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SearcHPV: A novel approach to identify and assemble human papillomavirus–host genomic integration events in cancer

dc.contributor.authorPinatti, Lisa M.
dc.contributor.authorGu, Wenjin
dc.contributor.authorWang, Yifan
dc.contributor.authorElhossiny, Ahmed
dc.contributor.authorBhangale, Apurva D.
dc.contributor.authorBrummel, Collin V.
dc.contributor.authorCarey, Thomas E.
dc.contributor.authorMills, Ryan E.
dc.contributor.authorBrenner, J. Chad
dc.date.accessioned2021-10-05T15:05:57Z
dc.date.available2022-11-05 11:05:54en
dc.date.available2021-10-05T15:05:57Z
dc.date.issued2021-10-01
dc.identifier.citationPinatti, Lisa M.; Gu, Wenjin; Wang, Yifan; Elhossiny, Ahmed; Bhangale, Apurva D.; Brummel, Collin V.; Carey, Thomas E.; Mills, Ryan E.; Brenner, J. Chad (2021). "SearcHPV: A novel approach to identify and assemble human papillomavirus–host genomic integration events in cancer." Cancer (19): 3531-3540.
dc.identifier.issn0008-543X
dc.identifier.issn1097-0142
dc.identifier.urihttps://hdl.handle.net/2027.42/170218
dc.publisherWiley Periodicals, Inc.
dc.publisherR Foundation for Statistical Computing
dc.subject.othervirus integration
dc.subject.otherpapillomavirus infections
dc.subject.othergenomics
dc.subject.otherDNA sequence analysis
dc.subject.otherbioinformatics
dc.subject.othersquamous cell carcinoma
dc.titleSearcHPV: A novel approach to identify and assemble human papillomavirus–host genomic integration events in cancer
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelOncology and Hematology
dc.subject.hlbsecondlevelPublic Health
dc.subject.hlbtoplevelHealth Sciences
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/170218/1/cncr33691-sup-0001-FigS1.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/170218/2/cncr33691.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/170218/3/cncr33691_am.pdf
dc.identifier.doi10.1002/cncr.33691
dc.identifier.sourceCancer
dc.identifier.citedreferenceKhanal S, Shumway BS, Zahin M, et al. Viral DNA integration and methylation of human papillomavirus type 16 in high‐grade oral epithelial dysplasia and head and neck squamous cell carcinoma. Oncotarget. 2018; 9: 30419 ‐ 30433. doi: 10.18632/oncotarget.25754
dc.identifier.citedreferenceHolmes A, Lameiras S, Jeannot E, et al. Mechanistic signatures of HPV insertions in cervical carcinomas. NPJ Genom Med. 2016; 1: 16004. doi: 10.1038/npjgenmed.2016.4
dc.identifier.citedreferenceMontgomery ND, Parker JS, Eberhard DA, et al. Identification of human papillomavirus infection in cancer tissue by targeted next‐generation sequencing. Appl Immunohistochem Mol Morphol. 2016; 24: 490 ‐ 495. doi: 10.1097/PAI.0000000000000215
dc.identifier.citedreferenceMorel A, Neuzillet C, Wack M, et al. Mechanistic signatures of human papillomavirus insertions in anal squamous cell carcinomas. Cancers (Basel). 2019; 11: 1846. doi: 10.3390/cancers11121846
dc.identifier.citedreferenceNkili‐Meyong AA, Moussavou‐Boundzanga P, Labouba I, et al. Genome‐wide profiling of human papillomavirus DNA integration in liquid‐based cytology specimens from a Gabonese female population using HPV capture technology. Sci Rep. 2019; 9: 1504. doi: 10.1038/s41598‐018‐37871‐2
dc.identifier.citedreferenceWalline HM, Goudsmit CM, McHugh JB, et al. Integration of high‐risk human papillomavirus into cellular cancer–related genes in head and neck cancer cell lines. Head Neck. 2017; 39: 840 ‐ 852. doi: 10.1002/hed.24729
dc.identifier.citedreferenceShuman AG, Gornick MC, Brummel C, et al. Patient and provider perspectives regarding enrollment in head and neck cancer research. Otolaryngol Head Neck Surg. 2020; 162: 73 ‐ 78.
