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Epigenetic modification such as DNA methylation plays a key role in disease susceptibility and gene regulation. However, the genetic regulation of DNA methylation in human is not fully appreciated. We describe the effects of genetic variants on the DNA methylome in human lung based on Based on the Environment And Genetics of Lung Etiology (EAGLE) study in the NCI’s Division of Cancer Epidemiology and Genetics (DCEG), we performed a methylation-quantitative trait loci (meQTL) analysesanalysis in 210 histologically normal human lung tissues. We identified 34,304 cis304 cis- and 585 trans-meQTLs, a genetic-epigenetic interaction of surprising magnitude. These findings are replicated in both breast and kidney tissues and show distinct patterns: cis-meQTLs mostly localize to CpG sites outside of genes, promoters and CpG islands (CGIs), while trans-meQTLs are over-represented in promoter CGIs. meQTL SNPs are enriched in CTCF-binding sites, DNaseI hypersensitivity regions and histone marks. Importantly, four of the five established lung cancer risk loci in European ancestry are cis-meQTLs and, in aggregate, cis-meQTLs are enriched for lung cancer risk in a genome-wide analysis of 11,587 subjects. Thus, inherited genetic variation may affect lung carcinogenesis by regulating the human methylome. We also develop developed a novel statistical algorithm and identified an association hotspot with replication in The Cancer Genome Atlas (TCGA) samples. |
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Jianxin Shi received a Ph.D. in Statistics from Stanford University in 2006. He was then pursued a postdoctoral research fellow fellowship at the Stanford University School of Medicine from 2006 to 2009, working on focusing his studies on the genetic mapping of psychiatric disorders from 2006 to 2009. Dr. Shi is currently a tenure track investigator in the Biostatistics Branch , of the Division of Cancer Epidemiology and Genetics at the National Cancer InstituteNCI. His research focuses on cancer genetics and genomics.
SUMMARY:
Topic: Characterizing the Genetic Basis of Methylome Diversity in Histologically Normal Human Lung Tissue
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Date: Wednesday, September 17, 2014
Time: 11 AM – 12 PM EDT
WebEx Meeting Link: https://cbiit.webex.com/cbiit/onstage/g.php?t=a&d=734325295
Password: speakerseries
Meeting ID: 734 325 295
Dial-In for Audio Only: 1-855-244-8681
You are invited to listen to Dr. Shi's presentation in Room 2W908 in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
Presentation: A screen cast of the presentation will be available for viewing after the event on our Speaker Series Videos page and on the NCI CBIIT Speaker Series YouTube Playlist
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The National Cancer Institute (NCI) Cente Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
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