Multisite long-read sequencing reveals the early contribution of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis

Somatic structural variations (SVs) represent a critical category of genomic mutations in hepatocellular carcinoma (HCC). However, the accurate identification of somatic SVs using short-read high-throughput sequencing (HTS) is challenging. Here, we applied long-read nanopore sequencing and multisite sampling in a cohort of 42 samples from five patients. We discovered a prominent presence of somatic SVs in adjacent nontumor tissues, which significantly differed from somatic single nucleotide variants (SNVs) and copy number variations (CNVs). The types of SVs were markedly different between adjacent nontumor and tumor tissues, with somatic insertions (INSs) and deletions (DELs) serving as early genomic alterations associated with HCC. Notably, hepatitis B virus (HBV) DNA integration frequently resulted in the generation of somatic SVs, particularly inducing interchromosomal translocations. While HBV DNA integration into the liver genome occurs randomly, multisite shared HBV-induced SVs are implicated as early driving events in the pathogenesis of HCC. Long-read RNA sequencing revealed that some HBV-induced SVs impact cancer-associated genes, with translocations being capable of inducing the formation of fusion genes. These findings enhance our understanding of somatic SVs in HCC and their role in early tumorigenesis.