Methylation levels at the transcription start site correlate with HLF expression and DNMT3A mutational status. (A, upper) Schematic overview of the localization of CpGs assessed by the Illumina 450K methylation array in the HLF gene (upper row shows entire HLF gene with exons and introns; lower row shows enlarged regions assessed for CpG methylation; CpG positions are indicated by triangles, and numbered black bars indicate gaps not shown in the enlarged regions). (A, lower) Methylation levels at indicated CpGs according to HLF mRNA expression levels in the TCGA patient cohort. Patients were grouped according to HLF expression (RPKM) into quartiles (n = 156, box plots according to Tukey method; see supplemental Table 8 for details). Only P values <.005 are shown. **P < .005; ***P < .0005. Correl r: Pearson correlation coefficients for direct correlation of methylation and HLF mRNA expression levels. (B) Methylation levels in DNMT3A R882-mutated (red, n = 27) and wild-type patients (blue, n = 145) from the TCGA patient cohort. DNMT3A mutations other than R882 were excluded from the analysis, given their undetermined effect on DNA methylation levels. Positions marked in red indicate CpGs with significant differences in methylation level between the 2 groups. P values were determined by Mann-Whitney U test and were Benjamini-Hochberg corrected. *P < .05; **P < .005; ***P < .0005.