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Rearrangements of Viral and Human Genomes at Human Papillomavirus Integration Events and Their Allele-Specific Impacts on Cancer Genome Regulation

We discovered genomic and epigenomic dysregulation originating at sites of human papillomavirus (HPV) integration following the Oxford Nanopore long-read analysis of 72 cervical cancer genomes. The integration events had allele-specific effects on the genome, methylome, and transcriptome, which sometimes resulted in the activation of cancer genes. We also examined the 72 samples using Illumina short-read analysis in phs000528. We also produced long-read cDNA-sequencing data on 29 cervical cancer samples from phs000528 (of which 27 also have long-read WGS data available) for further analysis of HPV-human transcripts derived from HPV integration events.