Optimized design and data analysis of tag-based cytosine methylation assays

Masako Suzuki, Qiang Jing, Daniel Lia, Marién Pascual, Andrew McLellan, John M. Greally

Research output: Contribution to journalArticle

62 Citations (Scopus)

Abstract

Using the type III restriction-modification enzyme EcoP15I, we isolated sequences flanking sites digested by the methylation-sensitive HpaII enzyme or its methylation-insensitive MspI isoschizomer for massively parallel sequencing. A novel data transformation allows us to normalise HpaII by MspI counts, resulting in more accurate quantification of methylation at >1.8 million loci in the human genome. This HELP-tagging assay is not sensitive to sequence polymorphism or base composition and allows exploration of both CG-rich and depleted genomic contexts.

Original languageEnglish (US)
Article numberr36
JournalGenome Biology
Volume11
Issue number4
DOIs
StatePublished - Apr 1 2010

Fingerprint

cytosine
Cytosine
methylation
Methylation
data analysis
assay
Type III Site Specific Deoxyribonucleases
assays
enzyme
High-Throughput Nucleotide Sequencing
tagging
Base Composition
Human Genome
enzymes
genomics
polymorphism
genome
genetic polymorphism
loci
Enzymes

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Optimized design and data analysis of tag-based cytosine methylation assays. / Suzuki, Masako; Jing, Qiang; Lia, Daniel; Pascual, Marién; McLellan, Andrew; Greally, John M.

In: Genome Biology, Vol. 11, No. 4, r36, 01.04.2010.

Research output: Contribution to journalArticle

Suzuki, Masako ; Jing, Qiang ; Lia, Daniel ; Pascual, Marién ; McLellan, Andrew ; Greally, John M. / Optimized design and data analysis of tag-based cytosine methylation assays. In: Genome Biology. 2010 ; Vol. 11, No. 4.
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