Identification of the TMPRSS2-ERG associated 3-Mb deletion on chromosome 21 and mapping of the breakpoints. Exemplary log2 ratio plots of chromosome 21 from plasma DNA of several patients (regions with log2 ratios >0.2 are shown in red and those with log2 ratios <-0.2 in blue). A deletion with size of 3 Mbp located at the TMPRSS2-ERG region was visible in patients CRPC1, CRPC5, CSPC4, and CSPC1. For comparison we also included chromosome 21 plots from CSPC2 and CRPC2 without this deletion. Mapping of the exact breakpoints was based on fusion transcripts identified with our GB-panel. In CRPC1, CRPC5, and CSPC4 the breakpoints were in exon 1 of the TMPRSS2 gene and exon 3 of the ERG gene, respectively (center panel). In CSPC1 the proximal breakpoint was approximately 24 Kb upstream of the ERG gene.