, Takahiro ;
Nakahara, Koichiro ;
Takahashi, Yuji ;
Frangopol, Dan M. .
STRUCTURE AND INFRASTRUCTURE ENGINEERING, 2006, 2 (01) :33-41
[6]  
Gonzalgo ML, 1997, CANCER RES, V57, P594
[7]   Genome-wide profiling of promoter methylation in human [J].
Hatada, I. ;
Fukasawa, M. ;
Kimura, M. ;
Morita, S. ;
Yamada, K. ;
Yoshikawa, T. ;
Yamanaka, S. ;
Endo, C. ;
Sakurada, A. ;
Sato, M. ;
Kondo, T. ;
Horii, A. ;
Ushijima, T. ;
Sasaki, H. .
ONCOGENE, 2006, 25 (21) :3059-3064
[8]   CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome [J].
Heisler, LE ;
Torti, D ;
Boutros, PC ;
Watson, J ;
Chan, C ;
Winegarden, N ;
Takahashi, M ;
Yau, P ;
Huang, THM ;
Farnham, PJ ;
Jurisica, I ;
Woodgett, JR ;
Bremner, R ;
Penn, LZ ;
Der, SD .
NUCLEIC ACIDS RESEARCH, 2005, 33 (09) :2952-2961
[9]   Mechanisms of disease: Gene silencing in cancer in association with promoter hypermethylation [J].
Herman, JG ;
Baylin, SB .
NEW ENGLAND JOURNAL OF MEDICINE, 2003, 349 (21) :2042-2054
[10]  
Kaneda A, 2002, CANCER RES, V62, P6645