Confirmed fusions in two bladder cancer cell lines. (a) RT-PCR amplifications of confirmed fusions in two bladder cancer cell lines. Marker (M), positive (β-actin) and negative (ddH2O) controls are also shown. Fusion events in red are detected in both cell lines. For fusions that have multiple RT-PCR products, genuine amplicons of a fusion transcript are boxed in yellow. One fusion, SNAP23-LRRC57, reported by deFuse, is further discussed in the text. (b-e) Fusion events that indicate potential chromosomal rearrangements, including potential inversion (b) and intrachromosomal translocations (c-e), are shown. Blue segments are upstream genes, and downstream genes are in orange. Gene symbols are followed with their DNA strands. Exons around the junction sites are drawn with a double slash indicating exons that are not shown. The start positions of upstream genes and end positions of downstream genes are noted with a colon separating chromosomal location and reference genome coordinate. The span-reads and junc-reads from RNA-Seq are shown over and under the junction sequences, respectively. Sanger sequencing of junction sequences are displayed under the junction sites.
Jia et al. Genome Biology 2013 14:R12 doi:10.1186/gb-2013-14-2-r12