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. Author manuscript; available in PMC: 2015 Oct 1.
Published in final edited form as: Nat Genet. 2015 Mar 2;47(4):367–372. doi: 10.1038/ng.3221

Table 2.

Donor Middle Acceptor
Samples Chr Position Strand Type Seq Chr Position Strand Breakpoint Genes Verification TERG ID
6_T1, 6_T2 21 39867180 + HOMOLOGY T 21 42877104 + deletion ERG-TMPRSS2 CS & P (6_T1); V (6_T1, 6_T2) A
6_T1, 6_T4 21 39877208 + HOMOLOGY T 21 42871170 + deletion ERG-TMPRSS2 P (6_T1); V (6_T1, 6_T4) B
6_T1, 6_T4 21 39877355 − HOMOLOGY CC 21 42819405 − insertion ERG-MX1 CS & P (6_T1); V (6_T1, 6_T4)
6_T1, 6_T4 21 39877745 + NTS CAT 21 39880855 + deletion ERG-ERG CS & P (6_T1); V (6_T1, 6_T4)
6_T3 20 10441211 − HOMOLOGY G 21 39872887 + translocation C20orf94-ERG CS & P & V (6_T3)
6_T3 20 10441429 + HOMOLOGY GT 21 42868518 − translocation C20orf94-TMPRSS2 CS & P & V (6_T3)
6_T3 21 39872930 + Exact --- 21 42868510 + deletion ERG-TMPRSS2 CS & P & V (6_T3) C
7_T1, 7_T2 1 205613440 + HOMOLOGY C 21 42857784 − translocation _-TMPRSS2 V (7_T1, 7_T2)
7_T1, 7_T2 2 204298424 − HOMOLOGY A 21 42849002 + translocation RAPH1-TMPRSS2 V (7_T1, 7_T2)
7_T1, 7_T2 2 204298476 + Exact --- 19 42797705 + translocation RAPH1-CIC P (7_T1); V (7_T1, 7_T2)
7_T1, 7_T2 10 120084722 − HOMOLOGY TG 21 42842154 + translocation C10orf84-TMPRSS2 CS & P (7_T1); V (7_T1, 7_T2)
7_T1, 7_T2 10 120084747 + HOMOLOGY AC 21 39872234 + translocation C10orf84-ERG CS & P (7_T2); V (7_T1, 7_T2)
7_T1, 7_T2 21 39872152 + HOMOLOGY A 21 42861527 + deletion ERG-TMPRSS2 CS & P (7_T1); V (7_T1, 7_T2) D
7_T1, 7_T2 21 42842403 + Exact --- 21 42848506 − inversion_+ TMPRSS2-TMPRSS2 CS & P (7_T1); V (7_T1, 7_T2)
7_T2 21 39831266 + HOMOLOGY AAAC 21 42875633 + deletion ERG-TMPRSS2 CS & P & V (7_T2) E
7_T3 21 39861568 + NTS TA 21 42865303 + deletion ERG-TMPRSS2 CS & P & V (7_T3) F
7_T4 21 39835734 + HOMOLOGY G 21 42867100 + deletion ERG-TMPRSS2 CS & P & V (7_T4) G
7_T4 21 42841552 − HOMOLOGY GGCT 21 42851963 + inversion_− TMPRSS2-TMPRSS2 CS & P & V (7_T4)
7_T4, 7_T5 21 39868722 + Exact --- 21 42870051 + deletion ERG-TMPRSS2 CS & P (7_T4); V (7_T4, 7_T5) H
8_T1, 8_T2 21 38745261 + HOMOLOGY T 21 42851601 − inversion_+ DYRK1A-TMPRSS2 P (8_T1); V (8_T1, 8_T2)
8_T1, 8_T2 21 38745286 − HOMOLOGY A 21 42859198 − insertion DYRK1A-TMPRSS2 CS & P (8_T1); V (8_T1, 8_T2)
8_T1, 8_T2 21 39831518 + Exact --- 21 42870497 − inversion_+ ERG-TMPRSS2 CS (8_T1); P & V (8_T1, 8_T2) I
8_T1, 8_T2 21 42844460 − HOMOLOGY T 21 42851648 + inversion_− TMPRSS2-TMPRSS2 V (8_T1, 8_T2)
8_T1, 8_T2 21 42863787 − HOMOLOGY G 21 42870663 + inversion_− TMPRSS2-TMPRSS2 CS & P (8_T1); V (8_T1, 8_T2)

Patterns of ERG alterations. Positions and structure of each ERG breakpoints and related rearrangements. The position and structure of the breakpoint was determined, in the majority of cases, by capillary sequencing using custom-designed PCR across the rearrangement breakpoint as previously described30 (“CS” in column “Verification”), and/or by in-silico reconstruction using local de novo assembly in Brass phase 2. Verification by sizing PCR products across the breakpoint using gel electrophoresis was also performed (“P”). All breakpoints were visually verified (“V”) to ensure the presence of discordant reads and checked that they did not occur in repeat regions.