TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration
dc.contributor.author | Lagström, Sonja | |
dc.contributor.author | Umu, Sinan Uğur | |
dc.contributor.author | Lepistö, Maija | |
dc.contributor.author | Ellonen, Pekka | |
dc.contributor.author | Meisal, Roger | |
dc.contributor.author | Christiansen, Irene Kraus | |
dc.contributor.author | Ambur, Ole Herman | |
dc.contributor.author | Rounge, Trine Ballestad | |
dc.date.accessioned | 2020-02-04T10:26:58Z | |
dc.date.accessioned | 2020-03-08T20:33:59Z | |
dc.date.available | 2020-02-04T10:26:58Z | |
dc.date.available | 2020-03-08T20:33:59Z | |
dc.date.issued | 2018-11-26 | |
dc.identifier.citation | Lagström SL, Umu SU, Lepistö M, Ellonen P, Meisal R, Christiansen IK, Ambur OH, Rounge TB. TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration. Scientific Reports. 2019;9:524:1-12 | en |
dc.identifier.issn | 2045-2322 | |
dc.identifier.issn | 2045-2322 | |
dc.identifier.uri | https://hdl.handle.net/10642/8243 | |
dc.description.abstract | HPV genomic variability and chromosomal integration are important in the HPV-induced carcinogenic process. 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). 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. For method validation, cell lines (n = 4), plasmids (n = 3), and HPV16, 18, 31, 33 and 45 positive clinical samples (n = 21) were analysed. Our results showed deep HPV genome-wide sequencing coverage. Chromosomal integration breakpoints and large deletions were identified in HPV positive cell lines and in one clinical sample. HPV genomic variability was observed in all samples allowing identification of low frequency variants. In contrast to other approaches, TaME-seq proved to be highly efficient in HPV target enrichment, leading to reduced sequencing costs. Comprehensive studies on HPV intra-host variability generated during a persistent infection will improve our understanding of viral carcinogenesis. 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. | en |
dc.description.sponsorship | This work was funded by a grant from South-Eastern Norway Regional Health Authority (project number 2016020). | en |
dc.language.iso | en | en |
dc.publisher | Nature Research (part of Springer Nature) | en |
dc.relation.ispartofseries | Scientific Reports;9, Article number: 524 (2019) | |
dc.rights | This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. | en |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | |
dc.subject | Cancer genomics | en |
dc.subject | Human papillomaviruses | en |
dc.subject | Next generation sequencing | en |
dc.title | TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration | en |
dc.type | Journal article | en |
dc.type | Peer reviewed | en |
dc.date.updated | 2020-02-04T10:26:58Z | |
dc.description.version | publishedVersion | en |
dc.identifier.doi | https://dx.doi.org/10.1038/s41598-018-36669-6 | |
dc.identifier.cristin | 1698618 | |
dc.source.journal | Scientific Reports |
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Except where otherwise noted, this item's license is described as This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.