High-throughput DNA methylation profiling using universal bead arrays.

Marina Bibikova; Zhenwu Lin; Lixin Zhou; Eugene Chudin; Eliza Wickham Garcia; Bonnie Wu; Dennis Doucet; Neal J Thomas; Yunhua Wang; Ekkehard Vollmer; Torsten Goldmann; Carola Seifart; Wei Jiang; David L Barker; Mark S Chee; Joanna Floros; Jian-Bing Fan

doi:10.1101/gr.4410706

PubMed · 16449502

High-throughput DNA methylation profiling using universal bead arrays.

Marina Bibikova·Zhenwu Lin·Lixin Zhou·Eugene Chudin·Eliza Wickham Garcia·Bonnie Wu·Dennis Doucet·Neal J Thomas·Yunhua Wang·Ekkehard Vollmer·Torsten Goldmann·Carola Seifart·Wei Jiang·David L Barker·Mark S Chee·Joanna Floros·Jian-Bing Fan

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Abstract

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.

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Base Sequence Chromosomes, Human, X CpG Islands DNA Fingerprinting DNA Methylation Gene Expression Regulation, Neoplastic Humans Lung Neoplasms Molecular Sequence Data Oligonucleotide Array Sequence Analysis Polymorphism, Single Nucleotide Reproducibility of Results Sulfites Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

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Marina Bibikova, Zhenwu Lin, Lixin Zhou, Eugene Chudin, Eliza Wickham Garcia, Bonnie Wu, Dennis Doucet, Neal J Thomas, Yunhua Wang, Ekkehard Vollmer, Torsten Goldmann, Carola Seifart, Wei Jiang, David L Barker, Mark S Chee, Joanna Floros, Jian-Bing Fan. 2006-01-31. High-throughput DNA methylation profiling using universal bead arrays.. https://doi.org/10.1101/gr.4410706

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