dc.identifier.citedreferenceHeft Neal ME, Bhangale AD, Birkeland AC, et al. Prognostic significance of oxidation pathway mutations in recurrent laryngeal squamous cell carcinoma. Cancers (Basel). 2020; 12: 3081. doi: 10.3390/cancers12113081
dc.identifier.citedreferencePapillomavirus Episteme. National Institute of Allergy and Infectious Diseases. Updated January 13, 2020. Accessed May 1, 2020. https://pave.niaid.nih.gov/
dc.identifier.citedreferenceVan Doorslaer K, Li Z, Xirasagar S, et al. The Papillomavirus Episteme: a major update to the papillomavirus sequence database. Nucleic Acids Res. 2017; 45: D499 ‐ D506. doi: 10.1093/nar/gkw879
dc.identifier.citedreferenceLi H, Durbin R. Fast and accurate short read alignment with Burrows‐Wheeler transform. Bioinformatics. 2009; 25: 1754 ‐ 1760. doi: 10.1093/bioinformatics/btp324
dc.identifier.citedreferencePicard toolkit. Broad Institute GitHub Repository. Accessed April 15, 2020. https://github.com/broadinstitute/picard
dc.identifier.citedreferenceMcKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next‐generation DNA sequencing data. Genome Res. 2010; 20: 1297 ‐ 1303. doi: 10.1101/gr.107524.110
dc.identifier.citedreferenceZhang J, Kobert K, Flouri T, Stamatakis A. PEAR: a fast and accurate Illumina Paired‐End reAd mergeR. Bioinformatics. 2014; 30: 614 ‐ 620. doi: 10.1093/bioinformatics/btt593
dc.identifier.citedreferenceHuang X, Madan A. CAP3: a DNA sequence assembly program. Genome Res. 1999; 9: 868 ‐ 877. doi: 10.1101/gr.9.9.868
dc.identifier.citedreferenceTeam RC. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing; 2019.
dc.identifier.citedreferenceVan Rossum G, Drake FL. Python 3 Reference Manual: Python Documentation Manual Part 2. CreateSpace Independent Publishing Platform; 2009.
dc.identifier.citedreferenceLiu J, Pan S, Hsieh MH, et al. Targeting Wnt‐driven cancer through the inhibition of porcupine by LGK974. Proc Natl Acad Sci U S A. 2013; 110: 20224 ‐ 20229.
dc.identifier.citedreferenceMyers JE, Guidry JT, Scott ML, et al. Detecting episomal or integrated human papillomavirus 16 DNA using an exonuclease V‐qPCR‐based assay. Virology. 2019; 537: 149 ‐ 156. doi: 10.1016/j.virol.2019.08.021
dc.identifier.citedreferenceOlthof NC, Huebbers CU, Kolligs J, et al. Viral load, gene expression and mapping of viral integration sites in HPV16‐associated HNSCC cell lines. Int J Cancer. 2015; 136: E207 ‐ E218. doi: 10.1002/ijc.29112
dc.identifier.citedreferencePoirson J, Biquand E, Straub M‐L, et al. Mapping the interactome of HPV E6 and E7 oncoproteins with the ubiquitin‐proteasome system. FEBS J. 2017; 284: 3171 ‐ 3201.
dc.identifier.citedreferenceThompson DA, Zacny V, Belinsky GS, et al. The HPV E7 oncoprotein inhibits tumor necrosis factor alpha–mediated apoptosis in normal human fibroblasts. Oncogene. 2001; 20: 3629 ‐ 3640.
dc.identifier.citedreferenceHu Z, Zhu D, Wang W, et al. Genome‐wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology‐mediated integration mechanism. Nat Genet. 2015; 47: 158 ‐ 163. doi: 10.1038/ng.3178
dc.identifier.citedreferenceFerber MJ, Thorland EC, Brink AA, et al. Preferential integration of human papillomavirus type 18 near the c‐myc locus in cervical carcinoma. Oncogene. 2003; 22: 7233 ‐ 7242. doi: 10.1038/sj.onc.1207006
dc.identifier.citedreferenceSchmitz M, Driesch C, Jansen L, Runnebaum IB, Durst M. Non‐random integration of the HPV genome in cervical cancer. PLoS One. 2012; 7: e39632. doi: 10.1371/journal.pone.0039632
dc.identifier.citedreferenceWalline HM, Komarck CM, McHugh JB, et al. Genomic integration of high‐risk HPV alters gene expression in oropharyngeal squamous cell carcinoma. Mol Cancer Res. 2016; 14: 941 ‐ 952. doi: 10.1158/1541‐7786.MCR‐16‐0105
dc.identifier.citedreferenceCancer Genome Atlas Network. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015; 517: 576 ‐ 582. doi: 10.1038/nature14129
