简化代表性亚硫酸氢盐测序与Sequenom EpiTyper甲基化分析之间DNA甲基化模式的比较评估。
Comparative assessment of DNA methylation patterns between reduced representation bisulfite sequencing and Sequenom EpiTyper methylation analysis.
作者信息
Chatterjee Aniruddha, Macaulay Erin C, Ahn Antonio, Ludgate Jackie L, Stockwell Peter A, Weeks Rob J, Parry Matthew F, Foster Timothy J, Knarston Ingrid M, Eccles Michael R, Morison Ian M
机构信息
Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand.
Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand.
出版信息
Epigenomics. 2017 Jun;9(6):823-832. doi: 10.2217/epi-2016-0176. Epub 2017 May 19.
AIM
Validation of sequencing-based DNA methylation data is an important step for meaningful translation of findings. However, there has been limited assessment of different platforms to validate methylation data from next generation sequencing.
METHODS
We performed a comparative methylation analysis between the genome-wide platform of reduced representation bisulfite sequencing with a targeted, Sequenom EpiTyper platform (four genes were analyzed in 15 cell lines covering 52 CpG sites).
RESULTS
We show that the accuracy of validation substantially improves if results from multiple and adjacent CpG sites are combined rather than at single CpG sites. We demonstrate increased read number improves accuracy of reduced representation bisulfite sequencing results. Further, by using series of replicates, we document variation in samples analyzed by Sequenom EpiTyper, indicating the importance of including replicates to increase precision.
CONCLUSION
The results reveal potential sources of bias and provide a guideline for refining study design for DNA methylation analysis.
目的
对基于测序的DNA甲基化数据进行验证是研究结果进行有意义转化的重要一步。然而，对于验证来自新一代测序的甲基化数据的不同平台，评估一直有限。
方法
我们在简化代表性亚硫酸氢盐测序的全基因组平台与靶向的Sequenom EpiTyper平台之间进行了比较甲基化分析（在15个细胞系中分析了4个基因，涵盖52个CpG位点）。
结果
我们表明，如果将多个相邻CpG位点的结果合并而非单个CpG位点的结果，验证的准确性会显著提高。我们证明增加读数数量可提高简化代表性亚硫酸氢盐测序结果的准确性。此外，通过使用一系列重复样本，我们记录了Sequenom EpiTyper分析的样本中的变异，表明纳入重复样本以提高精度的重要性。
结论
结果揭示了潜在的偏差来源，并为完善DNA甲基化分析的研究设计提供了指导。
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