DNA甲基化谱分析：全基因组测序方法与Infinium人类甲基化450芯片的比较

DNA methylation profiling: comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip.

作者信息

Walker Denise L, Bhagwate Aditya Vijay, Baheti Saurabh, Smalley Regenia L, Hilker Christopher A, Sun Zhifu, Cunningham Julie M

机构信息

Medical Genome Facility, Mayo Clinic, 200, 1st St, SW, Rochester, MN 55905, USA.

Division of Biomedical Statistics & Informatics, Mayo Clinic, Rochester, MN, USA.

出版信息

Epigenomics. 2015;7(8):1287-302. doi: 10.2217/EPI.15.64. Epub 2015 Jul 20.

DOI:10.2217/EPI.15.64

PMID:26192535

Abstract

AIMS

To compare the performance of four sequence-based and one microarray methods for DNA methylation profiling.

METHODS

DNA from two cell lines were profiled by reduced representation bisulfite sequencing, methyl capture sequencing (SS-Meth Seq), NimbleGen SeqCapEpi CpGiant(Nimblegen MethSeq), methylated DNA immunoprecipitation (MeDIP) and the Human Methylation 450 Bead Chip (Meth450K).

RESULTS & CONCLUSION: Despite differences in genome-wide coverage, high correlation and concordance were observed between different methods. Significant overlap of differentially methylated regions was identified between sequenced-based platforms. MeDIP provided the best coverage for the whole genome and gene body regions, while RRBS and Nimblegen MethSeq were superior for CpGs in CpG islands and promoters. Methylation analyses can be achieved by any of the five methods but understanding their differences may better address the research question being posed.

摘要

目的

比较四种基于序列的方法和一种微阵列方法在DNA甲基化谱分析中的性能。

方法

通过简化代表性亚硫酸氢盐测序、甲基捕获测序（SS-Meth Seq）、NimbleGen SeqCapEpi CpGiant（Nimblegen MethSeq）、甲基化DNA免疫沉淀（MeDIP）和人类甲基化450芯片（Meth450K）对两种细胞系的DNA进行分析。

结果与结论

尽管全基因组覆盖存在差异，但不同方法之间观察到高度的相关性和一致性。在基于测序的平台之间鉴定出差异甲基化区域的显著重叠。MeDIP为全基因组和基因体区域提供了最佳覆盖，而RRBS和Nimblegen MethSeq在CpG岛和启动子中的CpG方面表现更优。五种方法中的任何一种都可以实现甲基化分析，但了解它们之间的差异可能更有助于解决所提出的研究问题。