Skip to main content

Table 1 Identified and validated fusion gene candidates

From: Identification of fusion genes in breast cancer by paired-end RNA-sequencing

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
  1. 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.