dc.identifier.citedreferenceGroves IJ, Coleman N. Human papillomavirus genome integration in squamous carcinogenesis: what have next‐generation sequencing studies taught us? J Pathol. 2018; 245: 9 ‐ 18. doi: 10.1002/path.5058
dc.identifier.citedreferencePannunzio NR, Li S, Watanabe G, Lieber MR. Non‐homologous end joining often uses microhomology: implications for alternative end joining. DNA Repair (Amst). 2014; 17: 74 ‐ 80. doi: 10.1016/j.dnarep.2014.02.006
dc.identifier.citedreferenceCarvajal‐Garcia J, Cho JE, Carvajal‐Garcia P, et al. Mechanistic basis for microhomology identification and genome scarring by polymerase theta. Proc Natl Acad Sci U S A. 2020; 117: 8476 ‐ 8485. doi: 10.1073/pnas.1921791117
dc.identifier.citedreferenceGao G, Wang J, Kasperbauer JL, et al. Whole genome sequencing reveals complexity in both HPV sequences present and HPV integrations in HPV‐positive oropharyngeal squamous cell carcinomas. BMC Cancer. 2019; 19: 352. doi: 10.1186/s12885‐019‐5536‐1
dc.identifier.citedreferenceNulton TJ, Olex AL, Dozmorov M, Morgan IM, Windle B. Analysis of The Cancer Genome Atlas sequencing data reveals novel properties of the human papillomavirus 16 genome in head and neck squamous cell carcinoma. Oncotarget. 2017; 8: 17684 ‐ 17699. doi: 10.18632/oncotarget.15179
dc.identifier.citedreferenceParfenov M, Pedamallu CS, Gehlenborg N, et al. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A. 2014; 111: 15544 ‐ 15549. doi: 10.1073/pnas.1416074111
dc.identifier.citedreferencePinatti LM, Sinha HN, Brummel CV, et al. Association of human papillomavirus integration with better patient outcomes in oropharyngeal squamous cell carcinoma. Head Neck. 2021; 43: 544 ‐ 557. doi: 10.1002/hed.26501
dc.identifier.citedreferenceTian R, Cui Z, He D, et al. Risk stratification of cervical lesions using capture sequencing and machine learning method based on HPV and human integrated genomic profiles. Carcinogenesis. 2019; 40: 1220 ‐ 1228. doi: 10.1093/carcin/bgz094
dc.identifier.citedreferenceMcBride AA, Warburton A. The role of integration in oncogenic progression of HPV‐associated cancers. PLoS Pathog. 2017; 13: e1006211. doi: 10.1371/journal.ppat.1006211
dc.identifier.citedreferenceBodelon C, Untereiner ME, Machiela MJ, Vinokurova S, Wentzensen N. Genomic characterization of viral integration sites in HPV‐related cancers. Int J Cancer. 2016; 139: 2001 ‐ 2011. doi: 10.1002/ijc.30243
dc.identifier.citedreferenceAkagi K, Li J, Broutian TR, et al. Genome‐wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability. Genome Res. 2014; 24: 185 ‐ 199. doi: 10.1101/gr.164806.113
dc.identifier.citedreferencePinatti LM, Walline HM, Carey TE. Human papillomavirus genome integration and head and neck cancer. J Dent Res. 2018; 97: 691 ‐ 700. doi: 10.1177/0022034517744213
dc.identifier.citedreferenceLuft F, Klaes R, Nees M, et al. Detection of integrated papillomavirus sequences by ligation‐mediated PCR (DIPS‐PCR) and molecular characterization in cervical cancer cells. Int J Cancer. 2001; 92: 9 ‐ 17.
dc.identifier.citedreferenceKlaes R, Woerner SM, Ridder R, et al. Detection of high‐risk cervical intraepithelial neoplasia and cervical cancer by amplification of transcripts derived from integrated papillomavirus oncogenes. Cancer Res. 1999; 59: 6132 ‐ 6136.
dc.identifier.citedreferenceWang Q, Jia P, Zhao Z. VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. PLoS One. 2013; 8: e64465. doi: 10.1371/journal.pone.0064465
dc.identifier.citedreferenceWang Q, Jia P, Zhao Z. VERSE: a novel approach to detect virus integration in host genomes through reference genome customization. Genome Med. 2015; 7: 2. doi: 10.1186/s13073‐015‐0126‐6
dc.identifier.citedreferenceChen Y, Yao H, Thompson EJ, Tannir NM, Weinstein JN, Su X. VirusSeq: software to identify viruses and their integration sites using next‐generation sequencing of human cancer tissue. Bioinformatics. 2013; 29: 266 ‐ 267. doi: 10.1093/bioinformatics/bts665
dc.working.doiNOen
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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