Genomic structure, validation and functional significance of VAPB-IKZF3. (a) Exonic expression of VAPB-IKZF3 is indicated by sequencing coverage (red). Copy number changes measured by array comparative genomic hybridization (aCGH; black dots) in reference to normal copy number (horizontal grey line) and fusion break points (vertical grey line) are indicated. Gene structures are shown below the aCGH data. Arrows below gene structures indicate which strand the genes lie on. Fusion transcript structure is pictured below wild-type (wt) gene structures. (b) Interphase FISH showing amplification of VAPB and IKZF3 and the VAPB-IKZF3 fusion in BT-474. White arrows indicate gene fusions. (c) Expression of the 5' and 3' partner genes and the fusion gene. RPKM denotes reads per kilobase per million sequenced short reads. (d) Quantitative RT-PCR validation of small interfering RNA (siRNA) knock-down efficiency of cells transfected either with a scramble siRNA or with gene-specific siRNAs. Error bars show standard deviation. (e) CTG cell viability analysis of cells transfected either with a scramble siRNA or with gene-specific siRNAs. Asterisks indicate the statistical significance of growth reduction: ***P < 0.001. Error bars show standard deviation.
Edgren et al. Genome Biology 2011 12:R6 doi:10.1186/gb-2011-12-1-r6