Analysis of HBV DNA integration events in hepatocellular carcinoma cell lines by high throughput targeted capture sequencing

Objective To investigate the integration characteristics of hepatitis B virus (HBV) viral DNA in the host genome of hepatocellular carcinoma HepG2.2.15 cells and HepG2-derived cell line HepAD38 by probe-based capture and high-throughput sequencing technology. Methods After the genomic DNA of HepG2.2.15 and HepAD38 cells were extracted, probe-based capture technique was used to capture the integrated DNA fragments of HBV DNA in the obtained genomic sequences, and the intergrated fragments were further studied with high-throughput sequencing technology. The bioinformatics software such as Trimmatic, BBAP, and BWA (Burrows-Wheeler Aligner) were empolyed for data analysis. Finally, the characteristics of integrated DNA were validated through PCR and cloning and sequencing. Results The probe-based capture and high-throughput sequencing technology detected 12 and 7 integrated DNA fragments in HepG2.2.15 and HepAD38 cells, respectively. These integration events were randomly distributed on chromosomes chr1, chr2, chr7, chr9, chr16, chr17, chr19, and chrX. DPP7, TRIM56 and GPC3 appeared with higher frequencies at the upstream and downstream of the integration sites. Conclusion We successfully establish a method to detect and analyze the integrated DNA fragments of HBV DNA in host genome based on probe-based capture and high-throughput sequencing technology. HBV integration events occur randomly on the chromosomes in HepG2.2.15 and HepAD38 cells, and most of integration sites are in the X gene region of the HBV genome.