Extended Data Figure 8: Fine structure analysis of EGFRvIII amplification in extrachromosomal or chromosomal DNA in GBM39 cells.
From: Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity
a, FISH images showed the EGFR gene on ecDNA (top) and HSRs (bottom) in different passages of the GBM39 cell line. Analysis of the HSR FISH images shows evidence of multiple integration sites on different chromosomes. b, Next-generation sequencing of DNA from 4 independent cultures of GBM39 was used to analyse the fine structure of amplifications (Supplementary Information 4.3). In 3 biological replicates (rows 1–3) of these cultures, EGFRvIII was exclusively on ecDNA, whereas one of the later passage cultures (row 4) was found to contain EGFRvIII entirely on HSRs, with no detectable ecDNA. The DNA derived from different ecDNA cultures shows identical structure with some heterogeneity (P < 2.18 × 10−8 for all pairs), suggesting common origin. However, DNA derived from HSRs show a conserved structure that is identical to the ecDNA structure (P < 1.98 × 10−5, Supplementary Information 2.4), possibly with tandem duplications. c, A possible progression of normal genome to cancer genome with EGFRvIII ecDNA and amplification to a copy count of around 100 copies. The EGFRvIII ecDNA elements possibly aggregate into tandem duplications and reintegrate into multiple chromosomes as HSRs, so that 5–6 HSRs accommodate around 100 copies of EGFRvIII.
