Illustrating the EGFR exon 8 ITD event along with the reinterpretation of a sequence mutation.
Sample View of TCGA-06-0211-01A, focusing on the region around exon 8. This tumor has a SV leading to exon 8 ITD detected by CICERO from RNA-seq (magenta box). Pipeline analysis also identified a somatic SNV at exon 7 which is annotated to be Q276* nonsense mutation by VEP. The "nonsense" mutation is also cataloged in COSMIC under COSV51804002.
Exon 7 read alignment of WGS BAM from this tumor. The SNV only appears on reads with the soft-clips of tandem duplication SV, indicating the SNV and SV are one mutation event.