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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
...Rearrangements of viral and human s at human papillomavirus integration events and their allele-specific impacts on cancer regulation Vanessa L. Porter1,2,3, Michelle Ng1,3, Kieran O'Neill1, Signe MacLennan1,2,3, Richard D. Corbett1, Luka Culibrk1,4, Zeid Hamadeh5,6, Marissa Iden7,8, Rachel Schmidt...
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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
...@mdanderson.orgAbstractHuman papillomavirus (HPV) is a necessary but insufficient cause of a subset of oral squamous cell carcinomas (OSCCs) that is increasing markedly in frequency. To identify contributory, secondary genetic alterations in these cancers, we used comprehensive genomics methods to compare 149 HPV-positive and 335 HPV...
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Methods: Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes
- Katherine Elena Varley and
- Robi David Mitra
Genome Res. November 2008 18: 1844-1850; Published in Advance October 10, 2008, doi:10.1101/gr.078204.108
....E. ( 2000 ) Multiplex PCR: Optimization and application in diagnostic virology . Clin. Microbiol. Rev. 13 : 559 – 570 . ↵ Ewing, B. , Green, P. ( 1998 ) Base-calling of automated sequencer traces using phred . II. Error probabilities . Genome Res. 8 : 186 – 194 . Ewing, B. , Hillier, L. , Wendl, M...
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ARTICLE: PCR amplification from paraffin-embedded tissues: recommendations on fixatives for long-term storage and prospective studies.
- C E Greer,
- J K Lund,
- and M M Manos
Genome Res. August 1991 1: 46-50; doi:10.1101/gr.1.1.46
...addressed the possible effect of fixation on the integriW of the sequence in- formation in the amplif ied DNA. DNA damage resulting from fixation may cause replication errors, such as point mutations, during PCR. Furthermore, elegant work by P~i~ibo et a1.(16) demonstrated that DNA strand scission...
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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
...nested PCR or high-throughput sequencing (HTS), which may introduce bias and is restricted to detecting junctions between HBV and host s. Recently, the advancement of long-read sequencing has improved our understanding of HBV integration and its role in HCC development. HBV can integrate into the human...
REVIEW: Utility of PCR for DNA analysis from dried blood spots on filter paper blotters.
- E R McCabe
Genome Res. November 1991 1: 99-106; doi:10.1101/gr.1.2.99
...McCabe, E ER McCabe E R, McCabe E.R. McCabe McCabe E R E McCabe E R McCabe, E.R McCabe, ER McCabe, E R McCabe E R McCabe genome;1/2/99 10.1101/gr.1.2.99 1088-9051 Utility of PCR for DNA analysis from dried blood spots on filter paper blotters. Utility of PCR for DNA analysis from dried blood spots...
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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
.... Additionally, qPCR validation revealed that the expression level of the EVA1C gene in samples with DEL was significantly lower than in samples without DEL (Supplemental Fig. S11C). Furthermore, based on gene expression and clinical data obtained from the KM plotter database (Menyhart et al. 2018), survival...
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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA; 3Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA; 4Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; 5...
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Method: Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies
- Tsung-Kai Hung,
- Wan-Chi Liu,
- Sheng-Kai Lai,
- Hui-Wen Chuang,
- Yi-Che Lee,
- Hong-Ye Lin,
- Chia-Lang Hsu,
- Chien-Yu Chen,
- Ya-Chien Yang,
- Jacob Shujui Hsu,
- and Pei-Lung Chen
Genome Res. August 2024 34: 1211-1223; Published in Advance September 9, 2024, doi:10.1101/gr.278358.123
...*03501, including two inhibitory tyrosine-kinase motifs (ITIMs; I/VxYxxL/V), which are underscored and in bold in the alignment (Carr et al. 2005; Campbell and Purdy 2011; Oszmiana et al. 2016).We further confirmed the KIR2DS4/3DL1 fusion gene by PCR amplification with sequence-specific primers (PCR-SSP) (Gómez...
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Method: A virome-wide clonal integration analysis platform for discovering cancer viral etiology
- Xun Chen,
- Jason Kost,
- Arvis Sulovari,
- Nathalie Wong,
- Winnie S. Liang,
- Jian Cao,
- and Dawei Li
Genome Res. May 2019 29: 819-830; Published in Advance March 14, 2019, doi:10.1101/gr.242529.118
...integration events that were not originally detected (Fig. 3A; Supplemental Tables S11A, S12; Liang et al. 2014). All five integrations are present in the tumor, but not the paired normal tissue. All the newly identified integrations were validated via PCR and subsequent Sanger sequencing (Fig. 3B...

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