Classification of DNA methylation patterns in tumor cell genomes using a CpG island microarray

被引:20
作者
Adrien, L. R.
Schlecht, N. F.
Kawachi, N.
Smith, R. V.
Brandwein-Gensler, M.
Massimi, A.
Chen, S.
Prystowsky, M. B.
Childs, G.
Belbin, T. J.
机构
[1] Albert Einstein Coll Med, Dept Pathol, Bronx, NY 10461 USA
[2] Albert Einstein Coll Med, Dept Epidemiol & Populat Hlth, Bronx, NY 10461 USA
[3] Albert Einstein Coll Med, Dept Mol Genet, Bronx, NY 10461 USA
[4] Montefiore Med Ctr, Dept Otolaryngol, Bronx, NY 10467 USA
关键词
D O I
10.1159/000091923
中图分类号
Q2 [细胞生物学];
学科分类号
071009 ; 090102 ;
摘要
Our group has initiated experiments to epigenetically profile CpG island hypermethylation in genomic DNA from tissue specimens of head and neck squamous cell carcinoma (HNSCC) using a microarray of 12,288 CpG island clones. Our technique, known as a methylation-specific restriction enzyme (MSRE) analysis, is a variation of the differential methylation hybridization (DMH) technique, in that it is not an array comparison of two DNA samples using methylation-specific restriction enzymes. Instead, it is a comparison of a single DNA sample's response to a methylation-sensitive restriction enzyme (HpaII) and its corresponding methylation-insensitive isoschizomer (MspI). Estimation of the reproducibility of this microarray assay by intraclass correlation (ICC) demonstrated that in four replicate experiments for three tumor specimens, the ICC observed for a given tumor specimen ranged from 0.68 to 0.85 without filtering of data. Repeated assays achieved 87% concordance or greater for all tumors after filtering of array data by fluorescence intensity. We utilized hierarchical clustering on a population of 37 HNSCC samples to cluster tumor samples with similar DNA methylation profiles. Supervised learning techniques are now being utilized to allow us to identify associations between specific epigenetic signatures and clinical parameters. Such techniques will allow us to identify select groups of CpG island loci that could be used as epigenetic markers for both diagnosis and prognosis in HNSCC. Copyright (c) 2006 S. Karger AG, Basel.
引用
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页码:16 / 23
页数:8
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