High-throughput DNA methylation profiling using universal bead arrays.
We have developed a high-throughput method for analyzing the methylation status of hundreds of preselected genes simultaneously and have applied it to the discovery of methylation signatures that distinguish normal from cancer tissue samples. Through an adaptation of the GoldenGate genotyping assay implemented on a BeadArray platform, the methylation state of 1536 specific CpG sites in 371 genes (one to nine CpG sites per gene) was measured in a single reaction by multiplexed genotyping of 200 ng of bisulfite-treated genomic DNA. The assay was used to obtain a quantitative measure of the methylation level at each CpG site. After validating the assay in cell lines and normal tissues, we analyzed a panel of lung cancer biopsy samples (N = 22) and identified a panel of methylation markers that distinguished lung adenocarcinomas from normal lung tissues with high specificity. These markers were validated in a second sample set (N = 24). These results demonstrate the effectiveness of the method for reliably profiling many CpG sites in parallel for the discovery of informative methylation markers. The technology should prove useful for DNA methylation analyses in large populations, with potential application to the classification and diagnosis of a broad range of cancers and other diseases.
Bibikova
Marina
M
Illumina, Inc., San Diego, California 92121, USA.
Lin
Zhenwu
Z
Zhou
Lixin
L
Chudin
Eugene
E
Garcia
Eliza Wickham
EW
Wu
Bonnie
B
Doucet
Dennis
D
Thomas
Neal J
NJ
Wang
Yunhua
Y
Vollmer
Ekkehard
E
Goldmann
Torsten
T
Seifart
Carola
C
Jiang
Wei
W
Barker
David L
DL
Chee
Mark S
MS
Floros
Joanna
J
Fan
Jian-Bing
JB
D001483:Base Sequence; D041321:Chromosomes, Human, X / Q000378:metabolism; D018899:CpG Islands / Q000235:genetics; D016172:DNA Fingerprinting; D019175:DNA Methylation; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D013447:Sulfites / Q000378:metabolism
D013447:Sulfites; C042345:hydrogen sulfite