Detection of epigenetic field defects using a weighted epigenetic distance-based method
文献类型：期刊论文
| 作者 | Wang, Ya4; Qian, Min4; Wang, Shuang4; Ruan, Peifeng3; Teschendorff, Andrew E.1,2; , |
| 刊名 | NUCLEIC ACIDS RESEARCH
 |
| 出版日期 | 2019 |
| 卷号 | 47期号:1页码:e6 |
| 关键词 | NSCLC Cisplatin sensitivity Scribble Nox2 ROS PD-L1 |
| ISSN号 | 0305-1048 |
| DOI | 10.1093/nar/gky882 |
| 文献子类 | Article |
| 英文摘要 | Identifying epigenetic field defects, notably early DNA methylation alterations, is important for early cancer detection. Research has suggested these early methylation alterations are infrequent across samples and identifiable as outlier samples. Here we developed a weighted epigenetic distance-based method characterizing (dis)similarity in methylation measures at multiple CpGs in a gene or a genetic region between pairwise samples, with weights to up-weight signal CpGs and down-weight noise CpGs. Using distance-based approaches, weak signals that might be filtered out in a CpG site-level analysis could be accumulated and therefore boost the overall study power. In constructing epigenetic distances, we considered both differential methylation (DM) and differential variability (DV) signals. We demonstrated the superior performance of the proposed weighted epigenetic distance-based method over non-weighted versions and site-level EWAS (epigenome-wide association studies) methods in simulation studies. Application to breast cancer methylation data from Gene Expression Omnibus (GEO) comparing normal-adjacent tissue to tumor of breast cancer patients and normal tissue of independent age-matched cancer-free women identified novel epigenetic field defects that were missed by EWAS methods, when majority were previously reported to be associated with breast cancer and were confirmed the progression to breast cancer. We further replicated some of the identified epigenetic field defects. |
| 学科主题 | Biochemistry & Molecular Biology |
| WOS关键词 | GENE-EXPRESSION PATTERNS ; DNA METHYLATION ; BREAST-CANCER ; DOWN-REGULATION ; IDENTIFICATION ; ASSOCIATION ; REGRESSION ; DISEASE ; HYPERMETHYLATION ; MECHANISMS |
| 语种 | 英语 |
| WOS记录号 | WOS:000462586700008 |
| 出版者 | OXFORD UNIV PRESS |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.144/handle/331004/987]  |
| 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.Chinese Acad Sci, CAS Key Lab Computat Biol, Shanghai Inst Biol Sci, Shanghai, Peoples R China; 2.UCL, Stat Canc Genom, UCL Canc Inst, London, England, 3.George Washington Univ, Dept Stat, Columbian Coll Arts & Sci, Washington, DC 20052 USA; 4.Columbia Univ, Dept Biostat, Mailman Sch Publ Hlth, New York, NY 10027 USA; |
| 推荐引用方式 GB/T 7714 | Wang, Ya,Qian, Min,Wang, Shuang,et al. Detection of epigenetic field defects using a weighted epigenetic distance-based method[J]. NUCLEIC ACIDS RESEARCH,2019,47(1):e6. |
| APA | Wang, Ya,Qian, Min,Wang, Shuang,Ruan, Peifeng,Teschendorff, Andrew E.,&,.(2019).Detection of epigenetic field defects using a weighted epigenetic distance-based method.NUCLEIC ACIDS RESEARCH,47(1),e6. |
| MLA | Wang, Ya,et al."Detection of epigenetic field defects using a weighted epigenetic distance-based method".NUCLEIC ACIDS RESEARCH 47.1(2019):e6. |
入库方式： OAI收割
来源：上海营养与健康研究所
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