Reliability of DNA methylation measures from dried blood spots and mononuclear cells using the HumanMethylation450k BeadArray.
Reliability of DNA methylation measures from dried blood spots and mononuclear cells using the HumanMethylation450k BeadArray.
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DOI：
10.1038/srep30317
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发表时间：
2016-07-26
影响因子：
4.6
通讯作者：
Milne RL
中科院分区：
文献类型：
--
作者：
Dugué PA;English DR;MacInnis RJ;Jung CH;Bassett JK;FitzGerald LM;Wong EM;Joo JE;Hopper JL;Southey MC;Giles GG;Milne RL
广泛使用的HumanMethylation450 （HM450K）微阵列甲基化测量的可靠性尚未对来自干血斑（DBS）或外周血单个核细胞（PBMC）的DNA进行评估，也未对来自不同研究的综合数据进行评估。来自DBS和PBMC样本的DNA中重复的HM450K甲基化测量可从墨尔本合作队列研究中嵌套的六个病例对照研究的参与者中获得。采用混合效应模型计算基于技术重复（单个研究中重复的样本；126个PBMC， 136个DBS）和研究重复（多个研究中重复的样本；280个PBMC， 769个DBS）的类内相关系数（ICC）来评估单个CpGs的可靠性。PBMC基于技术重复的信度中等（ICC中位数= 0.42），但DBS的信度较低（ICC中位数= 0.20）。研究重复的ICCs低于技术重复。高度甲基化或未甲基化的CpGs通常具有较低的ICCs，这似乎主要与它们较低的变异性有关。全球甲基化测量的ICCs很高，通常大于0.70。由HM450K微阵列确定的甲基化测量的可靠性范围广泛，主要取决于单个CpG位点甲基化的可变性。在HM450K分析中，对于相当大比例的CpGs，关联研究的能力很低。
The reliability of methylation measures from the widely used HumanMethylation450 (HM450K) microarray has not been assessed for DNA from dried blood spots (DBS) or peripheral blood mononuclear cells (PBMC), nor for combined data from different studies. Repeated HM450K methylation measures in DNA from DBS and PBMC samples were available from participants in six case-control studies nested within the Melbourne Collaborative Cohort Study. Reliability was assessed for individual CpGs by calculating the intraclass correlation coefficient (ICC) based on technical replicates (samples repeated in a single study; 126 PBMC, 136 DBS) and study duplicates (samples repeated across studies; 280 PBMC, 769 DBS) using mixed-effects models. Reliability based on technical replicates was moderate for PBMC (median ICC = 0.42), but lower for DBS (median ICC = 0.20). Study duplicates gave lower ICCs than technical replicates. CpGs that were either highly methylated or unmethylated generally had lower ICCs, which appeared to be mostly related to their lower variability. The ICCs for global methylation measures were high, typically greater than 0.70. The reliability of methylation measures determined by the HM450K microarray is wide-ranging and depends primarily on the variability in methylation at individual CpG sites. The power of association studies is low for a substantial proportion of CpGs in the HM450K assay.