HBV integration–mediated large-scale deletions and chromosomal duplications. (A) Copy number loss at the HBV integration locus on Chr 11 in patient 1. (Left) Copy number (CN) profile of the tumor tissue; (right) CN profile of the paired nontumor tissue. (B) HBV–human chimeric read coverage (IGV) revealing a ∼0.3 Mb deletion mediated by HBV insertion. (C) HBV integration in NAV2, with the deleted region spanning Intron 1–30. (D) Relative NAV2 expression in tumor versus nontumor tissues. (E) CN amplification at the HBV integration site on Chr 1 in patient 2 (CN profiles: tumor vs. nontumor). (F) HBV–human chimeric read coverage. (G) Examples of HBV-mediated chromosomal rearrangements: (1) fragment deletion with head-tail reconnection; (2) chromosomal duplication. (H) Relative expression levels of genes in the Chr 1 HBV integration region.