Fig. 2
Integrative analysis of structural variation. a Multi-platform, multi-analysis approach for detecting SV by three-platform sequencing. SV detection is run using RNA-Seq and WES of the tumor sample, and integrated SV and CNA detection are run using WGS of the tumor and normal samples. b, c An example of linking three fusion transcripts of DIP2C-PDGFRA detected in RNA-Seq to DNA SVs detected in WGS in a high-grade glioma. The fusion transcripts are shown in protein view (b) with the domains marked in color and the vertical dotted lines marking the boundaries of each exon with chimeric RNA read counts indicated above the PDGFRA ideogram and wildtype exon 9–10 read counts below. The fusion transcript involving PDGFRA exon 10—marked by the gray line in the PDGFRA protein view (b)—is linked to a novel DNA SV involving chromosome 4, 11 and 10, shown using the gray line in (c), while the other two fusion transcripts, marked by the purple lines in (b), are linked to the same DNA SV involving chromosome 4 and 10, shown using the purple line in (c)
