Universität zu Köln

Bergmann, Larissa-Anna ORCID: 0009-0009-0866-7954, Pacholewska, Alicja ORCID: 0000-0002-4888-4883 and Schweiger, Michal R. ORCID: 0000-0002-4672-0623 (2025). Novel Avenues for the Detection of Cancer-Associated Viral Genome Integrations Using Long-Read Sequencing Technologies. Cancers, 17 (11). MDPI. ISSN 2072-6694

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Abstract

[Artikel-Nr.: 1740] Human papillomaviruses (HPVs), like many other viruses, are able to integrate their genomes into the host cellular genome. This integration can activate viral oncogenes or alter the function of cellular oncogenes and tumor suppressor genes, thereby increasing the likelihood of HPV-associated tumor development. In particular, HPV types 16 and 18 are responsible for over 70% of all cervical, anal, and oropharyngeal cancers worldwide, with rising incidence. Even more, high-resolution mapping of preferred integration sites using LR-Seq technologies offers deep insights into the molecular mechanisms of HPV integration. LR-Seq enables the detection of complex integration patterns, where the viral genome can be replicated and amplified into virus–host concatemers, including events within large structural variations or highly repetitive genomic regions. Furthermore, aligning LR-Seq data to the latest T2T reference genome (hs1) is necessary to provide new information about viral integration in genomic regions that were previously inaccessible, such as centromeres and other structurally complex repeat-rich loci. In this review, we provide insights into HPV genomic integration revealed by LR-Seq technologies, with a particular focus on how the use of the complete T2T reference genome enhances the detection of integration events in previously uncharacterized, repeat-rich regions of the human genome.

Item Type:	Article
Creators:	Creators Email ORCID ORCID Put Code Bergmann, Larissa-Anna UNSPECIFIED https://orcid.org/0009-0009-0866-7954 UNSPECIFIED Pacholewska, Alicja UNSPECIFIED https://orcid.org/0000-0002-4888-4883 UNSPECIFIED Schweiger, Michal R. UNSPECIFIED https://orcid.org/0000-0002-4672-0623 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-800004
Identification Number:	10.3390/cancers17111740
Journal or Publication Title:	Cancers
Volume:	17
Number:	11
Number of Pages:	18
Date:	22 May 2025
Publisher:	MDPI
ISSN:	2072-6694
Language:	English
Faculty:	Faculty of Medicine
Divisions:	Faculty of Medicine > Innere Medizin > Klinik I für Innere Medizin - Hämatologie und Onkologie Zentrum für Molekulare Medizin
Subjects:	Medical sciences Medicine
Uncontrolled Keywords:	Keywords Language HPV ; human papillomavirus ; LR-Seq ; long-read sequencing ; viral genome integration English
['eprint_fieldname_oa_funders' not defined]:	Publikationsfonds UzK
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/80000