Genome-wide methylation analysis of human breast cancer subtype group (Luminal A, Luminal B, HER2+ and TNBC)

To identify Differentially methylated regions (DMRs) in TNBCs, we performed methyl binding domain protein 2 enrichment of DNA followed by massively parallel sequencing (MBD-seq) using 10 breast tumors and 10 matched normal samples for each of the four subtypes (LumA, LumB, HER2, and TNBC), classified according to ER, PR, and HER2 expression. ~~. 468 genes were significantly hypomethylated and 353 genes were significantly hypermethylated in promoter and CDS regions in only TNBC. Overall design: The sonicated genomic DNA was immunoprecipitated with human MBD2 protein. Next, MBD2-enriched DNA for each breast cancer subtype was used to construct DNA libraries according to the Illumina protocol.