High-throughput method for analyzing methylation of CpGs in targeted genomic regions

Shivani Nautiyal, Victoria E.H. Carlton, Yontao Lu, James S. Ireland, Diane Flaucher, Martin Moorhead, Joe W. Gray, Paul Spellman, Michael Mindrinos, Paul Berg, Malek Faham

Research output: Contribution to journalArticle

28 Scopus citations

Abstract

A unique microarray-based method for determining the extent of DNA methylation has been developed. It relies on a selective enrichment of the regions to be assayed by target amplification by capture and ligation (mTACL). The assay is quantitatively accurate, relatively precise, and lends itself to high-throughput determination using nanogram amounts of DNA. The measurements using mTACLs are highly reproducible and in excellent agreement with those obtained by sequencing (r = 0.94). In the present work, the methylation status of >145,000 CpGs from 5,472 promoters in 221 samples was measured. The methylation levels of nearby CpGs are correlated, but the correlation falls off dramatically over several hundred base pairs. In some instances, nearby CpGs have very different levels of methylation. Comparison of normal and tumor samples indicates that in tumors, the promoter regions of genes involved in differentiation and signaling are preferentially hypermethylated, whereas those of housekeeping genes remain hypomethylated. mTACL is a platform for profiling the state of methylation of a large number of CpG in many samples in a cost-effective fashion, and is capable of scaling to much larger numbers of CpGs than those collected here.

Original languageEnglish (US)
Pages (from-to)12587-12592
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume107
Issue number28
DOIs
StatePublished - Jul 13 2010

Keywords

  • Array
  • Technology
  • Tumor

ASJC Scopus subject areas

  • General

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    Nautiyal, S., Carlton, V. E. H., Lu, Y., Ireland, J. S., Flaucher, D., Moorhead, M., Gray, J. W., Spellman, P., Mindrinos, M., Berg, P., & Faham, M. (2010). High-throughput method for analyzing methylation of CpGs in targeted genomic regions. Proceedings of the National Academy of Sciences of the United States of America, 107(28), 12587-12592. https://doi.org/10.1073/pnas.1005173107