Searching journal content for articles similar to Sakamoto et al. 30 (9): 1243.

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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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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
...sequencing for both germline and somatic cancer analysis. We provide an overview of the computational methodologies tailored to long-read data and highlight key discoveries and resources within cancer genomics that were previously inaccessible with prior technologies. We also address future opportunities...
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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
..., the current understanding of somatic SVs in HCC is still incomplete.Long-read sequencing (LRS) technology, represented by Oxford Nanopore Technologies (ONT) and Pacific Bioscience (PacBio), can produce continuous reads longer than 10,000 bp. These reads can completely span across genomic repetitive segments...
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Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
- Ju Heon Maeng,
- H. Josh Jang,
- Alan Y. Du,
- Shin-Cheng Tzeng,
- and Ting Wang
Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
...to improve cancer immunotherapy approaches; however, current genomics and computational tools are not optimized for their detection. Here we combined CAGE technology with full-length long-read transcriptome sequencing (long-read CAGE, or LRCAGE) and developed a suite of computational tools to significantly...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...short-read sequences. Recent advances in long-read isoform sequencing enable the detection of fusion transcripts at unprecedented resolution in bulk and single-cell samples. Here, we developed a new computational tool, CTAT-LR-Fusion, to detect fusion transcripts from long-read RNA-seq with or without...
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Method: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
- Alexander Zee,
- Dori Z.Q. Deng,
- Matthew Adams,
- Kayla D. Schimke,
- Russell Corbett-Detig,
- Shelbi L. Russell,
- Xuan Zhang,
- Robert J. Schmitz,
- and Christopher Vollmers
Genome Res. November/December 2022 32: 2092-2106; Published in Advance November 9, 2022, doi:10.1101/gr.277031.122
...∼600-nt-long cDNA molecules across dozens of flowcells and generated about 6 million reads per MinION flowcell. The Long-read RNA-seq Genome Annotation Assessment Project (LRGASP) Consortium (Pardo-Palacios et al. 2021) sequenced ∼520-nt-long cDNA molecules and generated about 18 million reads per...
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Research: The transcriptional landscape and mutational profile of lung adenocarcinoma
- Jeong-Sun Seo,
- Young Seok Ju,
- Won-Chul Lee,
- Jong-Yeon Shin,
- June Koo Lee,
- Thomas Bleazard,
- Junho Lee,
- Yoo Jin Jung,
- Jung-Oh Kim,
- Jung-Young Shin,
- Saet-Byeol Yu,
- Jihye Kim,
- Eung-Ryoung Lee,
- Chang-Hyun Kang,
- In-Kyu Park,
- Hwanseok Rhee,
- Se-Hoon Lee,
- Jong-Il Kim,
- Jin-Hyoung Kang,
- and Young Tae Kim
Genome Res. November 2012 22: 2109-2119; Published in Advance September 13, 2012, doi:10.1101/gr.145144.112
...tissue samples (Supplemental Table 2; Supplemental Material). All these sequencing experiments were done as described previously ( Ju et al. 2011). We generated 14,038,673,860 paired-end 101-bp-long reads from RNA sequencing of 164 samples (87 cancer and 77 corresponding normal tissues). On average...
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Research: Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
- Peter A. Audano and
- Christine R. Beck
Genome Res. January 2024 34: 7-19; Published in Advance January 4, 2024, doi:10.1101/gr.278203.123
...are subject to systematic bias affecting variant representation. To understand why SV breakpoints are inconsistent across samples, we reanalyzed 64 phased haplotypes constructed from long-read assemblies released by the Human Genome Structural Variation Consortium (HGSVC). We identify 882 SV insertions...
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Method: Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation
- Joseph B. Hiatt,
- Colin C. Pritchard,
- Stephen J. Salipante,
- Brian J. O'Roak,
- and Jay Shendure
Genome Res. May 2013 23: 843-854; Published in Advance February 4, 2013, doi:10.1101/gr.147686.112
...-read’’) for the captured target sequence that is robust to such errors. Table 1. Summary of clinical samples Cancer type Number of samples Colorectal/rectal adenocarcinoma 18 Non-small cell lung cancer 11 Melanoma 7 Gastrointestinal stromal tumor 4 Myeloproliferative disordera 3 Acute myeloid leukemiaa 2 Urothelial...
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Method: Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations
- Jonathan S. Brammeld,
- Mia Petljak,
- Inigo Martincorena,
- Steven P. Williams,
- Luz Garcia Alonso,
- Alba Dalmases,
- Beatriz Bellosillo,
- Carla Daniela Robles-Espinoza,
- Stacey Price,
- Syd Barthorpe,
- Patrick Tarpey,
- Constantine Alifrangis,
- Graham Bignell,
- Joana Vidal,
- Jamie Young,
- Lucy Stebbings,
- Kathryn Beal,
- Michael R. Stratton,
- Julio Saez-Rodriguez,
- Mathew Garnett,
- Clara Montagut,
- Francesco Iorio,
- and Ultan McDermott
Genome Res. April 2017 27: 613-625; Published in Advance February 8, 2017, doi:10.1101/gr.213546.116
...) and the development of statistical approaches for recurrencedetection innoncoding regions. Such algorithms are currently under development as part of the PanCancer Analysis of Whole Genomes (http://pancancer.info/) which is undertaking the analysis of more than 2000 whole s. Thus, in due course as whole- sequencing...
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