Fusion gene plots for four individual prostate cancer samples with the same fusion event. The four samples all had fusion transcripts with junctions between TMPRSS2 exon 1 and ERG exon 4. (A) Chimeric sequences plotted with increasing fusion scores. For the three first samples, the chimera of TMPRSS2:ERG exon1:4 had the highest ranking out of the 10,297 tested combinations. (B) Fusion map of each chimeric exon-exon junction of TMPRSS2 and ERG. Intensities of red indicate the relative values of the medians for the four replicate oligos for each chimeric exon-exon junction and the white arrows point to the correct fusion breakpoints. (C) Measurements from intragenic oligos (intra-exon probes) for ERG demonstrate a shift in intensities between exons three and four.