TaME-seq : An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration

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Lagström , S , Umu , S U , Lepistö , M , Ellonen , P , Meisal , R , Christiansen , I K , Ambur , O H & Rounge , T B 2019 , ' TaME-seq : An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration ' , Scientific Reports , vol. 9 , 524 . https://doi.org/10.1038/s41598-018-36669-6

Title: TaME-seq : An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration
Author: Lagström, Sonja; Umu, Sinan Ugur; Lepistö, Maija; Ellonen, Pekka; Meisal, Roger; Christiansen, Irene Kraus; Ambur, Ole Herman; Rounge, Trine B.
Contributor: University of Helsinki, Institute for Molecular Medicine Finland
University of Helsinki, Sekvensointiyksikkö
Date: 2019-01-24
Language: eng
Number of pages: 12
Belongs to series: Scientific Reports
ISSN: 2045-2322
URI: http://hdl.handle.net/10138/298924
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.
Subject: HUMAN-PAPILLOMAVIRUS TYPE-16
INVASIVE CERVICAL-CANCER
GENETIC-VARIATION
NATURAL-HISTORY
DNA INTEGRATION
SITES
CARCINOMAS
EXPRESSION
3111 Biomedicine
1184 Genetics, developmental biology, physiology
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