Fig. 2

Distribution of CNVs in our cohort. A Comparison of CNVs between the HPV-positive group and HPV-negative group. P = 0.840 is determined by the Mann–Whitney U test in copy number amplifications and P = 0.824 in copy number deletions. B Focal-level somatic CNV events. Red and blue denoted amplification and deletion, respectively. Chromosomal locations of peaks of significantly recurring focal amplification and deletion are filtered by FDRs. Peaks are annotated with amplification of candidate oncogenes or deletion of TSGs by cytoband (1q23.3(FCGR2B), 11q13.3(CCND1), 1q21.2(ARNT/JAK1), 5q13.2(MAP3K1/PIK3R1), 5q35.3(RAD17/APC), 6q16.3(CCNC), 11q22.3(ZBTB16/SDHD), 12p13.2(ETV6), and 13q21.1(RB1)). Heatmap of the CNAs of 10 HPV-positive samples (top) and 49 HPV-negative samples (bottom) in units of log2 (tumor/adjacent non-tumor) along the chromosomes. C, D Venn diagrams showing comparisons of recurrent peaks between the HPV-positive group and HPV-negative group