Evaluation of the Infinium Methylation 450K technology
Evaluation of the Infinium Methylation 450K technology
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DOI：
10.2217/epi.11.105
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发表时间：
2011-12-01
期刊：
影响因子：
3.8
通讯作者：
Fuks, Francois
中科院分区：
文献类型：
--
作者：
Dedeurwaerder, Sarah;Defrance, Matthieu;Fuks, Francois
目的：DNA甲基化组的研究对生物医学具有巨大的前景，但受到经济高效地分析众多样本的技术挑战的阻碍。近期，对之前的Infinium HumanMethylation27 BeadChip®（美国加利福尼亚州Illumina公司）进行了重大扩展，开发出了Infinium HumanMethylation450（Infinium甲基化450K；美国加利福尼亚州Illumina公司）。这种升级技术是两种不同化学检测方法——Infinium I和Infinium II检测的混合体，能够（对12个样本同时）评估分布在整个基因组的超过48万个胞嘧啶的甲基化状态。在本文中，我们在细胞系和组织样本上对Infinium甲基化450K进行了评估，强调了它的一些优势以及一些局限性。特别是，我们比较了Infinium I和Infinium II检测的甲基化值。
材料与方法：我们使用Infinium甲基化450K进行分析：首先是特征明确的HCT116野生型和双敲除细胞系，然后是16个乳腺组织样本（包括8个正常样本和8个原发性肿瘤样本）。使用GenomeStudio™软件提取绝对甲基化值（β值），然后进行详细分析。
结果：尽管如先前所示，该技术似乎具有很高的稳健性，但我们注意到从Infinium I型和II型检测中获取的β值之间存在差异。具体而言，从Infinium II探针获得的β值不如从Infinium I探针获得的准确和可重复。这表明在任何下游生物信息学分析中，应分别考虑来自I型和II型检测的数据。为了能够一起处理Infinium I和Infinium II的数据，我们开发并测试了一种新的校正技术，我们称之为“基于峰值的校正”。其思路是根据Infinium I数据对Infinium II数据进行重新调整。尽管这种技术应被视为一种近似方法，但它显著提高了Infinium II数据的质量。
结论：就试剂成本、劳动时间、样本通量和覆盖范围而言，Infinium 450K是一种强大的技术。它为更好地理解健康和疾病中的表观遗传成分带来了巨大希望。然而，由于其设计包含两种不同化学检测的性质，对整套数据的分析并不像最初预期的那样容易。校正策略，比如这里提出的基于峰值的方法，是朝着充分的输出数据分析迈出的一步。
Aims: Studies of DNA methylomes hold enormous promise for biomedicine but are hampered by the technological challenges of analyzing many samples cost-effectively. Recently, a major extension of the previous Infinium HumanMethylation27 BeadChip (R) (Illumina, Inc. CA, USA), called Infinium HumanMethylation450 (Infinium Methylation 450K; Illumina, Inc. CA, USA) was developed. This upgraded technology is a hybrid of two different chemical assays, the Infinium I and Infinium II assays, allowing (for 12 samples in parallel) assessment of the methylation status of more than 480,000 cytosines distributed over the whole genome. In this article, we evaluate Infinium Methylation 450K on cell lines and tissue samples, highlighting some of its advantages but also some of its limitations. In particular, we compare the methylation values of the Infinium I and Infinium II assays. Materials & methods: We used Infinium Methylation 450K to profile: first, the well-characterized HCT116 wild-type and double-knockout cell lines and then, 16 breast tissue samples (including eight normal and eight primary tumor samples). Absolute methylation values (beta-values) were extracted with the GenomeStudio (TM) software and then subjected to detailed analysis. Results: While this technology appeared highly robust as previously shown, we noticed a divergence between the b-values retrieved from the type I and type II Infinium assays. Specifically, the b-values obtained from Infinium II probes were less accurate and reproducible than those obtained from Infinium I probes. This suggests that data from the type I and type II assays should be considered separately in any downstream bioinformatic analysis. To be able to deal with the Infinium I and Infinium II data together, we developed and tested a new correction technique, which we called `peak-based correction'. The idea was to rescale the Infinium II data on the basis of the Infinium I data. While this technique should be viewed as an approximation method, it significantly improves the quality of Infinium II data. Conclusion: Infinium 450K is a powerful technique in terms of reagent costs, time of labor, sample throughput and coverage. It holds great promise for the better understanding of the epigenetic component in health and disease. Yet, due to the nature of its design comprising two different chemical assays, analysis of the whole set of data is not as easy as initially anticipated. Correction strategies, such as the peak-based approach proposed here, are a step towards adequate output data analysis.