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Method: FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data
- Can Luo,
- Zimeng Jamie Zhou,
- Yichen Henry Liu,
- and Xin Maizie Zhou
Genome Res. October 2025 35: 2252-2272; Published in Advance August 13, 2025, doi:10.1101/gr.280282.124
...FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data Can Luo1,3, Zimeng Jamie Zhou2,3, Yichen Henry Liu2 and Xin Maizie Zhou1,2 1Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA; 2...
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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
...practice to predict therapeutic response, highlighting the incomplete understanding of the mutational landscape of HCC.Structural variants (SVs) are large genomic alterations (>50 bp), distinct from small variants like SNVs and short insertions and deletions (indels), as they often arise from different...
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Research: Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer
- Gabriela D.A. Guardia,
- Carlos H. dos Anjos,
- Aline Rangel-Pozzo,
- Filipe F. dos Santos,
- Alexander Birbrair,
- Paula F. Asprino,
- Anamaria A. Camargo,
- and Pedro A.F. Galante
Genome Res. September 2025 35: 1942-1958; Published in Advance July 15, 2025, doi:10.1101/gr.280304.124
...dimension of this challenge. This study aims to comprehensively characterize the landscape of HER2 alternative splicing isoforms in breast cancer and to investigate their potential role in mediating resistance to anti-HER2 therapies, particularly ADCs. By employing long-read sequencing technology...
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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
...Bio) Single Molecule Real Time sequencing and Oxford Nanopore Technologies (ONT) sequencing, have emerged as powerful alternatives to short-read sequencing (Fig. 1; van Dijk et al. 2023). Their extended read lengths can span difficult-to-resolve regions, improving the identification performance of structural...
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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
...of genomic structures and epigenomic and transcriptional changes associated with HPV integration events in cervical tumors harboring various HPV types. We used ONT long-read sequencing to generate reads that could span the distances between HPV–human breakpoints, thereby enabling the reconstruction...
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Research: Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T
- Luis F. Paulin,
- Jeremy Fan,
- Kieran O'Neill,
- Erin Pleasance,
- Vanessa L. Porter,
- Steven J.M. Jones,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 621-631; Published in Advance March 17, 2025, doi:10.1101/gr.279352.124
...://creativecommons.org/licenses/by-nc/4.0/.References ↵Aganezov S, Goodwin S, Sherman RM, Sedlazeck FJ, Arun G, Bhatia S, Lee I, Kirsche M, Wappel R, Kramer M, et al. 2020. Comprehensive analysis of structural variants in breast cancer s using single-molecule sequencing. Genome Res 30: 1258–1273. doi:10.1101/gr.260497.119 ↵Aganezov S...
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Method: Analytical validation of germline small variant detection using long-read HiFi genome sequencing
- Nathan Hammond,
- Linda Liao,
- Pun Wai Tong,
- Zena Ng,
- Thuy-Mi P. Nguyen,
- Chandler Ho,
- Yao Yang,
- and Stuart A. Scott
Genome Res. June 2025 35: 1391-1399; Published in Advance April 11, 2025, doi:10.1101/gr.278836.123
..., Bhatia S, Lee I, Kirsche M, Wappel R, Kramer M, et al. 2020. Comprehensive analysis of structural variants in breast cancer s using single-molecule sequencing. Genome Res 30: 1258–1273. doi:10.1101/gr.260497.119 ↵Ameur A, Kloosterman WP, Hestand MS. 2019. Single-molecule sequencing: towards clinical...
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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
...advantages of long-read technologies is its ability to generate highly contiguous sequences of large genomic regions, including complex and repetitive regions that are difficult to resolve using short-read technologies. This is particularly useful for applications such as structural variant (SV) detection...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge CB10 1SA, United Kingdom Corresponding author: ana.conesa@csic.esAbstractLong-read sequencing (LRS) technologies have revolutionized transcriptomic research by enabling the comprehensive sequencing of full...
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Research: Long-read sequencing for non-small-cell lung cancer genomes
- Yoshitaka Sakamoto,
- Liu Xu,
- Masahide Seki,
- Toshiyuki T. Yokoyama,
- Masahiro Kasahara,
- Yukie Kashima,
- Akihiro Ohashi,
- Yoko Shimada,
- Noriko Motoi,
- Katsuya Tsuchihara,
- Susumu S. Kobayashi,
- Takashi Kohno,
- Yuichi Shiraishi,
- Ayako Suzuki,
- and Yutaka Suzuki
Genome Res. September 2020 30: 1243-1257; Published in Advance September 4, 2020, doi:10.1101/gr.261941.120
...reported the precise analysis of complicated genomic regions, and large-scale aberration detection is enabled by long-read sequencing. For example, a single-molecule real-time (SMRT) sequencer, Pacific Biosciences (PacBio) RS, has been used to analyze BCR-ABL1 rearranged transcripts and their TKI...
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