通过与单个样品的比较,评估Infinium MethylationEPIC BeadChip阵列的混合样品方法。

IF 5.7 2区 医学 Q1 Medicine
Shota Nishitani, Takashi X Fujisawa, Akiko Yao, Shinichiro Takiguchi, Akemi Tomoda
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引用次数: 0

摘要

背景:混合样本法用于表观基因组研究和表达分析,是一种低成本的少量DNA筛选方法。使用Illumina Infinium Methylation 450K BeadChip阵列对表观基因组研究中的混合样本方法进行评估;然而,关于更新后的850K阵列的后续报告缺乏。先前的一项研究表明,从单个样本中获得的甲基化水平可以使用汇总样本准确地复制,但没有解决全表观基因组关联研究(EWAS)统计问题。DNA定量方法对于混合样本方法中DNA的均匀混合很重要,现在已经成为基于荧光的方法,需要考虑其他因素,包括微阵列芯片批次效应的分辨率和DNA样本来源的细胞比例的异质性。在本研究中,从44个个体样本中创建了4个合并样本,并对单个样本进行了差异甲基化位置(dmp)和区域(DMRs)的EWAS统计,并与合并样本的统计结果进行了比较。结果:在混合样品中甲基化水平可以很好地重现。这是整个数据集的情况,仅限于前100个CpG站点,与之前使用450K BeadChip阵列的研究一致。然而,EWAS对单个样本的DMP的统计结果不能在合并样本中复制。定性分析强调甲基化在任意候选基因是可复制的。关注chr 20, EWAS对单个样本DMR的统计结果显示,只要它们被限制在具有足够效应量的区域,就可以在合并样本中复制。结论:混合样本法可很好地复制甲基化值,可用于DMR的EWAS。该方法具有样本量有效和成本效益高的特点,通过仔细了解混合样本法的有效特点和缺点,并结合候选基因分析,可以用于筛选。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Evaluation of the pooled sample method in Infinium MethylationEPIC BeadChip array by comparison with individual samples.

Evaluation of the pooled sample method in Infinium MethylationEPIC BeadChip array by comparison with individual samples.

Evaluation of the pooled sample method in Infinium MethylationEPIC BeadChip array by comparison with individual samples.

Evaluation of the pooled sample method in Infinium MethylationEPIC BeadChip array by comparison with individual samples.

Background: The pooled sample method is used in epigenomic research and expression analysis and is a cost-effective screening approach for small amounts of DNA. Evaluation of the pooled sample method in epigenomic studies is performed using the Illumina Infinium Methylation 450K BeadChip array; however, subsequent reports on the updated 850K array are lacking. A previous study demonstrated that the methylation levels obtained from individual samples were accurately replicated using pooled samples but did not address epigenome-wide association study (EWAS) statistics. The DNA quantification method, which is important for the homogeneous mixing of DNA in the pooled sample method, has since become fluorescence-based, and additional factors need to be considered including the resolution of batch effects of microarray chips and the heterogeneity of the cellular proportions from which the DNA samples are derived. In this study, four pooled samples were created from 44 individual samples, and EWAS statistics for differentially methylated positions (DMPs) and regions (DMRs) were conducted for individual samples and compared with the statistics obtained from the pooled samples.

Results: The methylation levels could be reproduced fairly well in the pooled samples. This was the case for the entire dataset and when limited to the top 100 CpG sites, consistent with a previous study using the 450K BeadChip array. However, the statistical results of the EWAS for the DMP by individual samples were not replicated in pooled samples. Qualitative analyses highlighting methylation within an arbitrary candidate gene were replicable. Focusing on chr 20, the statistical results of EWAS for DMR from individual samples showed replicability in the pooled samples as long as they were limited to regions with a sufficient effect size.

Conclusions: The pooled sample method replicated the methylation values well and can be used for EWAS in DMR. This method is sample amount-effective and cost-effective and can be utilized for screening by carefully understanding the effective features and disadvantages of the pooled sample method and combining it with candidate gene analyses.

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来源期刊
Clinical Epigenetics
Clinical Epigenetics Biochemistry, Genetics and Molecular Biology-Developmental Biology
CiteScore
8.90
自引率
5.30%
发文量
150
审稿时长
12 weeks
期刊介绍: Clinical Epigenetics, the official journal of the Clinical Epigenetics Society, is an open access, peer-reviewed journal that encompasses all aspects of epigenetic principles and mechanisms in relation to human disease, diagnosis and therapy. Clinical trials and research in disease model organisms are particularly welcome.
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