TitleHigh-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers.
Publication TypeJournal Article
Year of Publication2009
AuthorsOda, Mayumi, Glass Jacob L., Thompson Reid F., Mo Yongkai, Olivier Emmanuel N., Figueroa Maria E., Selzer Rebecca R., Richmond Todd A., Zhang Xinmin, Dannenberg Luke, Green Roland D., Melnick Ari, Hatchwell Eli, Bouhassira Eric E., Verma Amit, Suzuki Masako, and Greally John M.
JournalNucleic Acids Res
Date Published2009 Jul
KeywordsCells, Cultured, Cytosine, Deoxyribonuclease HpaII, DNA, DNA Methylation, Genome, Human, Humans, Polymerase Chain Reaction

<p>Many genome-wide assays involve the generation of a subset (or representation) of the genome following restriction enzyme digestion. The use of enzymes sensitive to cytosine methylation allows high-throughput analysis of this epigenetic regulatory process. We show that the use of a dual-adapter approach allows us to generate genomic representations that includes fragments of <200 bp in size, previously not possible when using the standard approach of using a single adapter. By expanding the representation to smaller fragments using HpaII or MspI, we increase the representation by these isoschizomers to more than 1.32 million loci in the human genome, representing 98.5% of CpG islands and 91.1% of refSeq promoters. This advance allows the development of a new, high-resolution version of our HpaII-tiny fragment Enrichment by Ligation-mediated PCR (HELP) assay to study cytosine methylation. We also show that the MspI representation generates information about copy-number variation, that the assay can be used on as little as 10 ng of DNA and that massively parallel sequencing can be used as an alternative to microarrays to read the output of the assay, making this a powerful discovery platform for studies of genomic and epigenomic abnormalities.</p>

Alternate JournalNucleic Acids Res
PubMed ID19386619
PubMed Central IDPMC2709560
Grant ListR01 HG004401 / HG / NHGRI NIH HHS / United States
R01 AG18728 / AG / NIA NIH HHS / United States
R01 HL082946 / HL / NHLBI NIH HHS / United States
P01 AG027734 / AG / NIA NIH HHS / United States
T32 GM007288 / GM / NIGMS NIH HHS / United States