Validation of a DNA methylation reference panel for the estimation of nucleated cells types in cord blood.
Validation of a DNA methylation reference panel for the estimation of nucleated cells types in cord blood.
复制标题
对DNA甲基化参考面板的验证，以估算脐带血中核细胞类型的估计。
DOI：
10.1080/15592294.2016.1233091
复制
发表时间：
2016-11
期刊：
影响因子：
3.7
通讯作者：
Hivert MF
中科院分区：
文献类型：
--
作者：
Cardenas A;Allard C;Doyon M;Houseman EA;Bakulski KM;Perron P;Bouchard L;Hivert MF
脐带血被广泛用作产前条件的表观基因组关联研究中的替代组织。样本间的细胞类型组成变化可能是构成细胞混合物的血液中表观基因组范围关联研究的重要混淆因素。我们评估了一种新开发的脐带血参考组，以根据DNA甲基化水平估算细胞类型组成，包括有核红细胞（nRBC）。我们从154个独特的脐带血样本中估计了细胞类型组成，这些样本具有可用的DNA甲基化数据以及有核细胞类型的直接测量。我们观察到nRBC的估计和测量组成之间的高度相关性（r = 0.92，R2 = 0.85），淋巴细胞（r = 0.77，R2 = 0.58），粒细胞（r = 0.72，R2 = 0.52），单核细胞中度相关（r = 0.51，R2 = 0.25），以及相对较低的均方根误差从1.4%至5.4%的残差。这些结果验证了脐带血参考组的使用，并强调了其实用性和局限性的流行病学研究。
Cord blood is widely used as surrogate tissue in epigenome-wide association studies of prenatal conditions. Cell type composition variation across samples can be an important confounder of epigenome-wide association studies in blood that constitute a mixture of cells. We evaluated a newly developed cord blood reference panel to impute cell type composition from DNA methylation levels, including nucleated red blood cells (nRBCs). We estimated cell type composition from 154 unique cord blood samples with available DNA methylation data as well as direct measurements of nucleated cell types. We observed high correlations between the estimated and measured composition for nRBCs (r = 0.92, R2 = 0.85), lymphocytes (r = 0.77, R2 = 0.58), and granulocytes (r = 0.72, R2 = 0.52), and a moderate correlation for monocytes (r = 0.51, R2 = 0.25) as well as relatively low root mean square errors from the residuals ranging from 1.4 to 5.4%. These results validate the use of the cord blood reference panel and highlight its utility and limitations for epidemiological studies.