Identification of methylation states of DNA regions for Illumina methylation BeadChip

BMC Genomics
Ximei LuoYuming Zhao

Abstract

Methylation of cytosine bases in DNA is a critical epigenetic mark in many eukaryotes and has also been implicated in the development and progression of normal and diseased cells. Therefore, profiling DNA methylation across the genome is vital to understanding the effects of epigenetic. In recent years the Illumina HumanMethylation450 (HM450K) and MethylationEPIC (EPIC) BeadChip have been widely used to profile DNA methylation in human samples. The methods to predict the methylation states of DNA regions based on microarray methylation datasets are critical to enable genome-wide analyses. We report a computational approach based on the two layers two-state hidden Markov model (HMM) to identify methylation states of single CpG site and DNA regions in HM450K and EPIC BeadChip. Using this mothed, all CpGs detected by HM450K and EPIC in H1-hESC and GM12878 cell lines are identified as un-methylated, middle-methylated and full-methylated states. A large number of DNA regions are segmented into three methylation states as well. Comparing the identified regions with the result from the whole genome bisulfite sequencing (WGBS) datasets segmented by MethySeekR, our method is verified. Genome-wide maps of chromatin states show that methy...Continue Reading

References

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Datasets Mentioned

BETA
GM12878

Methods Mentioned

BETA
methylation profiling
chip
WGBS
ChIP-seq

Software Mentioned

MethylSeekR
EPIC
Varley
Bioconductor
HMM
Fisher
DMRcate
ENCODE
minfi
R

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