Copy number and gene expression profiles for rob(15;21)c and r(21)c iAMP21-ALL cases. (A) Example of the copy number and rearrangement profile of the der(15;21) chromosome for patient SJALL062714 with rob(15;21)c. Copy number is indicated on the y-axis, and the chromosome 15 and 21 ideograms are shown along the bottom of the plot to indicate breakpoint location. Rearrangements are separated based on their orientation: (B) Volcano plot comparing gene expression pattern between rob(15;21)c and typical subgroups. Only those cases in the main iAMP21-ALL cluster of Figure 1B with matched WGS and WTS were used in this analysis. Two hundred sixty-four genes showed significant differences (adjusted P value < .05), including 95 (36%) on chromosome 15 (84 and 11 upregulated and downregulated, respectively in rob(15;21)c compared with typical groups). (C) Heatmap showing the copy-number profile of chromosome 15 for 3 rob(15;21)c cases with matched WGS and WTS. Log₂ ratios of copy number calculated based on the tumor and germ line samples for each case were used, with red and blue showing copy number amplification/gain and deletion, respectively. Each row represents a sample. The ideogram for chromosome 15 is shown on the top of the heatmap. Genes with significantly higher and lower expression in rob(15;21)c compared with those in typical cases are shown in red and blue, respectively, and listed in supplemental Table 8. (D-E) Rearrangement and copy number patterns of 2 cases with r(21)c: SJALL062717 (D) and SJALL049622 (E). Somatic and germ line profiles are shown at the top and bottom, respectively. Rearrangements are separated based on their orientation. D, deletion; HH, head-to-head inverted; TD, tandem duplication; TT, tail-to-tail inverted.