DNA hypomethylation is associated to overexpression of trisomic genes. (A) Visualization on the University of California at Santa Cruz (UCSC) genome browser of DNA methylation changes detected by the HELP assay on 4 genes localized in neighboring regions of the DSCR. Each custom track represents the mean HELP values measured for that group. Negative deflections below the zero line represent negative log ratios (methylated regions), and positive deflections above the zero line represent positive log ratios (hypomethylated regions). Red arrows indicate HELP probesets with detectable differences in methylation between control samples (FL-MNC and non–DS-AMKL) and DS-related samples (Tri21 FL-MNC, DS-AMKL, and DS-TMD). (B) Boxplots representing gene expression values for genes differentially methylated in and around the DS critical region. P values are for t test comparisons between each of the 2 DS-related conditions vs the non–DS-AMKL values. (C) Gene set enrichment analysis using positional gene sets MSigDB collections (c1) showing significant enrichment for genes localized in 21q22 band in DS-AMKL samples from a publicly available DS-AMKL microarray dataset.²⁹