Influence of genetic background and tissue types on global DNA methylation patterns.
Recent studies have shown a genetic influence on gene expression variation, chromatin, and DNA methylation. However, the effects of genetic background and tissue types on DNA methylation at the genome-wide level have not been characterized extensively. To study the effect of genetic background and tissue types on global DNA methylation, we performed DNA methylation analysis using the Affymetrix 500K SNP array on tumor, adjacent normal tissue, and blood DNA from 30 patients with esophageal squamous cell carcinoma (ESCC). The use of multiple tissues from 30 individuals allowed us to evaluate variation of DNA methylation states across tissues and individuals. Our results demonstrate that blood and esophageal tissues shared similar DNA methylation patterns within the same individual, suggesting an influence of genetic background on DNA methylation. Furthermore, we showed that tissue types are important contributors of DNA methylation states.
Yang
Howard H
HH
Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America.
Hu
Nan
N
Wang
Chaoyu
C
Ding
Ti
T
Dunn
Barbara K
BK
Goldstein
Alisa M
AM
Taylor
Philip R
PR
Lee
Maxwell P
MP
D002294:Carcinoma, Squamous Cell / Q000097:blood / Q000235:genetics*; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000097:blood / Q000235:genetics*; D004938:Esophageal Neoplasms / Q000097:blood / Q000235:genetics*; D004947:Esophagus / Q000378:metabolism; D020869:Gene Expression Profiling; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis
D004273:DNA, Neoplasm