Fig. 1: Identification and characterization of focal amplifications from whole-genome sequencing data of the GCA cohort.

a Schematic of the experiment design for detecting focal amplifications from WGS data of 36 pairs of GCA tumor and tumor-adjacent normal tissue from a high incidence GCA rate region in the northern region of China. b Detailed characterization of focal amplifications from 36 GCAs, where ecDNA amplicons are further classified into circular (ecDNA), complex, linear, breakage-fusion-bridge (BFB), and invalid. c Genomic annotation of all focal amplifications, where the annotation was defined by overlapping gene regions and regions of focal amplifications. d Distribution of high-frequency oncogene focal amplifications across all 36 samples. e The summary of oncogene focal amplifications co-amplification in our cohort, where co-amplification is defined when two or more than two oncogenes are in the same focal amplifications; f EGFR and CDK6 are located in the same circular focal amplification (ecDNA), where the genome coverage on the left panel represents gene amplification of EGFR and CDK6, and the circular structure on the right panel is the reconstruction of EGFR and CDK6 in the same ecDNA. Source data are provided as a Source Data file for Fig. 1b–f.