Validation of somatic structural breakpoints by PCR (images were inverted for better presentation). (A) Agarose gel of PCR products amplified from genomic DNA, targeting breakpoints detected by SMASH in NPC-5989. Because the breakpoints are somatic, specific PCR bands only occur in the tumor sample (pointed out by red arrows). (T) tumor sample; (N) matched normal sample from blood; (W) no-DNA control; (L) 1 kb plus ladder. (B) Agarose gel of PCR products amplified by RT-PCR on tumor RNA corresponding to somatic gene fusions in NPC-5989 and NPC-5421. RT primers were ∼200 bp downstream from the fusion points. PCR primers were within 150 bp upstream of and downstream from the fusion points to specifically amplify across it. (T) tumor; (C) control sample (different tumor); (L) 1 kb plus ladder. Specific products within the expected size range are pointed out by red arrows.
