A novel cell-type deconvolution algorithm reveals substantial contamination by immune cells in saliva, buccal and cervix
文献类型：期刊论文
| 作者 | Zheng, Shijie C.4,5; Dong, Danyue4,5; Teschendorff, Andrew E.1,4; Webster, Amy P.2; Beck, Stephan2; Feber, Andy3; Graham, David G.3; Sullivan, Roisin3; Jevons, Sarah3; Lovat, Laurence B.3 |
| 刊名 | EPIGENOMICS
 |
| 出版日期 | 2018 |
| 卷号 | 10期号:7页码:925-940 |
| 关键词 | buccal cell-type heterogeneity cervix DNA methylation EWAS immune cell saliva surrogate tissue |
| ISSN号 | 1750-1911 |
| DOI | 10.2217/epi-2018-0037 |
| 文献子类 | Article |
| 英文摘要 | Aim: An outstanding challenge in epigenome studies is the estimation of cell-type proportions in complex epithelial tissues. Materials & methods: Here, we construct and validate a DNA methylation reference and algorithm for complex tissues that contain epithelial, immune and nonimmune stromal cells. Results: Using this reference, we show that easily accessible tissues such as saliva, buccal and cervix exhibit substantial variation in immune cell (IC) contamination. We further validate our reference in the context of oral cancer, where it correctly predicts an increased IC infiltration in cancer but suppressed in patients with highest smoking exposure. Finally, our method can improve the specificity of differentially methylated CpG calls in epithelial cancer. Conclusion: The degree and variation of IC contamination in complex epithelial tissues is substantial. We provide a valuable resource and tool for assessing the epithelial purity and IC contamination of samples and for identifying differential methylation in such complex tissues. |
| 学科主题 | Genetics & Heredity |
| WOS关键词 | EPIGENOME-WIDE ASSOCIATION ; DNA METHYLATION DATA ; HUMAN BREAST-TUMORS ; GENE-EXPRESSION ; CANCER ; HETEROGENEITY ; METHYLOME ; DISCOVERY ; DISEASES ; SUBSETS |
| 语种 | 英语 |
| WOS记录号 | WOS:000438759200006 |
| 出版者 | FUTURE MEDICINE LTD |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.144/handle/331004/629]  |
| 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.UCL, Dept Womens Canc, 74 Huntley St, London WC1E 6AU, England, 2.UCL, UCL Canc Inst, Paul OGorman Bldg,72 Huntley St, London WC1E 6BT, England; 3.UCL, Div Surg & Intervent Sci, London WC1E 6BT, England; 4.Shanghai Inst Biol Sci, CAS Key Lab Computat Biol, CAS MPG Partner Inst Computat Biol, 320 Yue Yang Rd, Shanghai 200031, Peoples R China; 5.Univ Chinese Acad Sci, 19A Yuquan Rd, Beijing 100049, Peoples R China; |
| 推荐引用方式 GB/T 7714 | Zheng, Shijie C.,Dong, Danyue,Teschendorff, Andrew E.,et al. A novel cell-type deconvolution algorithm reveals substantial contamination by immune cells in saliva, buccal and cervix[J]. EPIGENOMICS,2018,10(7):925-940. |
| APA | Zheng, Shijie C..,Dong, Danyue.,Teschendorff, Andrew E..,Webster, Amy P..,Beck, Stephan.,...&,.(2018).A novel cell-type deconvolution algorithm reveals substantial contamination by immune cells in saliva, buccal and cervix.EPIGENOMICS,10(7),925-940. |
| MLA | Zheng, Shijie C.,et al."A novel cell-type deconvolution algorithm reveals substantial contamination by immune cells in saliva, buccal and cervix".EPIGENOMICS 10.7(2018):925-940. |
入库方式： OAI收割
来源：上海营养与健康研究所
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