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  1. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ...that integrates into host genomic DNA and forms virus–virus and virus–host genomic structural rearrangements, which are unstable and lead to further intratumoral heterogeneity and clonal evolution; through long-read sequencing, unique breakpoints shared across structural variants were also observed in HPV...
  2. Research: Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers
    • David E. Symer,
    • Keiko Akagi,
    • Heather M. Geiger,
    • Yang Song,
    • Gaiyun Li,
    • Anne-Katrin Emde,
    • Weihong Xiao,
    • Bo Jiang,
    • André Corvelo,
    • Nora C. Toussaint,
    • Jingfeng Li,
    • Amit Agrawal,
    • Enver Ozer,
    • Adel K. El-Naggar,
    • Zoe Du,
    • Jitesh B. Shewale,
    • Birgit Stache-Crain,
    • Mark Zucker,
    • Nicolas Robine,
    • Kevin R. Coombes,
    • and Maura L. Gillison
    Genome Res. January 2022 32: 55-70; Published in Advance December 13, 2021, doi:10.1101/gr.275911.121
    ...that HPV integrants recurrently flank or bridge focal regions of extensive host genomic instability, including copy number variation (CNV) and structural variation (SV) (Akagi et al. 2014; Parfenov et al. 2014; The Cancer Genome Atlas Research Network 2017). We proposed a mechanistic looping model...
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  3. Research: Human papillomavirus and the landscape of secondary genetic alterations in oral cancers
    • Maura L. Gillison,
    • Keiko Akagi,
    • Weihong Xiao,
    • Bo Jiang,
    • Robert K.L. Pickard,
    • Jingfeng Li,
    • Benjamin J. Swanson,
    • Amit D. Agrawal,
    • Mark Zucker,
    • Birgit Stache-Crain,
    • Anne-Katrin Emde,
    • Heather M. Geiger,
    • Nicolas Robine,
    • Kevin R. Coombes,
    • and David E. Symer
    Genome Res. January 2019 29: 1-17; Published in Advance December 18, 2018, doi:10.1101/gr.241141.118
    ...as a consequence of host genomic instability induced by HPV oncoproteins, APOBEC induced host editing, and other forms of DNA mutagenesis. HPV E6*1, E6, E7, and E5 oncoproteins and these recurrent somatic variants in host genes and pathways cooperatively disrupt host genomic stability, apoptosis, cellular...
  4. Research: Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation
    • Vanessa L. Porter,
    • Michelle Ng,
    • Kieran O'Neill,
    • Signe MacLennan,
    • Richard D. Corbett,
    • Luka Culibrk,
    • Zeid Hamadeh,
    • Marissa Iden,
    • Rachel Schmidt,
    • Shirng-Wern Tsaih,
    • Carolyn Nakisige,
    • Martin Origa,
    • Jackson Orem,
    • Glenn Chang,
    • Jeremy Fan,
    • Ka Ming Nip,
    • Vahid Akbari,
    • Simon K. Chan,
    • James Hopkins,
    • Richard A. Moore,
    • Eric Chuah,
    • Karen L. Mungall,
    • Andrew J. Mungall,
    • Inanc Birol,
    • Steven J.M. Jones,
    • Janet S. Rader,
    • and Marco A. Marra
    Genome Res. April 2025 35: 653-670; Published in Advance December 5, 2024, doi:10.1101/gr.279041.124
    ..., we performed Oxford Nanopore Technologies long-read sequencing on 72 cervical cancer s from a Ugandan data set that was previously characterized using short-read sequencing. We find recurrent structural rearrangement patterns at HPV integration events, which we categorize as del(etion)-like, dup...
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  5. Research: Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression
    • Suhaida A. Selamat,
    • Brian S. Chung,
    • Luc Girard,
    • Wei Zhang,
    • Ying Zhang,
    • Mihaela Campan,
    • Kimberly D. Siegmund,
    • Michael N. Koss,
    • Jeffrey A. Hagen,
    • Wan L. Lam,
    • Stephen Lam,
    • Adi F. Gazdar,
    • and Ite A. Laird-Offringa
    Genome Res. July 2012 22: 1197-1211; Published in Advance May 21, 2012, doi:10.1101/gr.132662.111
    ...: Transcriptional inhibitor, interacts with activated SMADs Rodenhiser et al. 2008 First report of DNA methylation in lung cancer shown in bold. aHuman Genome Organization nomenclature. bGene function from GeneCards website, http://www.genecards.org/. cPreviously reported studies in order of relevance...
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