Fig. 2: Clonality and distribution of HPV16 integration.
From: Intratumor heterogeneity of HPV integration in HPV-associated head and neck cancer
a Circos plot of HPV16 integration breakpoints. The circle shows the positions of 396 integration breakpoints and their CCFs in the HPV16 and human genomes. Breakpoints for which CCFs could not be estimated are assigned a value of 0. The color of the dots indicates the HPV16 gene region where each breakpoint is located. Inside the circle, breakpoints in the HPV16 genome are connected with their corresponding locations in the human genome, with each tumor indicated by a different color. b Pie chart showing the clonality of integration breakpoints (nCCF≥0.1 = 339). Breakpoints for which CCF could not be estimated or with CCF < 0.1 (nCCF<0.1 = 57) were excluded as false positives, and breakpoints with CCF ≥ 0.8 were classified as clonal. BP, breakpoint. c,e Scatter plots of observed vs. expected proportions of integration breakpoints (nCCF≥0.1 = 339) for each HPV16 gene and each human genomic region, with 95% confidence interval (CI) represented by error bars. The expected proportion of breakpoints per HPV16 gene or human genomic region is plotted on the x-axis, assuming that breakpoints are equally distributed across each HPV16 gene or each human genomic region. The observed proportion is plotted on the y-axis. Left and right panels show results restricted to clonal and subclonal breakpoints, respectively. Two-sided binomial tests were performed for each HPV16 gene and each human genomic region. The slope of the dashed line is 1. Observed and expected values, as well as two-sided P-values, are provided in Supplementary Tables 5 and 7. URR upstream regulatory region, NC noncoding region. d Pie chart showing distribution of integration breakpoints (nCCF≥0.1 = 339) in the human genome. UTR untranslated region, CDS coding sequence. Source data are provided as a Source Data file.
