TCF3:PBX1 in a leukemia cell line. (A) The highest ranking fusion score (y-axis) among 10,297 chimeric combinations (ranked along the x-axis) indicated a fusion event between exons 16 and 3 of TCF3 and PBX1, respectively. (B) Fusion map of each chimeric exon-exon junction of TCF3 and PBX1. Intensities of red indicate the relative values of the medians for the four replicate oligos for each chimeric exon-exon junction, and the square with strongest intensity indicates the correct fusion breakpoint. (C) Measurements from intragenic oligos (intra-exon probes) for each of the two fusion partners are indicative of the same fusion breakpoints as seen from the chimeric oligos. (D) The exact fusion breakpoint between TCF3 and PBX1 was confirmed by cDNA sequencing. (E) Chromosome banding and fluorescence in situ hybridization analyses of the same cell line demonstrated rearranged chromosomes from the translocation t(1;19)(q23;p13), which implicates the loci of TCF3 and PBX1.