Cell type specific DNA methylation in cord blood: A 450K-reference data set and cell count-based validation of estimated cell type composition

Epigenome-wide association studies of prenatal exposure to different environmental factors are becoming increasingly common. These studies are usually performed in umbilical cord blood. Since blood comprises multiple cell types with specific DNA methylation patterns, confounding caused by cellular heterogeneity is a major concern. This can be adjusted for using reference data consisting of DNA methylation signatures in cell types isolated from blood. However, the most commonly used reference data set is based on blood samples from adult males and is not representative of the cell type composition in neonatal cord blood. The aim of this study was to generate a reference data set from cord blood to enable correct adjustment of the cell type composition in samples collected at birth. The purity of the isolated cell types was very high for all samples (>97.1%), and clustering analyses showed distinct grouping of the cell types according to hematopoietic lineage. We explored whether this cord blood and the adult peripheral blood reference data sets impact the estimation of cell type composition in cord blood samples from an independent birth cohort (MoBa, n = 1092). This revealed significant differences for all cell types. Importantly, comparison of the cell type estimates against matched cell counts both in the cord blood reference samples (n = 11) and in another independent birth cohort (Generation R, n = 195), demonstrated moderate to high correlation of the data. This is the first cord blood reference data set with a comprehensive examination of the downstream application of the data through validation of estimated cell types against matched cell counts.

针对产前暴露于不同环境因素的表观全基因组关联研究（Epigenome-wide Association Study, EWAS）正日益普及。此类研究通常以脐带血为实验材料。由于血液包含多种具有特定DNA甲基化模式的细胞类型，细胞异质性引发的混杂偏倚是该类研究的核心顾虑。该偏倚可通过使用源自分离血液细胞的DNA甲基化特征参考数据集进行校正。然而，当前最常用的参考数据集基于成年男性的血液样本，无法反映新生儿脐带血的细胞类型组成。本研究旨在构建源自脐带血的参考数据集，以实现对出生采集样本中细胞类型组成的准确校正。所有分离得到的细胞样本纯度均极高（>97.1%），聚类分析结果显示细胞类型依照造血谱系形成了清晰的聚类分组。我们探究了本脐带血参考数据集与成人外周血参考数据集，对独立出生队列MoBa（n=1092）的脐带血样本细胞类型组成估算的影响。结果显示所有细胞类型的估算值均存在显著差异。尤为重要的是，分别将脐带血参考样本（n=11）与另一独立出生队列Generation R（n=195）中的细胞类型估算值与匹配的细胞计数进行对比后发现，数据呈现中等至高度的相关性。本研究构建的脐带血参考数据集是首个通过将估算细胞类型与匹配细胞计数进行验证，从而全面考察该数据集下游应用场景的参考数据集。