Fig. 6

Heterogeneity of focal amplification in renal cancer tissue. a Sequencing reads depth and RNA expression level in typical focal amplification regions of a renal cancer tissue sample. The y-axis represents the reads count that was normalized based on the total number of reads mapped per sample. b Circos plots of the chromatin interactions mediated by focal amplification regions across all 23 chromosomes in renal cancer tissue. c Circos plots of the split reads mediated by focal amplification regions across all 23 chromosomes. The split reads aligned to the PD-L1 amplified region are marked with red lines. d Chromatin contact matrix between the amplified regions of chr1, chr9, and chr12, and sequencing reads depth within these amplified regions. e Coamplification network of amplified oncogenes in the renal cancer tissue sample. Different amplified oncogenes are assembled by split reads. The thickness of the line indicates the chromatin contact strength