Identifying IKZF1 deletions using RNA-seq data. (A) Schematic of the IKZF1 canonical transcript (IK1) and augmented deletion transcripts, del4-7, del4-8, del2-7, and del2-8. Each coding exon is colored, and noncoding exons are gray. The exons encoding the N-terminal DNA-binding, and C-terminal dimerization domains are indicated by arrows. (B) Expression levels of IK1 (ENST00000331340) in all B-ALL samples (including 99 diagnosis samples and matched relapse for 2 samples). Plot shows transcripts per million (TPM) on the y-axis. (C-D) Relationship between expression of the IKZF1 del 4-7 transcript and IKZF1 del 4-8 and total IKZF1 expression (the sum of all IKZF1 transcripts). Samples that have the respective IKZF1 deletion transcript are colored and all other samples are shown in gray. The legend for panels B-D is shown at top right. Samples are colored by IKZF1 deletion status based on primary and secondary RQ-PCR results, according to the key. Samples that have not been tested for IKZF1 deletion (unknown) or are confirmed nondeletions (undetected) are gray. Samples that were identified in primary RQ-PCR analysis, as part of clinical diagnostics (clinical RQ-PCR result) are depicted by circles, and samples that were predicted by RNA-seq and validated by secondary RQ-PCR (RNA-seq predicted and validated) are depicted by triangles. Samples that were predicted by RNA-seq to have an IKZF1 deletion but were not validated by RQ-PCR (unvalidated) are depicted by unfilled triangles.