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).