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Figure 4 | BMC Medical Genomics

Figure 4

From: Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines

Figure 4

Expression profile of WWC1 and ADRBK2. We studied the gene expression profiles of WWC1 and ADRBK2: (A) Expression plot of WWC1 exons as measured by the log2 fold change (FC) between the RPKM values of each exon in HCC3153 versus the average of all other WWC1-ADRBK2-negative samples. The predicted gene fusion junction is marked by an arrow. It can be seen that exons downstream of exon 19 in WWC1 is underrepresented in HCC3153. (B) Similarly, the same can be observed in the exons upstream of exon 10 in ADRBK2. Moreover, the 3' end of the gene appears to be overexpressed. (C) Two sets of primers were designed to test for expression. The first set, F1 and R1, spanned exons 9 and 10 of ADRBK2 to test for wild-type expression. Similarly, the second set, F2 and R2, spanned exons 19 and 20 of WWC1. Both sets were also combined to test for expression of predicted WWC1-ADRBK2 fusion. The expected fragment sizes are shown in brackets. (D) Exon-exon RT-PCR results: a normal control was tested for the wild-type expression of ADRBK2 by F1/R1 (lane 1), the wild-type expression of WWC1 by F2/R2 (2), and with both sets together (3). In lane 4, both primer sets were applied on HCC3153 and confirmed expression of the expected fusion fragment but no wild-type expression.

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