Identification of differentially methylated cell types in epigenome-wide association studies
文献类型：期刊论文
| 作者 | Zheng, Shijie C.3; Teschendorff, Andrew E.3,4; Breeze, Charles E.1; Beck, Stephan4; Teschendorff, Andrew E.2; , |
| 刊名 | NATURE METHODS
 |
| 出版日期 | 2018 |
| 卷号 | 15期号:12页码:1059-+ |
| 关键词 | FX-5000T tension system endplate chondrocytes intermittent cyclic mechanical tension chondrocyte degeneration cell morphology |
| ISSN号 | 1548-7091 |
| DOI | 10.1038/s41592-018-0213-x |
| 文献子类 | Article |
| 英文摘要 | An outstanding challenge of epigenome-wide association studies (EWASs) performed in complex tissues is the identification of the specific cell type(s) responsible for the observed differential DNA methylation. Here we present a statistical algorithm called CeIIDMC (https://github.com/sjczheng/EpiDISH), which can identify differentially methylated positions and the specific cell type(s) driving the differential methylation. We validated CeIIDMC on in silico mixtures of DNA methylation data generated with different technologies, as well as on real mixtures from epigenome-wide association and cancer epigenome studies. CeIIDMC achieved over 90% sensitivity and specificity in scenarios where current state-of-the-art methods did not identify differential methylation. By applying CeIIDMC to an EWAS performed in buccal swabs, we identified smoking-associated differentially methylated positions occurring in the epithelial compartment, which we validated in smoking-related lung cancer. CeIIDMC may be useful in the identification of causal DNA-methylation alterations in disease. |
| 学科主题 | Biochemistry & Molecular Biology |
| WOS关键词 | DNA METHYLATION ; GENE-EXPRESSION ; GENOMIC CHARACTERIZATION ; CPG SITES ; HETEROGENEITY ; VALIDATION ; MICROARRAY ; SUBSETS |
| 语种 | 英语 |
| WOS记录号 | WOS:000451826200032 |
| 出版者 | NATURE PUBLISHING GROUP |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.144/handle/331004/805]  |
| 专题 | 中国科学院上海生命科学研究院营养科学研究所 |
| 作者单位 | 1.Altius Inst Biomed Sci, Seattle, WA USA; 2.UCL, Dept Womens Canc, London, England, 3.Chinese Acad Sci, CAS Key Lab Computat Biol, CAS MPG Partner Inst Computat Biol,Univ Chinese A, Shanghai Inst Nutr & Hlth,Shanghai Inst Biol Sci, Shanghai, Peoples R China; 4.UCL, UCL Canc Inst, Paul OGorman Bldg, London, England; |
| 推荐引用方式 GB/T 7714 | Zheng, Shijie C.,Teschendorff, Andrew E.,Breeze, Charles E.,et al. Identification of differentially methylated cell types in epigenome-wide association studies[J]. NATURE METHODS,2018,15(12):1059-+. |
| APA | Zheng, Shijie C.,Teschendorff, Andrew E.,Breeze, Charles E.,Beck, Stephan,Teschendorff, Andrew E.,&,.(2018).Identification of differentially methylated cell types in epigenome-wide association studies.NATURE METHODS,15(12),1059-+. |
| MLA | Zheng, Shijie C.,et al."Identification of differentially methylated cell types in epigenome-wide association studies".NATURE METHODS 15.12(2018):1059-+. |
入库方式： OAI收割
来源：上海营养与健康研究所
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