Genomic instability at the viral integration site near the caspase locus. (A) DNA-seq coverage and transcription around a chr11q22 HBV integration site in patient 31656. (Top panel) Normalized, GC-corrected DNA-seq coverage values in 50-kb windows, with the horizontal red line representing the resulting copy-number segments. There is a copy-number breakpoint right at the HBV integration site, with a copy-number loss of the chromosomal region 3′ from the integration site. Red and blue bar plots show transcription (RNA-seq read coverage) in this locus in the tumor and matched normal, respectively. (B) Genes closest to the integration site within this deletion were significantly down-regulated, including CASP12, CASP4, CASP5, CASP1, CARD16, and CARD17.