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) |