Multiple Sequencing Approaches for HPV Analyses

Nicole Rossi & Michael Dean presented at Nanopore Community Meeting 2021 on: “Resolution of complex human papillomavirus and human sequences.” Rossi and Dean are from the National Cancer Institute. Rossi spoke about the impact of human papilloma virus (HPV). Cervical cancer causes numerous deaths. The HPV genome has two oncogenes and promotes genome instability. HPV can integrate The use of Oxford Nanopore Technologies to sequence the genome is possible. Rossi and Dean used the CaSki Cervical Cancer Cell Line which is known to have regions of HPV. The HPV genome produces abnormal extrachromosomal genome forms. Sequencing can be used to detect these genomes. HPV16, Rossi noted, does not integrate in at least one-third of cervical tumors. How does HPV16 cause cancer without integration? This is one of the questions Rossi and Dean wanted to address. Rossi used the tagmentation and ligation sequencing approaches to sequence the HPV virus. The team also used ultra-HMW DNA sequencing using the kit and Circulomics kits. They also used adaptive sampling for the first time according to ONT, obtaining 300 kb+ adaptive sampling reads. The team lso used Nanopore Direct cDNA sequencing to study HPV expression patterns. With Magalodon, they detected modified bases. HPV whole genome methylation in different cell lines was analyzed. Also, the team’s preliminary analysis indicates 5hm-C in gene regulation. The group also used Pore-C to learn about chromosomal structure. I was impressed with the number of different sequencing approaches that the team used.

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Which sequencing approaches can be used to learn about HPV infection? Photo by Edward Jenner on Pexels.com