Extended Data Figure 3: Copy number alterations in cervical cancer.

a, A log₂-centred heatmap of somatic copy number alterations across 178 core-set cervical tumours. The x axis includes samples that have been ordered based on the cluster assignment. The y axis is based on genomic position, from 1p to Xq. Features associated with copy number clusters are annotated with asterisks; *P < 0.05; **P < 0.01. b, GISTIC2.0 amplification and deletion plots within copy number clusters. Chromosomal locations for peaks of significantly recurrent focal amplifications (red) and deletions (blue) are plotted by −log₁₀ q value for the high (CN High) and low (CN Low) copy number clusters. Peaks are annotated with cytoband and candidate driver genes. The total number of genes in the peak region is indicated in parentheses. Peaks with more than 30 genes in the peak region are excluded. Any genes annotated have a significant positive correlation with mRNA expression. c, Chromosomal locations for peaks of significantly recurrent focal amplifications (red) and deletions (blue) are plotted by −log₁₀ q value for all core set samples. Peaks are annotated with cytoband and candidate driver genes. The total number of genes in the peak region is indicated in parentheses. Peaks consisting of more than 30 genes in the peak region are excluded. Annotated genes have a significant positive correlation with mRNA expression. d, Cytolytic activity (CYT) associations with PD-L1 and/or PD-L2 amplification. Each bar represents a single tumour and the height of that bar represents the z score of the cytolytic activity of that tumour compared to the rest of the cohort. Bars are coloured according to their PD-L1 and/or PD-L2 amplification status and sorted from the highest to the lowest z score.