MECOM rearrangements, EVI1 overexpression, and absence of MDS1-EVI1 expression in atypical 3q26-rearranged AML. (A) Normalized EVI1 expression (counts per million [CPM] from RNA-seq data) determined in inv(3)/t(3;3) (n = 11), atypical 3q26 (n = 26) compared with non-3q26 AML (n = 111). (B) Allele-specific expression analysis using DNA-seq and RNA-seq data. The major allele is the allele of which the most SNPs were measured; the minor allele represents the allele that was underrepresented in the measurements. In order to perform this analysis, SNPs needed to be present in the sample. In 15 out of 33 cases, this analysis could be carried out. Asterisk (*) indicates significant differential expression between alleles (P < .05, χ² test). VAF, variant allele frequency. (C) Relative EVI1 and MDS1-EVI1 expression (CPM, RNA-seq) in atypical 3q26 AMLs (n = 26). The red crossbar represents the mean and the red box the standard deviation. (D) Schematic depiction of the breakpoints within the MECOM locus (3q26) determined by 3q-capture. The breakpoints could be determined in 23 AML cases. In 6 cases, the breakpoint was 3′ of EVI1 and in 15 cases 5′ of the EVI1 promoter but 3′ of the MDS1-EVI1 promoter and in 2 AMLs 5′ of the MDS1-EVI1 promoter.