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PMID: 19776032 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't

Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns.

Human molecular genetics ·Vol. 18 ·No. 24 ·2009-12-15 ·Pages 4808-17

Byun HM, Siegmund KD, Pan F, Weisenberger DJ, Kanel G, Laird PW, Yang AS

Abstract

DNA methylation is known to be associated with cell differentiation, aging, disease and cancer. There exists an expanding base of knowledge regarding tissue-specific DNA methylation, but we have little information about person-specific DNA methylation. Here, we analyze the DNA methylation patterns of multiple tissues from multiple individuals using a high-throughput quantitative assay of genome-wide DNA methylation, namely the Illumina GoldenGate BeadArray. DNA methylation patterns were largely conserved across 11 different tissues (r = 0.852) and across six individuals (r = 0.829), and we found that DNA was highly methylated in non-CpG islands and/or CpG sites that are not occupied by either H3K4me3 or H3K27me3 (P < 0.05). Finally, we found that the Illumina GoldenGate assay features a large number of probes (265/1505 probes, 17.6%) that contain single-nucleotide polymorphisms, which may interfere with DNA methylation analyses in genome-wide studies.

MeSH Terms
Autopsy CpG Islands DNA Methylation Epigenesis, Genetic Genome-Wide Association Study/methods Humans Polymorphism, Single Nucleotide
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Byun Hyang-Min
Jane Anne Nohl Division of Hematology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
Siegmund Kimberly D
Pan Fei
Weisenberger Daniel J
Kanel Gary
Laird Peter W
Yang Allen S
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Article Info
Journal
Human molecular genetics
Abbr.
Hum Mol Genet
ISSN
1460-2083
DOI
10.1093/hmg/ddp445
Published
2009-12-15
Epub
2009-00-23
Pages
4808-17
Language
English
Region
England
NLM ID
9208958
PMCID
PMC4481584
Subset
IM
Grants
NCI NIH HHS · R01 CA118699 · United States
External Links
PubMed source DOI: 10.1093/hmg/ddp445 PMC Full Text View journal details
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