Comparison of Methyl-capture Sequencing vs. Infinium 450K methylation array for methylome analysis in clinical samples.
Comparison of Methyl-capture Sequencing vs. Infinium 450K methylation array for methylome analysis in clinical samples.
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DOI：
10.1080/15592294.2015.1132136
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Karnani N
中科院分区：
文献类型：
--
作者：
Teh AL;Pan H;Lin X;Lim YI;Patro CP;Cheong CY;Gong M;MacIsaac JL;Kwoh CK;Meaney MJ;Kobor MS;Chong YS;Gluckman PD;Holbrook JD;Karnani N
表观基因组的个体间变异因其在病理生理学研究、疾病诊断和临床干预评估中的潜力而受到极大关注。 DNA 甲基化是全表观基因组关联研究 (EWAS) 中研究最多的表观遗传标记，因为它可以从有限的起始材料中检测到。 Infinium 450K 甲基化芯片是在临床样本中对该标记进行高通量分析的最受欢迎的平台，因为它具有成本效益并且需要少量的 DNA。然而，该方法存在基因组覆盖率低和探针交叉杂交引入的错误。全基因组亚硫酸氢盐测序可以克服这些限制，但会极大地提高成本。甲基捕获测序 (MC Seq) 是一种颇具吸引力的中间解决方案，可提高大样本集中的甲基化覆盖率。在这里，我们首先证明 MC Seq 的 DNA 用量与 Infinium 450K 的用量相当。其次，为了在 EWAS 的 2 个平台之间进行选择时提供指导，我们在覆盖范围、技术差异和临床样本中甲基化调用的一致性方面评估和比较 MC Seq 和 Infinium 450K。最后，由于 EWAS 的重点是研究个体间变异，因此我们展示了 MC Seq 在研究不同种族受试者个体间变异方面的实用性。
Interindividual variability in the epigenome has gained tremendous attention for its potential in pathophysiological investigation, disease diagnosis, and evaluation of clinical intervention. DNA methylation is the most studied epigenetic mark in epigenome-wide association studies (EWAS) as it can be detected from limited starting material. Infinium 450K methylation array is the most popular platform for high-throughput profiling of this mark in clinical samples, as it is cost-effective and requires small amounts of DNA. However, this method suffers from low genome coverage and errors introduced by probe cross-hybridization. Whole-genome bisulfite sequencing can overcome these limitations but elevates the costs tremendously. Methyl-Capture Sequencing (MC Seq) is an attractive intermediate solution to increase the methylome coverage in large sample sets. Here we first demonstrate that MC Seq can be employed using DNA amounts comparable to the amounts used for Infinium 450K. Second, to provide guidance when choosing between the 2 platforms for EWAS, we evaluate and compare MC Seq and Infinium 450K in terms of coverage, technical variation, and concordance of methylation calls in clinical samples. Last, since the focus in EWAS is to study interindividual variation, we demonstrate the utility of MC Seq in studying interindividual variation in subjects from different ethnicities.