Table 2

Seventy-six candidate fusions reported by TopHat-Fusion in four breast cancer cell lines

SAMPLE ID

Fusion genes (left-right)

Chromosomes (left-right)

5' position

3' position

Spanning reads

Spanning pairs


BT474

TRPC4AP-MRPL45

20-17

33665850

36476499

2

9

BT474

TOB1-SYNRG

17-17

48943418

35880750

26

47

SKBR3

TATDN1-GSDMB

8-17

125551264

38066175

311

555

BT474

THRA-SKAP1

17-17

38243102

46384689

28

46

MCF7

BCAS4-BCAS3

20-17

49411707

59445685

105

284

BT474

ACACA-STAC2

17-17

35479452

37374425

57

59

BT474

STX16-RAE1

20-20

57227142

55929087

6

24

BT474

MED1-ACSF2

17-17

37595419

48548386

10

12

MCF7

ENSG00000254868-FOXA1

14-14

38184710

38061534

2

22

SKBR3

ANKHD1-PCDH1

5-5

139825557

141234002

4

15

BT474

ZMYND8-CEP250

20-20

45852972

34078459

10

53

BT474

AHCTF1-NAAA

1-4

247094879

76846963

10

42

SKBR3

SUMF1-LRRFIP2

3-3

4418012

37170638

3

12

KPL4

BSG-NFIX

19-19

580779

13135832

12

27

BT474

VAPB-IKZF3

20-17

56964574

37922743

4

14

BT474

DLG2-HFM1

11-1

85195025

91853144

2

10

SKBR3

CSE1L-ENSG00000236127

20-20

47688988

47956855

13

31

MCF7

RSBN1-AP4B1

1-1

114354329

114442495

6

7

BT474

MED13-BCAS3

17-17

60129899

59469335

3

14

MCF7

ARFGEF2-SULF2

20-20

47538545

46365686

17

20

BT474

HFM1-ENSG00000225630

1-1

91853144

565937

2

43

KPL4

MUC20-ENSG00000249796

3-3

195456606

195352198

13

46

KPL4

MUC20-ENSG00000236833

3-3

195456612

197391649

8

15

MCF7

RPS6KB1-TMEM49

17-17

57992061

57917126

4

3

SKBR3

WDR67-ZNF704

8-8

124096577

81733851

3

3

BT474

CPNE1-PI3

20-20

34243123

43804501

2

6

BT474

ENSG00000229344-RYR2

1-1

568361

237766339

1

19

BT474

LAMP1-MCF2L

13-13

113951808

113718616

2

6

MCF7

SULF2-ZNF217

20-20

46415146

52210647

11

32

BT474

WBSCR17-FBXL20

7-17

70958325

37557612

2

8

MCF7

ENSG00000224738-TMEM49

17-17

57184949

57915653

5

6

MCF7

ANKRD30BL-RPS23

2-5

133012791

81574161

2

6

BT474

ENSG00000251948-SLCO5A1

19-8

24184149

70602608

2

6

BT474

GLB1-CMTM7

3-3

33055545

32483333

2

6

KPL4

EEF1DP3-FRY

13-13

32520314

32652967

2

4

MCF7

PAPOLA-AK7

14-14

96968936

96904171

3

3

BT474

ZNF185-GABRA3

X-X

152114004

151468336

2

3

KPL4

PPP1R12A-SEPT10

12-2

80211173

110343414

3

8

BT474

SKA2-MYO19

17-17

57232490

34863349

5

12

MCF7

LRP1B-PLXDC1

2-17

142237963

37265642

2

5

BT474

NDUFB8-TUBD1

10-17

102289117

57962592

1

49

BT474

ENSG00000225630-NOTCH2NL

1-1

565870

145277319

1

18

SKBR3

CYTH1-EIF3H

17-8

76778283

117768257

18

37

BT474

PSMD3-ENSG00000237973

17-1

38151673

566925

1

12

BT474

STARD3-DOK5

17-20

37793479

53259992

2

10

BT474

DIDO1-TTI1

20-20

61569147

36634798

1

10

BT474

RAB22A-MYO9B

20-19

56886176

17256205

8

20

KPL4

PCBD2-ENSG00000240967

5-5

134259840

99382129

1

32

SKBR3

RARA-PKIA

17-8

38465535

79510590

1

5

BT474

MED1-STXBP4

17-17

37607288

53218672

13

11

KPL4

C1orf151-ENSG00000224237

1-3

19923605

27256479

1

5

SKBR3

RNF6-FOXO1

13-13

26795971

41192773

2

13

SKBR3

BAT1-ENSG00000254406

6-11

31499072

119692419

2

30

BT474

KIAA0825-PCBD2

5-5

93904985

134259811

1

19

SKBR3

PCBD2-ANKRD30BL

5-2

134263179

133012790

1

5

BT474

ENSG00000225630-MTRNR2L8

1-11

565457

10530147

1

35

BT474

PCBD2-ENSG00000251948

5-19

134260431

24184146

2

6

BT474

ANKRD30BL-ENSG00000237973

2-1

133012085

567103

2

8

KPL4

ENSG00000225972-HSP90AB1

1-6

564639

44220780

1

7

BT474

MTIF2-ENSG00000228826

2-1

55470625

121244943

1

11

BT474

ENSG00000224905-PCBD2

21-5

15457432

134263223

2

7

BT474

RPS6KB1-SNF8

17-17

57970686

47021335

48

57

BT474

MTRNR2L8-PCBD2

11-5

10530146

134263156

1

6

BT474

RPL23-ENSG00000225630

17-1

37009355

565697

3

19

BT474

MTRNR2L2-PCBD2

5-5

79946288

134259832

1

5

SKBR3

ENSG00000240409-PCBD2

1-5

569005

134260124

2

4

SKBR3

PCBD2-ENSG00000239776

5-12

134263289

127650986

2

3

BT474

ENSG00000239776-MTRNR2L2

12-5

127650981

79946277

2

3

BT474

JAK2-TCF3

9-19

5112849

1610500

1

46

KPL4

NOTCH1-NUP214

9-9

139438475

134062675

3

5

BT474

MTRNR2L8-TRBV25OR92

11-9

10530594

33657801

4

4

BT474

MTRNR2L8-AKAP6

11-14

10530179

32953468

1

5

BT474

ENSG00000230916-PCBD2

X-5

125606246

134263219

1

5

MCF7

ENSG00000226505-MRPL36

2-5

70329650

1799907

5

20

SKBR3

CCDC85C-SETD3

14-14

100002351

99880270

5

6

BT474

RPL23-ENSG00000230406

17-2

37009955

222457168

109

5


The 76 candidate fusion genes found by TopHat-Fusion in four breast cancer cell lines (BT474, SKBR3, KPL4, MCF7), with previously reported fusions [12] shown in boldface. The remaining 51 fusion genes are novel. The fusions are sorted by the scoring scheme described in Materials and methods.

Kim and Salzberg Genome Biology 2011 12:R72   doi:10.1186/gb-2011-12-8-r72

Open Data