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Carcinogenesis Advance Access originally published online on October 14, 2004
Carcinogenesis 2005 26(2):471-479; doi:10.1093/carcin/bgh310
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Carcinogenesis vol.26 no.2 © Oxford University Press 2005; all rights reserved.

ARTICLE

High throughput screening of methylation status of genes in prostate cancer using an oligonucleotide methylation array

Yan Ping Yu, Shirish Paranjpe, Joel Nelson1, Sydney Finkelstein, Baoguo Ren, Demetrius Kokkinakis, George Michalopoulos and Jian-Hua Luo2

Department of Pathology and 1 Department of Urology, University of Pittsburgh School of Medicine, 3550 Terrace Street, Pittsburgh, PA 15261, USA

2 To whom correspondence should be addressed. Tel: +1 412 648 8791; Fax: +1 412 648 5997; Email: luoj{at}msx.upmc.edu

Recent work using high-throughput microarray technology has discovered altered expression of a large number of genes in prostate cancer. Many of these alterations may be the consequence of changes in methylation status in the CpG islands of promoter or exon 1 regions of these genes. In order to determine the methylation status of a large number of genes and ESTs we combined the principle of match/mismatch hybridization with the technique of whole genome labeling to develop a highly specific oligonucleotide-based methylation microarray. Using this array, we analyzed the methylation status of 105 genes and ESTs in three prostate cancer cell lines. Between 32 and 47% of these genes and ESTs were methylated in these cell lines. By correlating the methylation status of this array with the results of Affymetrix expression arrays of three prostate cancer cell lines, we determined that methylation of genes played a significant role (37%) in down-regulating the expression of certain genes in prostate cancer. We also tested this array on a number of primary prostate tissue samples. Our results indicated that a subset of genes in this microarray (25/105) were methylated in all prostate cancer samples but not in normal prostate, suggesting the potential significance of alterations in the methylation status of certain genes in the development of prostate cancer.


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