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Methods. 2010 Nov;52(3):203-12. doi: 10.1016/j.ymeth.2010.04.009. Epub 2010 Apr 27.

Whole genome DNA methylation analysis based on high throughput sequencing technology.

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  • 1Beijing Genomics Institute at Shenzhen, Shenzhen 518000, China.

Abstract

There are numerous approaches to decipher a whole genome DNA methylation profile ("methylome"), each varying in cost, throughput and resolution. The gold standard of these methods, whole genome bisulfite-sequencing (BS-seq), involves treatment of DNA with sodium bisulfite combined with subsequent high throughput sequencing. Using BS-seq, we generated a single-base-resolution methylome in human peripheral blood mononuclear cells (in press). This BS-seq map was then used as the reference methylome to compare two alternative sequencing-based methylome assays (performed on the same donor of PBMCs): methylated DNA immunoprecipitation (MeDIP-seq) and methyl-binding protein (MBD-seq). In our analysis, we found that MeDIP-seq and MBD-seq are complementary strategies, with MeDIP-seq more sensitive to highly methylated, high-CpG densities and MDB-seq more sensitive to highly methylated, moderate-CpG densities. Taking into account the size of a mammalian genome and the current expense of sequencing, we feel 3gigabases (Gbp) 45bp paired-end MeDIP-seq or MBD-seq uniquely mapped reads is the minimum requirement and cost-effective strategy for methylome pattern analysis.

Copyright © 2010 Elsevier Inc. All rights reserved.

PMID:
20430099
[PubMed - indexed for MEDLINE]
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