Methylation Profiles of YWHA Genes

Methylation levels on CpGs located in the seven YWHA genes were extracted from the methylomic data previously obtained for a subset of this cohort^{4 (link)}. Briefly, for each individual, genomic DNA (500 ng) was extracted from whole blood and treated with sodium bisulfite using the EZ-96DNA Methylation KIT (Catalog No D5004, Zymo Research, Irvine, CA, USA) following the manufacturer’s standard protocol. Genome-wide DNA methylation was assessed using Illumina Infinium HumanMethylation450 BeadChip (Illumina, San Diego, CA, USA), which interrogates the DNA methylation profile of >485 000 CpG loci across the genome at single-nucleotide resolution. Illumina GenomeStudio software (Illumina) was used to extract signal intensities for each probe. For details about preprocessing and clean up steps, please refer to Kebir et al.^{4 (link)}. Methylation and expression data were available for 25 patients (12 converters and 13 non converters) at both baseline and at the end of follow-up. A total of 122 CpGs were located in the promoter or the body of one of the seven YWHA genes. Methylation levels on these CpG were correlated with their corresponding gene expressions using Pearson’s test.