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 |
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