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Table 2 Genes disrupted by sequence validated somatic rearrangements discovered in breast cancers

From: Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing

  Sample ID Chr 1 Breakpoint 1 Chr 2 Breakpoint 2 Disrupted genes
       (affected regions/breakpoint locations)
Deletion 153 T 11 106618805   106622567 GUCY1A2 (exon 7)
  154 T 8 72214170   72217978 EYA1 (intron 7–8)
  119 T 5 134715922   134720809 H2AFY (intron 2–3)
  149 T 2 12526265   12528008  
  149 T 2 65366656   65369602  
  149 T 10 22889925   22892366 PIP4K2A (intron 3–4)
  149 T 15 45915722   45917969  
  152 T 12 2130488   2133385  
Inversion 120 T 2 120331908   120335057 PCDP1 (intron 6–7)
  116 T 5 129549038   129552347  
  149 T 10 24436405   24438757 KIAA1217 (intron 2–3)
  153 T 2 172893909   175831452 METAP1D (intron 1–2), CHN1 (intron 1–2)
  116 T 3 168893755   170864487 MECOM (intron 2–3), TNIK (intron 12–13)
  151 T 5 137738030   137744577 KDM3B (intron 11–12)
Translocation 153 T 2 42052398 4 66411362 EPHA5 (intron 3–4)
  153 T 6 104501617 X 152223450  
  153 T 7 54909974 19 29832131  
  153 T 8 57916723 19 30951050 ZNF536 (intron 2–3)
  153 T 12 48517177 19 30945107 PFKM (intron 3–4), ZNF536 (intron 2–3)
  153 T 19 30355201 X 153152399 LCA10 (intron 5–6)
  153 T 5 174245601 10 65204015 JMJD1C (intron 1–2)
  116 T 2 199768975 5 28258969  
  118 T 7 90081994 17 25904801 KSR1 (intron 3–4)
  118 T 15 60231305 21 47148999 PCBP3 (intron 1–2)
  118 T 15 60833617 21 35917066 RCAN1 (intron 1–2), RORA (intron 2–3)
  118 T 15 61356378 21 41870300 DSCAM (intron 3–4), RORA (intron 1–2)
  118 T 15 61375512 21 27982153 RORA (intron 1–2)
  118 T 15 71750638 21 18023846 THSD4 (intron 6–7)
  119 T 2 42052196 4 66411644 EPHA5 (intron 3–4)
  119 T 4 4714578 17 38990874 TMEM99 (exon 3)
  119 T 8 32833459 18 64563574  
  120 T 8 127068558 11 112588800  
  120 T 11 108583473 13 21735983 DDX10 (intron 10–11), SKA3 (exon 5)
  120 T 13 103233303 16 77586406  
  148 T 2 65563071 8 80378299 SPRED2 (intron 2–3)
  148 T 9 13526912 17 57745082 CLTC (intron 13–14)
  149 T 1 247997045 10 27944748  
  149 T 3 47806974 4 151298580 LRBA (intron 48–49), SMARCC1 (intron 2–3)
  149 T 5 15946143 17 67928932  
  149 T 11 108583658 13 21742368 DDX10 (intron 10–11), SKA3 (exon 4)
  1. Chr 1, the lower numbered chromosome in a rearrangement; Breakpoint 1, the breakpoint position on Chr 1 determined by Sanger sequencing; Chr 2, the other chromosome in a rearrangement; Breakpoint 2, the breakpoint position on Chr 2. Chromosome coordinates are based on human genome build HG19.