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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
...two uninterrupted copies of MYC, as illustrated in Figure 4E.HPV integration events show consistent orientation-dependent regulatory patternsONT sequencing simultaneously yields DNA methylation information along with DNA sequence data (Simpson et al. 2017). We therefore investigated methylation...
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Research: DNA methylation contributes to natural human variation
- Holger Heyn,
- Sebastian Moran,
- Irene Hernando-Herraez,
- Sergi Sayols,
- Antonio Gomez,
- Juan Sandoval,
- Dave Monk,
- Kenichiro Hata,
- Tomas Marques-Bonet,
- Liewei Wang,
- and Manel Esteller
Genome Res. September 2013 23: 1363-1372; Published in Advance August 1, 2013, doi:10.1101/gr.154187.112
...for primary samples of normal breast (n = 78), colon (n = 38), and lung (n = 32) tissues were obtained from The Cancer Genome Atlas (TCGA) data portal (https://tcga-data.nci.nih.gov/tcga). Infinium HumanMethylation450 BeadChip All DNA samples were assessed for integrity, quantity, and purity...
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Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
- Tianfu Zeng,
- Haotian Liao,
- Lin Xia,
- Siyao You,
- Yanqun Huang,
- Jiaxun Zhang,
- Yahui Liu,
- Xuyan Liu,
- and Dan Xie
Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
...studies have suggested that HBV DNA methylation could influence the expression patterns of viral genes (Fernandez et al. 2009; Mirabello et al. 2012). However, we did not observe significant differences between adjacent nontumor and tumor tissues in the methylation status of integrated HBV DNA sequences...
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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...
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LETTER: A Dominant Modifier of Transgene Methylation Is Mapped by QTL Analysis to Mouse Chromosome 13
- Pascale Valenza-Schaerly,
- Benjamin Pickard,
- Jörn Walter,
- Martin Jung,
- Lucille Pourcel,
- Wolf Reik,
- Dominique Gauguier,
- Gilles Vergnaud,
- and Christine Pourcel
Genome Res. March 1, 2001 11: 382-388; doi:10.1101/gr.163801
...markers for whole- scans and radiation hybrid mapping and a mouse family tree. Genome Res. 9 : 878 – 887 . ↵ Schweizer J. , Valenza-Schaerly P. , Goret F. , Pourcel C. ( 1998 ) Control of expression and methylation of a Hepatitis B viral transgene by strain-specific modifiers. DNA Cell Biol. 17 : 427...
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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
...of HPV integration with host DNA) are identified in genomic DNA of 81 (77%) tumors, based on detection of split and/or discordant WGS sequencing reads mapping both to HPV and the reference human (Supplemental Fig. S1.1). As we previously observed in cultured HPV-positive cancer cells (Akagi et al. 2014...
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Review: Leveraging the power of long reads for targeted sequencing
- Shruti V. Iyer,
- Sara Goodwin,
- and William Richard McCombie
Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
...) integration using PacBio sequencing. In this case, guides were designed specifically to the 8 kb HPV and not to the host. The authors demonstrated that by targeting HPV only, hundreds of DNA bases upstream and downstream from the integration site are also enriched. Analysis of the host flanking regions...
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Research: L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis
- Stephanie N. Schauer,
- Patricia E. Carreira,
- Ruchi Shukla,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Francisco J. Sanchez-Luque,
- Paola Nicoli,
- Michaela Kindlova,
- Serena Ghisletti,
- Alexandre Dos Santos,
- Delphine Rapoud,
- Didier Samuel,
- Jamila Faivre,
- Adam D. Ewing,
- Sandra R. Richardson,
- and Geoffrey J. Faulkner
Genome Res. May 2018 28: 639-653; Published in Advance April 11, 2018, doi:10.1101/gr.226993.117
...accumulation of L1 DNA has been observed in HIV-1 infected cultured cells, suggesting that in some cases viral infection may render cells susceptible to increased L1 activity (Jones et al. 2013). Other liver malignancies, such as intra-hepatic cholangiocarcinoma (ICC), which is the second most common type...
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Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
- Shudi Zhao,
- Yuedong Li,
- Guanping Chen,
- Xingyang Wang,
- Nan Chen,
- and Xiaofeng Wu
Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
...conduce to viral assembly and egress. Homologous regions (hrs) are conserved and interspersed repetitive sequences in the baculovirus (Cochran and Faulkner 1983). They have been reported in earlier studies with pivotal roles in viral DNA replication, progeny production, and transcriptional enhancement...
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Research: The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages
- Musa A. Hassan,
- Vincent Butty,
- Kirk D.C. Jensen,
- and Jeroen P.J. Saeij
Genome Res. March 2014 24: 377-389; Published in Advance November 18, 2013, doi:10.1101/gr.166033.113
...at specific loci and show that, beyond DNA sequence and structural changes, differential isoform usage and mRNA editing can contribute to intra-species genomic and phenotypic diversity. [Supplemental material is available for this article.] Splicing is an obligatory step in the processing of both coding...

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