Identification of representative IKZF1 deleted cases by splice junction track analysis. (A) Schematic representation of Sashimi plot for 1 IKZF1 nondeleted case displaying all expected arcs connecting IKZF1 exons. The vertical peaks represent coverage depth on IKZF1 exons. Arcs represent splice junctions that connect exons, and the numbers on curved lines show the junction read depth that split across the junction. (B) Schematic view and Sashimi plots obtained in the IGV software for a representative IKZF1 Δ4-7 case (red) displaying abnormal splice junction arcs connecting exon 3-8, which it is not seem in the IKZF1 nondeleted case (black). The upper panel displays all exon-exon junctions. The lower panel display selected exon junctions, which distinguish a particular IKZF1 deletion. This is accomplished in IGV by clicking on the specific exon, as indicated by the red arrowhead. (C) Schematic view and Sashimi plots for a representative IKZF1 Δ4-8 case (red) displaying the abnormal splice junctions connecting exon 3 to downstream genes FIGNL1 and DDC. Note that the abnormal splice junction arcs are only seen in IKZF1 deleted cases. Results for the whole group of patients are summarized in supplemental Figure 6 and supplemental Table 6. Genomic coordinates plotted on the last track of each panel correspond to RefSeq, Hg19.