Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation
Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation
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DOI：
10.1080/15592294.2017.1417710
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发表时间：
2018-01-01
期刊：
影响因子：
3.7
通讯作者：
Bakulski, Kelly M.
中科院分区：
文献类型：
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作者：
Dou, John;Schmidt, Rebecca J.;Bakulski, Kelly M.
脐带血DNA甲基化与许多健康结果和环境暴露有关。整个脐带血DNA反映了所有有核血细胞类型，而全血离心分离红细胞，产生白血细胞的灰白色外衣。这两种样品类型都用于DNA甲基化研究。细胞类型具有独特的甲基化模式和加工可以影响细胞分布，这可能会影响可比性。我们评估了脐带血灰白色和全脐带血样本之间细胞组成和DNA甲基化的差异。使用Infinium EPIC BeadChip （Illumina）对8个个体的脐带血DNA甲基化进行了测量，每个个体都提供了褐色皮毛和全血样本。我们分析了甲基化的主成分（PC），进行了分层聚类，并计算了对之间平均中心甲基化的相关性。我们对单个位点进行了适度的t检验，并估计了细胞组成。DNA甲基化pc与个体相关(P-PC1 = 1.4x 10(-9)；P-PC2 = 2.9x 10(-5)；P-PC3 = 3.8x 10(-5)；P-PC4 = 4.2 × 10(-6)；P-PC5 = 9.9 × 10(-13), P-PC6 = 1.3 × 10(-11))，与样品类型无关（PPC1-6>0.7）。样本按个体分层聚类。配对样本间平均中心甲基化的Pearson相关性r = 0.66至r = 0.87。在对多个比较进行校正后，棕毛被和全脐带血之间没有个体的显著差异（5个位点的P值未校正）
Cord blood DNA methylation is associated with numerous health outcomes and environmental exposures. Whole cord blood DNA reflects all nucleated blood cell types, while centrifuging whole blood separates red blood cells, generating a white blood cell buffy coat. Both sample types are used in DNA methylation studies. Cell types have unique methylation patterns and processing can impact cell distributions, which may influence comparability. We evaluated differences in cell composition and DNA methylation between cord blood buffy coat and whole cord blood samples. Cord blood DNA methylation was measured with the Infinium EPIC BeadChip (Illumina) in eight individuals, each contributing buffy coat and whole blood samples. We analyzed principal components (PC) of methylation, performed hierarchical clustering, and computed correlations of mean-centered methylation between pairs. We conducted moderated t-tests on single sites and estimated cell composition. DNA methylation PCs were associated with individual (P-PC1 = 1.4x 10(-9); P-PC2 = 2.9x 10(-5); P-PC3 = 3.8x 10(-5); P-PC4 = 4.2x 10(-6); P-PC5 = 9.9x 10(-13), P-PC6 = 1.3x 10(-11)) and not with sample type (PPC1-6>0.7). Samples hierarchically clustered by individual. Pearson correlations of mean-centered methylation between paired samples ranged from r = 0.66 to r = 0.87. No individual site significantly differed between buffy coat and whole cord blood when adjusting for multiple comparisons (five sites had unadjusted P