Results of FusionSeq. (a) A subset of the PE reads connecting TMPRSS2 and ERG are shown for four samples (106_T, NCI-H660, 1700_D, 580_B). (b) PE reads connecting ERG and SLC45A3 for sample 2621_D. The outer circle reports all chromosomes, whereas the inset shows only the region of ERG and SLC45A3. The gray lines depict the intra-transcript PE reads, whereas the red ones represent the inter-transcript PE reads. Note that for illustration purposes, only the inter-transcript reads are shown for SLC45A3. The inset also depicts the composite model (blue line) and its exons (green boxes). (c) Results of the junction-sequence identifier. The location of the breakpoints for the four samples with the TMPRSS2-ERG fusion are reported as bars (not to scale). Moreover, the sequence of the junctions as well as a subset of the aligned reads for two samples is reported (106_T, 580_B). (d) The locations of the PCR primers used for the validation are depicted as red arrows. The isoforms consist of TMPRSS2 and ERG exons fused to form different exon combinations as depicted schematically. For both samples NCI-H660 and 1700_D, isoform III is detected, whereas, for samples 106_T and 580_B, isoforms I and VI are determined, respectively (Table S7 in Additional file 1) [46, 56]. The transcript isoforms were validated by a PCR assay for each sample separately (gel images). A 50-nt length standard (lane 1) is shown here for the determination of the approximate fragment size. The identity of the PCR products was validated by Sanger sequencing.