Allele-specific expression analysis of FLT3 in BCP ALL. (A) Scatterplot of allelic ratio (x-axis) and log-scale binomial P values (y-axis) of FLT3 in BCP ALL (n = 77) with informative SNVs. The horizontal line represents the binomial P value of .05 (log₁₀ scale) and the vertical lines represent the ratio for the expressed reference/nonreference allele (log₂ scale). All 7 cases with clonal 13q12.2 deletions displayed allele-specific expression of FLT3 (top right quadrant). (B) FLT3 mutant allele frequencies observed by RNA-seq (y-axis) and by genomic-sequencing data (x-axis) of 9 BCP ALL cases. The line y=x is shown in black. The 3 cases with concurrent FLT3 mutation and 13q12.2 deletion showed increased expression of the mutated allele.