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Influence of Genetic Background and Tissue Types on Global DNA Methylation Patterns

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  • Howard H Yang
  • Nan Hu
  • Chaoyu Wang
  • Ti Ding
  • Barbara K Dunn
  • Alisa M Goldstein
  • Philip R Taylor
  • Maxwell P Lee

Abstract

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.

Suggested Citation

  • Howard H Yang & Nan Hu & Chaoyu Wang & Ti Ding & Barbara K Dunn & Alisa M Goldstein & Philip R Taylor & Maxwell P Lee, 2010. "Influence of Genetic Background and Tissue Types on Global DNA Methylation Patterns," PLOS ONE, Public Library of Science, vol. 5(2), pages 1-8, February.
    • Handle: RePEc:plo:pone00:0009355
    DOI: 10.1371/journal.pone.0009355
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    References listed on IDEAS

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    1. Mitsutaka Kadota & Howard H Yang & Nan Hu & Chaoyu Wang & Ying Hu & Philip R Taylor & Kenneth H Buetow & Maxwell P Lee, 2007. "Allele-Specific Chromatin Immunoprecipitation Studies Show Genetic Influence on Chromatin State in Human Genome," PLOS Genetics, Public Library of Science, vol. 3(5), pages 1-11, May.
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    Cited by:

    1. Sarah M. Orton & Kimberly Millis & Peter Choate, 2023. "Epigenetics of Trauma Transmission and Fetal Alcohol Spectrum Disorder: What Does the Evidence Support?," IJERPH, MDPI, vol. 20(17), pages 1-25, September.
    2. Wen Yalu & Li Ming & Fu Wenjiang J, 2011. "MA-SNP -- A New Genotype Calling Method for Oligonucleotide SNP Arrays Modeling the Batch Effect with a Normal Mixture Model," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-23, August.
    3. Wei Perng & Mercedes Mora-Plazas & Constanza Marín & Laura S Rozek & Ana Baylin & Eduardo Villamor, 2013. "A Prospective Study of LINE-1DNA Methylation and Development of Adiposity in School-Age Children," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-7, April.

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