Methylation Profiling with Infinium EPIC BeadChip

Bisulfite-converted DNA samples from step 1 were assessed using Infinium Human Methylation EPIC Bead Chip (Illumina, California, USA) according to the manufacturer’s instructions. Illumina Genome Studio software V.2011.1 was used to extract the raw signal intensities of each probe (without background correction or normalization). The resulting raw data were normalized (control normalization) and background corrected by the manufacturer software to generate β-values for representing methylation status of each CpG site. The data preprocessing of MethylationEPIC BeadChip was performed by R package “ChAMP” V.2.18.2, including filter and normalization.22 (link) It filtered out (1) probes with detection p value (>0.01), (2) probes with <3 beads in at least 5% of samples per probe, (3) all non-CpG probes, (4) all SNP-related probes,23 24 (link) (5) all multihit probes,25 (link) (6) cross-reactive probes cohybridizing to the sex chromosomes.23 (link) MethylationEPIC BeadChip normalization (sample normalization, using the parameter “BMIQ”), calling differentially methylated points and calling DMRs (using the parameter “Bumphunter”) were performed.

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Lin C.H., Lee Y.S., Huang Y.Y, & Tsai C.N. (2021). Methylation status of vault RNA 2-1 promoter is a predictor of glycemic response to glucagon-like peptide-1 analog therapy in type 2 diabetes mellitus. BMJ Open Diabetes Research & Care, 9(1), e001416.

Publication 2021

Infinium Human Methylation EPIC Bead Chip Genome Studio software V.2011.1

Bisulfite Chip Cross reactive Genome Human Sex chromosomes

Corresponding Organization : Taipei City Hospital

Other organizations : Linkou Chang Gung Memorial Hospital, Chang Gung Memorial Hospital, Ming Chuan University

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Variable analysis

independent variables

Bisulfite-converted DNA samples from step 1

dependent variables

Methylation status of each CpG site

control variables

Sample normalization using the parameter "BMIQ"
Calling differentially methylated points and calling DMRs using the parameter "Bumphunter"

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