Table 1

Identified and validated fusion gene candidates

Sample

5' gene

5' chromosome

3' gene

3' chromosome

Number of paired-end reads

Number of junction reads

In frame

Amplified

Genetic rearrangement validated


BT-474

ACACA

17

STAC2

17

57

72

Yes

Yes

Yes

BT-474

RPS6KB1

17

SNF8

17

43

68

Yes

Yes

Yes

BT-474

VAPB

20

IKZF3

17

41

26

Yes

Yes

Yes

BT-474

ZMYND8

20

CEP250

20

35

14

No

Yes

Yes

BT-474

RAB22A

20

MYO9B

19

9

12

No

Yes

Yes

BT-474

SKA2

17

MYO19

17

8

7

Yes

Yes

Yes

BT-474

DIDO1

20

KIAA0406

20

8

1

Yes

No

BT-474

STARD3

17

DOK5

20

4

6

Yes

Yes

Yes

BT-474

LAMP1

13

MCF2L

13

5

3

No

No

Yes

BT-474

GLB1

3

CMTM7

3

6

2

Yes

No

Yes

BT-474

CPNE1

20

PI3

20

4

2

No

Yes

Yes

SK-BR-3

TATDN1

8

GSDMB

17

28

447

Yes

Yes

Yes

SK-BR-3

CSE1L

20

ENSG00000236127

20

10

20

Yes

Yes

SK-BR-3

RARA

17

PKIA

8

13

10

Yes

Yes

Yes

SK-BR-3

ANKHD1

5

PCDH1

5

12

6

Yes

No

Yes

SK-BR-3

CCDC85C

14

SETD3

14

6

6

Yes

No

Yes

SK-BR-3

SUMF1

3

LRRFIP2

3

14

5

Yes

No

SK-BR-3

WDR67

8

ZNF704

8

3

3

Yes

Yes

Yes

SK-BR-3

CYTH1

17

EIF3H

8

38

2

Yes

Yes

Yes

SK-BR-3

DHX35

20

ITCH

20

3

2

Yes

No

Yes

SK-BR-3

NFS1

20

PREX1

20

5

9

Yes

Yes

KPL-4

BSG

19

NFIX

19

22

14

Yes

No

Yes

KPL-4

PPP1R12A

12

SEPT10

2

2

6

Yes

No

Yes

KPL-4

NOTCH1

9

NUP214

9

4

6

Yes

No

Yes

MCF-7

BCAS4

20

BCAS3

17

133

142

Yes

Yes

Previously reported

MCF-7

ARFGEF2

20

SULF2

20

17

25

Yes

Yes

Previously reported

MCF-7

RPS6KB1

17

TMEM49

17

2

7

Yes

Yes

Previously reported


A total of 24 novel fusion genes were identified in BT-474, SK-BR-3 and KPL-4. Three fusion genes detected in MCF-7 have been reported before and served as positive controls in our study. Two paired-end reads and two fusion junction spanning short reads were required for selecting a fusion candidate for further validation. In-frame prediction, copy number amplification (at least one of the fusion partner genes) and validation of the genomic rearrangement are indicated. Lower level copy number gains were excluded.

Edgren et al. Genome Biology 2011 12:R6   doi:10.1186/gb-2011-12-1-r6

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