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Research on HPV integration is hampered by current integration detection technologies and their unsuitability for formalin\u2010fixed paraffin\u2010embedded (FFPE) tissues. This study aims to develop and validate a novel targeted proximity\u2010ligation based sequencing method (targeted locus amplification\/capture [TLA\/TLC]) for HPV integration detection in cell lines and FFPE OPSCCs. For the identification of HPV integrations, TLA\/TLC was applied to 7 cell lines and 27 FFPE OPSCCs. Following preprocessing steps, a polymerase chain reaction (PCR)\u2010based HPV enrichment was performed on the cell lines and a capture\u2010based HPV enrichment was performed on the FFPE tissues before paired\u2010end sequencing. TLA was able to sequence up to hundreds of kb around the target, detecting exact HPV integration loci, structural variants, and chromosomal rearrangements. In all cell lines, one or more integration sites were identified, in accordance with detection of integrated papillomavirus sequences PCR data and the literature. TLC detected integrated HPV in 15\/27 FFPE OPSCCs and identified simple and complex integration patterns. In general, TLA\/TLC confirmed PCR data and detected additional integration sites. In conclusion TLA\/TLC reliably and robustly detects HPV integration in cell lines and FFPE OPSCCs, enabling large, population\u2010based studies on the clinical relevance of HPV integration. Furthermore, this approach might be valuable for clonality assessment of HPV\u2010related tumors in clinical diagnostics.<\/jats:p>","DOI":"10.1002\/jmv.29837","type":"journal-article","created":{"date-parts":[[2024,8,6]],"date-time":"2024-08-06T10:31:51Z","timestamp":1722940311000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Proximity ligation\u2010based sequencing for the identification of human papillomavirus genomic integration sites in formalin\u2010fixed paraffin embedded oropharyngeal squamous cell carcinomas"],"prefix":"10.1002","volume":"96","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9531-8414","authenticated-orcid":false,"given":"Imke","family":"Demers","sequence":"first","affiliation":[{"name":"Department of Pathology GROW\u2010School for Oncology and Developmental Biology, Maastricht University Medical Center Maastricht The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harini","family":"Balaji","sequence":"additional","affiliation":[{"name":"Jean\u2010Uhrmacher\u2010Institute for Otorhinolaryngological Research University of Cologne Cologne Germany"},{"name":"Department of Otorhinolaryngology Head and Neck Surgery, Medical Faculty, University of Cologne Cologne Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Harma","family":"Feitsma","sequence":"additional","affiliation":[{"name":"Cergentis B.V. 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M.","family":"van den Hout","sequence":"additional","affiliation":[{"name":"Department of Pathology GROW\u2010School for Oncology and Developmental Biology, Maastricht University Medical Center Maastricht The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steffen","family":"Wagner","sequence":"additional","affiliation":[{"name":"Department of Otorhinolaryngology Head and Neck Surgery, Medical Faculty, University of Giessen Giessen Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernd","family":"Kremer","sequence":"additional","affiliation":[{"name":"Department of Otorhinolaryngology and Head and Neck Surgery Erasmus MC Cancer Institute, University Medical Center Rotterdam Rotterdam The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jens P.","family":"Klussmann","sequence":"additional","affiliation":[{"name":"Department of Otorhinolaryngology Head and Neck Surgery, Medical Faculty, University of Cologne 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