Table 5

CRAC and TopHat-fusion predictions for the set of validated chimeric junctions from breast cancer libraries

Library

Fused genes

Chromosomes

5' position

5' strand

3' position

3' strand

Average supporta

CRACb

TopHat-fusionc


BT-474

SNF8-RPS6KB1

17-17

47,021,337

1

57,970,686

-1

36

Yes

Yes

BT-474

CMTM7-GLB1

3-3

32,483,329

-1

33,055,545

1

2

Yes

Yes

BT-474

SKA2-MYO19

17-17

57,232,490

-1

34,863,351

-1

6

Yes

Yes

BT-474

ZMYND8-CEP250

20-20

45,852,968

-1

34,078,459

1

9

Yes

Yes

BT-474

VAPB-IKZF3

20-17

56,964,572

1

37,934,021

-1

6

Yes

Yes

BT-474

ACACA-STAC2

17-17

35,479,452

-1

37,374,427

-1

46

Yes

Yes

BT-474

DIDO1-TTI1

20-20

61569147

-1

36,634,800

-1

2

Yes

Yes

BT-474

RAB22A-MYO9B

20-19

56,886,178

1

17,256,205

1

9

Yes

Yes

BT-474

MCF2L-LAMP1

13-13

11,371,8616

-1

113,951,811

-1

2

Yes

No

KPL-4

NOTCH1-NUP214

9-9

139,438,475

-1

134,062,675

1

2

Yes

Yes

KPL-4

BSG-NFIX

19-19

580,782

1

13,135,832

1

9

Yes

Yes

MCF-7

RPS6KB1-TMEM49

17-17

57,992,064

1

57,917,126

1

5

Yes

Yes

MCF-7

ARFGEF2-SULF2

20-20

47,538,548

1

46,365,686

-1

10

Yes

Yes

SK-BR-3

PKIA-RARA

8-17

79,485,042

-1

38,465,537

-1

7

Yes

Yes

SK-BR-3

TATDN1-GSDMB

8-17

125,551,264

-1

38,066,177

-1

334

Yes

Yes

SK-BR-3

KCNB1-CSE1L

20-20

47,956,856

-1

47,688,990

-1

6

Yes

No

SK-BR-3

CYTH1-EIF3H

17-8

76,778,283

-1

117,768,258

-1

11

Yes

Yes

SK-BR-3

SUMF1-LRRFIP2

3-3

4,418,012

-1

37,170,640

-1

4

Yes

Yes

SK-BR-3

SETD3-CCDC85C

14-14

99,880,273

1

100,002,353

1

3

Yes

No

SK-BR-3

PCDH1-ANKHD1

5-5

141,234,002

1

139,825,559

-1

2

Yes

Yes

BT-474

CPNE1-P13

20-20

34,243,123

NA

43,804,501

NA

1

No

Yes

BT-474

STARD3-DOK5

17-17

37,793,479

NA

53,259,992

NA

1

No

Yes

SK-BR-3

WDR67-ZNF704

8-8

124,096,577

NA

81,733,851

NA

1

No

Yes

MCF-7

BCAS4-BCAS3

20-17

49,411,707

NA

59,445,685

NA

3

No

Yes

KPL-4

PPP1R12A-SEPT10

12-2

80,211,173

NA

11,034,3414

NA

1

No

No

SK-BR-3

DHX35-ITCH

20-20

Unknown

NA

Unknown

NA

NA

No

No

SK-BR-3

NFS1-PREX1

20-20

Unknown

NA

Unknown

NA

NA

No

No


NA: not applicable

a Average support value over the junction k-mers

b Detected by CRAC

c Detected by TopHat-fusion

CRAC and TopHat-fusion predictions on the set of validated chimeric junctions from four breast cancer libraries [27]. The first 20 cases were found by CRAC, and the 7 remaining ones were not predicted by CRAC; however, for the final 2, we could not detect any read matching the 15 to 20 nt over the junction. A short read length penalizes CRAC: indeed, with k = 22, only the 6 (= 50 - 2 × 22) middle positions of a read could be used to locate any event (splices or mutations) exactly. Hence we expect that the spanning reads by which a chRNA is amenable to detection by CRAC to be rare. NA: not applicable. Columns: library, fused genes ID, annotation of the junction points, chromosomes, 5' position and strand, 3' position and strand, average support value over the junction k-mers, detection by CRAC and by TopHat-fusion (THF).

Philippe et al. Genome Biology 2013 14:R30   doi:10.1186/gb-2013-14-3-r30

Open Data