RT Journal
A1 Cheng, Yu-Wei
A1 Shawber, Carrie
A1 Notterman, Dan
A1 Paty, Philip
A1 Barany, Francis
T1 Multiplexed profiling of candidate genes for CpG island methylation status using a flexible PCR/LDR/Universal Array assay
JF Genome Research 
JO Genome Research 
YR 2006 
FD February 01 
VO 16 
IS 2 
SP 282 
OP 289 
DO 10.1101/gr.4181406 
UL http://genome.cshlp.org/content/16/2/282.abstract 
AB DNA methylation in CpG islands is associated with transcriptional silencing. Accurate determination of cytosine methylation status in promoter CpG dinucleotides may provide diagnostic and prognostic value for human cancers. We have developed a quantitative PCR/LDR/Universal Array assay that allows parallel evaluation of methylation status of 75 CpG dinucleotides in the promoter regions of 15 tumor suppressor genes (CDKN2B, CDKN2A, CDKN2D, CDKN1A, CDKN1B, TP53, BRCA1, TIMP3, APC, RASSF1, CDH1, MGMT, DAPK1, GSTP1, and RARB). When compared with an independent pyrosequencing method at a single promoter, the two approaches gave good correlation. In a study using 15 promoter regions and seven blinded tumor cell lines, our technology was capable of distinguishing methylation profiles that identified cancer cell lines derived from the same origins. Preliminary studies using 96 colorectal tumor samples and 73 matched normal tissues indicated CpG methylation is a gene-specific and nonrandom event in colon cancer. This new approach is suitable for clinical applications where sample quantity and purity can be limiting factors.