Table 1_Challenges in the detection and assembly of virus integration structures in human genomes.xlsx

Long-read sequencing technologies offer new opportunities to reconstruct these intricate integration structures, but the performance of existing assembly strategies remains incompletely evaluated. In this study, we systematically review sequencing platforms and their application for detecting structural variants and evaluate long-read assembly tools for reconstructing HPV integration structures. Using three synthetic Oxford Nanopore DNA sequencing datasets representing different levels of integration complexity together with the UMSCC47 cell line as an authentic long-read sequencing dataset, we assess whether structural-variant detection methods and genome assembly can accurately identify complex integration structures, particularly under conditions of high copy number and structural rearrangement.

Our results provide practical guidance for selecting sequencing technologies and computational approaches for viral integration detection and structural resolution, enabling a more comprehensive understanding of virus-driven genome remodeling in cancer.</p>