Fig. 3

Features of breakpoints associated with SMARCB1 structural variants. a Schematic depicting the sites of DNA breaks corresponding to SMARCB1 translocations. The two DNA break hotspots in the SMARCB1 gene are as indicated. b Heatmap depicting the SMARCB1 alteration identified in each allele, the genomic features associated with each SMARCB1-related breakpoint, and the impact of these alterations on the creation of fusion transcripts. Top: the type of SMARCB1 alteration identified in each allele. Middle: genomic features associated with each SMARCB1-associated breakpoints. Whether the breakpoint localizes to a genic/intergenic region, whether or not the breakpoint is transcribed, the type of repeat element which overlaps with the breakpoint, whether the pair of breakpoints occurs on a pair of homologous genes, and the number of base-pairs of microhomology sequence detected at the site of DNA fusion are as indicated. Bottom: the impact of SMARCB1-associated deletions and translocations on the occurrence of fusion transcripts