Table 1 |
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|
Identified and validated fusion gene candidates |
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|
Sample |
5' gene |
5' chromosome |
3' gene |
3' chromosome |
Number of paired-end reads |
Number of junction reads |
In frame |
Amplified |
Genetic rearrangement validated |
|
|
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|
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 |
|
|
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|
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. |
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|
Edgren et al. Genome Biology 2011 12:R6 doi:10.1186/gb-2011-12-1-r6 |
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