We have established a simple assay that can concurrently profile variants of TMPRSS2:ERG fusion transcripts by combining a single RT-PCR with an exon array. The modified 'Round ABC' protocol, which was TMPRRS2e1R  TMPRRS2e1/2R  TMPRRS2e2R  TMPRRS2e3R  ERGe1R  ERGe2R  ERGe3R  ERGe4R  ERGe5R  ERGe6R  T1G1R  T1G2R  T1G3R  T1G4R  T1G5R  T1G6R  T2G1R  T2G2R  T2G3R  T2G4R  T2G5R  T2G6R   #1  #15  #17  #4  #13 #10 #18 Figure 4 . Cluster analysis of seven prostate cancer samples having fusion transcripts. The signal intensity of each feature is divided by the intensity of a nonspecific control (herring sperm DNA) to normalize the data for cluster analysis. The result is shown in Table 3 . The samples having similar fusion transcript variants were clustered together by the program. 1  30  7  T1-G4; T2-G4  2  2 0  5  3  5 0  5  4  20  6  T1-G4  5  8 0  9  6  1  6  7  9 0  8  8  2 0  4  9  8 0  8  10  1  6  T1-G2  11  2  6  12  70  7  13  20  9  T1-G4  14  1  6  15  70  8  T1-G4; T2-G4  16  20  8  17  80  8  T1-G4; T2-G4  18  50  7  T1-G2; T1-G3; T1-G4  19  80  7  20 80 7 Figure 5 . Heterogeneity of FISH patterns of interstitial deletion between TMPRSS2 and ERG in a primary prostate tumor. An unpaired green dot (TMPRSS2 probe, indicated by arrows) suggests an interstitial deletion. Nonrandom variation of FISH patterns is shown by the fact that most of the green and red signals (two different but nearby probes) are paired in each panel. This variation is expected on a heterogeneous aneuploid cancer cell population, which often makes it difficult to distinguish meaningful events from random background aberrations.