Table 1

Verified expressed gene fusions in the breast cancer cell line ZR-75-30 predicted from structural analysis
5’ gene 3’ gene Chromosomes involveda Expression In framee Fusion (F) or Runthrough fusion (R)
5’ 3’
APPBP2 PHF20L1 17 8 yes yes F
COL14A1 SKAP1 8 17 yes yes F
TAOK1 PCGF2 17 17 yes b,d yes F
USP32 CCDC49 17 17 yes d no F
BCAS3 HOXB9 17 17 yes d see text F
TRPS1 LASP1 8 17 yes yes R
ERBB2 BCAS3 17 17 yes c no R
DDX5 DEPDC 17 8 yes c yes R
PLEC1 ENPP2 8 8 yes c yes F
TIAM1 NRIP1 21 21 yes b yes F
ZMYM4 OPRD1 1 1 yes no F
TIMM23 ARHGAP32 10 11 yes no R
TMEM74 APPBP2 8 17 no F
TRAPPC9 STARD3 8 17 no F
SSH2 PLXDC1 17 17 no F
TAOK1 CA10 17 17 no F
HYLS1 TIMM23 11 10 no b F
USP32 RALYL 17 8 no F
TMEM74 ACACA 8 17 no F
NUDCD1 TAC4 8 17 no R
TRAPPC9 HOXB6 8 17 no R
SSH2 NFE2L1 17 17 no R
TTC35 MKS1 8 17 no R
TMEM71 CRYBA1 8 17 no R
CA3 KIAA1429 8 8 no R
GRHL2 NUDCD1 8 8 no R
SUPT6H GPIHBP1 8 17 no R
PGAP3 NOV 8 17 no R
KIAA0100 LY6H 8 17 no R
TG ERBB2 8 17 no R

All genomic junctions tested were positive by PCR; those marked c were not tested.

a Precise chromosomal positions are given in Additional file 2 and Additional file 5 and the exon structure in Figure 2.

b 5’ gene is untranslated sequence only.

c Fusions not predicted by our analysis but detected by transcriptome sequencing by Robinson et al. (2011) and confirmed here by RT-PCR. Genomic breakpoints were detected in the present dataset on additional inspection—they had not met our stringent criteria or were complex rearrangements.

d Fusions also reported by Robinson et al. (2011).

e Predicted from annotations; not experimentally verified.

Schulte et al.

Schulte et al. BMC Genomics 2012 13:719   doi:10.1186/1471-2164-13-719

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