Extended Data Fig. 2: VAF scatterplots of SNV and indels, and patterns of CNVs of matched tumour and tumour-free SVZ tissue.
From: Human glioblastoma arises from subventricular zone cells with low-level driver mutations
a–c, Scatterplots from seven patients with IDH-wild-type GBM with tumour-free SVZ (a), meningioma with tumour-free SVZ (b), anaplastic oligodendroglioma, and IDH-mutant with tumour-free SVZ (c). Shared and private somatic mutations in paired SVZ and tumour (x and y axes, respectively) tissue specimens are indicated as a function of the VAF. A single point represents an individual mutation. Red dots indicate cancer-driver mutations (see Methods). d, Quantitative analysis of CNVs in EGFR in patients with IDH-wild-type GBM who harboured driver mutations thereof in tumour-free SVZ. The bar graph shows relative fold changes in EGFR copy numbers in patients GBM26, GBM187, GBM245, GBM276, GBM499 and GBM520 (relative to the matched normal control) based on qPCR. e, Genome-wide CNV plots for patients with IDH-wild-type GBM and matching tumour-free SVZs harbouring shared mutations in WES. Red and blue boxes indicate shared and tumour-private CNVs between tumour-free SVZ and tumour, respectively. f, Genome-wide CNV plots for a patient with IDH-wild-type GBM and a GBM-invaded SVZ. g, EGFR amplification was found at the cellular level through FISH of the tumour-free SVZ specimen from one patient (GBM520). FISH was performed in patients GBM26, GBM276, GBM499 and GBM520. EGFR and control probes were red and green, respectively. Scale bars, 10 µm.
