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

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.

SUBMITTER: Suzuki M 

PROVIDER: S-EPMC2884539 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature