A persistent infection with HPV high-risk genotypes is recognised as a necessary cause of cancer development 4. Human papillomavirus (HPV) is the main cause of cervical cancer 1, one of the most common cancers in women worldwide, causing more than 200,000 deaths each year 2, 3. Efficient identification of both HPV variability and integration sites will be important for the study of HPV evolution and adaptability and may be an important tool for use in cervical cancer diagnostics. Comprehensive studies on HPV intra-host variability generated during a persistent infection will improve our understanding of viral carcinogenesis. In contrast to other approaches, TaME-seq proved to be highly efficient in HPV target enrichment, leading to reduced sequencing costs. HPV genomic variability was observed in all samples allowing identification of low frequency variants. Chromosomal integration breakpoints and large deletions were identified in HPV positive cell lines and in one clinical sample. Our results showed deep HPV genome-wide sequencing coverage. For method validation, cell lines (n = 4), plasmids (n = 3), and HPV16, 18, 31, 33 and 45 positive clinical samples (n = 21) were analysed. TaME-seq combines tagmentation and multiplex PCR enrichment for simultaneous analysis of HPV variation and chromosomal integration, and it can also be adapted to other viruses. To uncover these genomic events in an HPV infection, we have developed an innovative and cost-effective sequencing approach named TaME-seq (tagmentation-assisted multiplex PCR enrichment sequencing). HPV genomic variability and chromosomal integration are important in the HPV-induced carcinogenic process.
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