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Fig. S1 Identification of TMPRSS2-ERG translocations with RT-PCR, ERG expression analysis and exons ratioing. (A) RT-PCR analysis on RNA extracted from five prostate cancer tissue specimens (low-grade, one; high-grade, two; metastatic, one and CPRC, one) with a forward primer located in TMPRSS2 exon 1 and a reverse primer located in ERG exon 4. The PCR products were separated by agarose gel electrophoresis. Lane 1, M, 100 bp DNA ladder (Promega); lanes 2–6, prostate cancer tissue specimens; lane 7, negative control. The most common fusion transcript from TMPRSS2 exon 1 to ERG exon 4 can be seen in lanes 2, 3 and 5 (180 bp). Lane 4 contains a transcript between TMPRSS2 exon 1 and ERG exon 2 (368 bp) together with a fusion transcript of TMPRSS2 exon 2 and ERG exon 2 (439 bp). The nature of all fusion transcripts was confirmed by sequence analysis. (B) The log2 expression level was calculated for exons 2–11 of the ERG gene. Then the mean ERG expression level was assessed together with ERG exons ratio (ex4/ex2). ERG gene expression by itself, unlike ERG ex4/ex2 ratio, was able to identify the less frequent variants of the TMPRSS2-ERG fusion transcripts containing ERG exon 2.

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