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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
...the increased complexity of the human , particularly in repetitive DNA regions, which could now be more completely and accurately resolved with long-read sequencing.In the decade following, further advances in generating longer, more accurate reads enabled the T2T consortium to achieve the first complete human...
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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
...limitations in our sample size or sequencing depth. In comparison to adjacent nontumor tissues, HBV DNA integration in HCC leads to a higher incidence of gene fusion events (Zhuo et al. 2021). Using long-read RNA-seq, we confirmed the formation of fusion transcripts between HBV and human genes. Previous...
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Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
- Alicja Pacholewska,
- Matthias Lienhard,
- Mirko Brüggemann,
- Heike Hänel,
- Lorina Bilalli,
- Anja Königs,
- Felix Heß,
- Kerstin Becker,
- Karl Köhrer,
- Jesko Kaiser,
- Holger Gohlke,
- Norbert Gattermann,
- Michael Hallek,
- Carmen D. Herling,
- Julian König,
- Christina Grimm,
- Ralf Herwig,
- Kathi Zarnack,
- and Michal R. Schweiger
Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
...inaccessible AG′ within the RNA secondary structure (Kesarwani et al. 2017). Despite these hypotheses, the exact mechanism of the effect of mutations in SF3B1 is still not resolved.Here, we aimed to comprehensively characterize the effects of SF3B1 mutations in cancer using long-read transcriptome sequencing...
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Research: Nanopore direct RNA sequencing reveals METTL2A-mediated m³C sites in poly(A) RNA
- Shuhei Mitsutomi,
- Anzu Sugawara,
- Masahide Seki,
- Yutaka Suzuki,
- Sotaro Miyao,
- Haozhe Du,
- Kenji Takahashi,
- Yusuke Mizukami,
- Kenzui Taniue,
- and Nobuyoshi Akimitsu
Genome Res. November 2025 35: 2406-2417; Published in Advance October 30, 2025, doi:10.1101/gr.280269.124
...sequencing by replacing the standard DNA polymerase with a reverse transcriptase (Vilfan et al. 2013), although this approach has not been widely adopted. Nanopore direct RNA sequencing has made it possible to directly sequence full-length native RNA molecules without reverse transcription and amplification...
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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...editing efficiency, we amplified genomic DNA from puromycin-selected, doubly transfected C1 cells using primers targeting regions surrounding sites recognized by sgRNAs in RE1, -2, or -3 (Supplemental Fig. S49A). PCR products were analyzed by gel electrophoresis, purified, and sequenced (Supplemental Fig...
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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
...in the transcriptome, we newly generated and analyzed full-length cDNA sequencing data using MinION. We also used the previous Illumina short-read RNA-seq and ChIP-seq data. In RERF-LC-KJ cells, short-read sequences indicated that the STK11 transcript is abnormally spliced at intron 1 and that transcription jumped...
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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
...Table S2).View larger version: In this window In a new window Figure 1. Detection and categorization of HPV integration events in cervical cancers. (A) The number of HPV integration events detected in the DNA (# of events) and detected in DNA and RNA (# of expressed events) across the HTMCP samples...
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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
...and developed nanopore Cas9-targeted sequencing (nCATS), which was available as the SQK-CS9109 kit from ONT (discontinued early 2024) and is the most widely used Cas9-based excision approach. nCATS is an amplification-free approach wherein targets are excised from dephosphorylated gDNA with crRNA guides...
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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
...their cDNA, or in the case of ONT, the option of direct RNA sequencing. Early applications of these technologies have been constrained due to low throughput and high error rates. Recent advances in both long-read platforms have enabled high-throughput long-read transcriptome sequencing at high sequencing...
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Research: Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing
- Sergey Aganezov,
- Sara Goodwin,
- Rachel M. Sherman,
- Fritz J. Sedlazeck,
- Gayatri Arun,
- Sonam Bhatia,
- Isac Lee,
- Melanie Kirsche,
- Robert Wappel,
- Melissa Kramer,
- Karen Kostroff,
- David L. Spector,
- Winston Timp,
- W. Richard McCombie,
- and Michael C. Schatz
Genome Res. September 2020 30: 1258-1273; Published in Advance September 4, 2020, doi:10.1101/gr.260497.119
....Organoid DNA and RNA extractionRNA was extracted using TRIzol (Thermo Fisher Scientific 15596018) RNA extraction protocol. DNA was extracted by removing matrigel from organoids using ice cold PBS or TrypLE following by DNA extraction using Qiagen DNeasy Blood and Tissue kit (Qiagen 69504).SKBR3 growthSKBR3...

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