Fig. 2

Circos plot of the gene-level copy number alteration. Top: Gene-level CNA events (pre-NAC) that were different between the ERC and NRC group with a p-value of less than 0.05 are shown. Cytoband regions that were observed to be over-represented with genomic alterations are labeled, including 17q25, 1q24-24, and 4p15.2-.32. The -log10 p values from the Fisher’s test of the copy gains are presented in the outer track (blue), and the -log10 p values of the Fisher’s test of copy losses are shown in the inner circle (deep red). Gains on chr1q and chr17q were observed in 3 out of 4 recurrent patient tumors. Bottom panels showed two regions (chr17q on the left and chr1q on the right) with copy gains (dark red, top) that were observed only among the ERC group but not in the NRC. Across these two regions, we also observed consistent higher gene expression, presented as logFC for ERC vs NRC (dark blue, bottom)