We used FISH analysis to independently confirm our array approach. Our FISH procedure (28) employed 50-mer probes that were labeled with small haptens for target hybridization in conjunction with individual hapten-specific, quantum dot conjugated antibodies for signal detection. The resolution of this method is $50 kb. We designed two probes for the FISH assays, one at the promoter region of TMPRSS2 (green in Figure 5 ) and the other at exon 2 of ERG (red in Figure 5 ). We observed heterogeneity of the FISH patterns in some primary prostate cancer samples ( Figure 5 ). It is more difficult to find interstitial deletions between TMPRSS2 and ERG in tumor samples containing low percentages of cancer cells by FISH. Therefore, we used samples that contained 480% cancer cells without detectable fusion genes to confirm the results of the arrays. The FISH experiments revealed no genomic deletions at this location for all the selected samples (#5, #7, #9, #19 and #20) that were similarly nondeleted by array hybridization.