Methylation of ID4 promoter-associated CpG island in CLL patients. (A) Schematic representation of the ID4 gene showing the location of the CpG island (CGI; black bar) and the amplicons used for MassARRAY based methylation analysis (ID4-0.1, 0.2, 1, 2, and 3; blue bars). The arrowhead indicates the predicted transcription start site. (B) Graphical display of quantitative DNA methylation data on amplicons ID4-1, 2, and 3. Each square represents a CpG unit, and each row represents a sample. Gray indicates unavailable data. Color coding for DNA methylation levels is explained by the bar on the left. Samples included 85 CLL PBMC samples obtained from patients seen at OSU; normal control patients were 9 sorted CD19⁺ B-cell samples and 8 CD3⁺ T-cell samples from healthy donors. (C) Plot of average percentage methylation over amplicons ID4-1, 2, and 3, in OSU CLL sample set and controls (normal B and T cells), and further separated by treatment status. P values were based on Mann-Whitney U tests. (D) Graphical display of DNA methylation in amplicons ID4-0.1, 0.2, 2, and 3. Included are 82 PBMC pretreatment samples from CLL patients enrolled on CALGB 9712, and same controls used for Figure 1B. (E) Plot of average percentage methylation over amplicons ID4-0.1, 0.2, 2, and 3, in CLL and controls (normal B and T cells) samples. P values were determined on the basis of Mann-Whitney U tests.