Fig. 2: RB1 disruption by multiple mechanisms.

a Schematic summary of RB1 disruption events observed in each sample (column) by different methods (row). The rightmost sample is PSCCE_33T, the only tumor positive for Rb, yet not evaluated by RNA-seq. b (From top to bottom) Schematic plot of exon deletions, Sanger sequencing validation of exon deletion breakpoints, sashimi plot of subsequent splicing abnormalities in RB1 mRNA and Rb IHC of three representative tumors. Schematic summary of disrupting mechanism is shown on the right. Black rectangles represent RB1 exons and gray dashed line represent deleted genomic regions. Green, red, blue, and black peaks in Sanger sequencing chromatograms represent bases A, T, C, and G, respectively. Genomic coordinates are in hg19 assembly. Curves in sashimi plot represent reads spanning exon junction with numbers of reads denoted. Abnormal exon junctions are plotted in red. Rb IHC of matched normal sample is provided as control. Scale bar: 50 μm. c Schematic plot and Sanger sequencing validation of exon deletions (left), sashimi plot and validation of abnormal mRNA exon junctions (middle) and Rb IHC staining (right) of PSCCE_10T. Two alleles of RB1 are plotted separately to show different ranges of exon deletions. Exons of ITM2B are plotted in green. Sanger sequencing chromatograms and sashimi plots are plotted in the same way described above. Scale bar: 50 μm.