Multiplexed profiling of candidate genes for CpG island methylation status using a flexible PCR/LDR/Universal Array assay Journal Article
| Authors: | Cheng, Y. W.; Shawber, C.; Notterman, D.; Paty, P.; Barany, F. |
| Article Title: | Multiplexed profiling of candidate genes for CpG island methylation status using a flexible PCR/LDR/Universal Array assay |
| Abstract: | 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. ©2006 by Cold Spring Harbor Laboratory Press. |
| Keywords: | controlled study; human tissue; unclassified drug; gene sequence; human cell; promoter region; polymerase chain reaction; reproducibility of results; gene expression profiling; protein; colonic neoplasms; cancer cell culture; cell line, tumor; brca1 protein; protein p53; uvomorulin; dna methylation; tumor suppressor gene; gene expression regulation, neoplastic; correlation analysis; cpg island; cpg islands; colorectal tumor; cyclin dependent kinase inhibitor 1b; colon cancer; tumor suppressor proteins; tumor cell line; intermethod comparison; gene silencing; methylated dna protein cysteine methyltransferase; genetic procedures; dinucleotide; apc protein; tissue inhibitor of metalloproteinase 3; glutathione transferase p1; ras association domain family protein 1a; gene technology; cyclin dependent kinase inhibitor 1; promoter regions (genetics); protein p14arf; death associated protein kinase; protein p16ink4a; ligase detection reaction; protein p16ink4b; quantitative genetics; universal array assay |
| Journal Title: | Genome Research |
| Volume: | 16 |
| Issue: | 2 |
| ISSN: | 1088-9051 |
| Publisher: | Cold Spring Harbor Laboratory Press |
| Date Published: | 2006-02-01 |
| Start Page: | 282 |
| End Page: | 289 |
| Language: | English |
| DOI: | 10.1101/gr.4181406 |
| PUBMED: | 16369045 |
| PROVIDER: | scopus |
| PMCID: | PMC1361724 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 24" - "Export Date: 4 June 2012" - "CODEN: GEREF" - "Source: Scopus" |
