and Somatic Sniper ([@bb0155]) (Supplementary Table 3). SNVs that were detected by at least three variant calling tools were designated as high confidence SNVs ([@bb0260]) (Supplementary Table 4). SNVs that resulted in missense mutations, nonsense mutations (stop gain) and mutations affecting splice sites are presented in Supplementary Table 5. Indels, defined as small insertion and deletions of up to 300 bps, detected by single reads that were called by Strelka are listed in Supplementary Table 6. Somatic SVs, defined as large deletions, inversions, insertions, translocations detected by anomalous paired-end reads, were called by Genomatix Mapper and BreakDancer (www.genomatix.de). Genes with intergenic breakpoints, inversion and deletions that were called are presented in Supplementary Table 7. Structural variation breakpoints for *ERG*, *LSAMP* and *PTEN* that were detected by whole genome sequencing are tabulated in Supplementary Table 8. A subset of base-pair mutations and rearrangements were validated using Sanger sequencing (Supplementary Fig. 2) in order to assess the specificity of the detection algorithms (primers used are listed in Supplementary Table 1).

2.5. Detection of transcripts from ZBTB20 and LSAMP promoters by 5′ RACE {#s0035}
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mRNA transcripts initiating from *ZBTB20* and *LSAMP* promoters were detected by 5′-rapid amplification of cDNA ends (RACE) ([@bb0095], [@bb0230]) using the SMARTer® RACE 5′/3′ kit (Clontech). In a coupled reaction, 10 ng of total RNA from patients reverse transcribed in the presence SMARTer IIA oligo into first-strand cDNA incorporated with the SMARTer sequence at the 5′ end. The first-strand cDNA is amplified in the presence of the universal primer and gene specific 5′ primers using two cycles of 94 °C for 30 s and 68 °C for 3 min followed by 28 cycles of 94 °C for 30 s, 68 °C for 30 s and 72 °C for 3 min. The absence of distinct bands prompted another round of amp