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  1. Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
    • Xuyan Liu,
    • Lin Xia,
    • Yixin Qiao,
    • Yang Li,
    • Yan Huang,
    • Bingyan Yue,
    • Xi Liang,
    • Xin Yang,
    • Honghui Zhang,
    • Jiaxun Zhang,
    • Xiao Chen,
    • Dan Xie,
    • and Jifeng Liu
    Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
    ...of centromeric regions that limits 319 DNA accessibility and favors conserved repair mechanisms, reducing the occurrence 320 of large-scale SVs (Kashi and King 2006). Sequence annotation revealed that over 60% 321 of INS inserted in satellite/center, satellite, and simple repeat regions harbored 322 inserted...
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  2. Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
    • Judith Arres,
    • Santosh Elavalli,
    • Shalini Behl,
    • Daniel Matias Sanchez,
    • Ayesha Al Ali,
    • Abdelrahman Ahmed Yehia Abdelaziz Saad,
    • Azza Attia,
    • Cyla Minas,
    • Sharika Pariyachery,
    • Shariq Ahmed,
    • Fatmah Aldhuhoori,
    • Nitu Thulasidharan,
    • Gurunath Katagi,
    • Omar Soliman,
    • Shilp Purohit,
    • Vinay Kusuma,
    • Raony Cardenas,
    • Thyago Cardoso,
    • Luis F. Paulin,
    • Philippe Sanio,
    • Joseph Mafofo,
    • Haiguo Wu,
    • Val Zvereff,
    • Albarah El-Khani,
    • Fahed Al Marzooqi,
    • Tiago R. Magalhães,
    • Fritz J. Sedlazeck,
    • and Javier Quilez
    Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
    ....Although our study presents promising results, there are some limitations to consider. First, we used cell lines rather than blood or saliva, which may not fully reflect the challenges of working with clinical samples. LRS requires high-molecular-weight DNA, often more difficult to extract from blood or saliva...
  3. Method: PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
    • Gianluca Mattei,
    • Marta Baragli,
    • Barbara Gega,
    • Alessandra Mingrino,
    • Martina Chieca,
    • Tommaso Ducci,
    • Gianmaria Frigè,
    • Luca Mazzarella,
    • Romina D'Aurizio,
    • Francesco De Logu,
    • Romina Nassini,
    • Pier Giuseppe Pelicci,
    • and Alberto Magi
    Genome Res. November 2025 35: 2501-2512; Published in Advance October 20, 2025, doi:10.1101/gr.280259.124
    ...with Salmon v. 0.14.1 and the reference transcriptome GRCh37 from Ensembl. Normalization and statistical analysis were performed with DESeq2 (v. 1.30.1). DEGs with adjusted P-value < 0.05, as scored by the Benjamin–Hopkins formula, and absolute log2FC > 0.5 were selected. DNA and RNA nanopore sequencing data...
  4. Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
    • Sergey Koren,
    • Zhigui Bao,
    • Andrea Guarracino,
    • Shujun Ou,
    • Sara Goodwin,
    • Katharine M. Jenike,
    • Julian Lucas,
    • Brandy McNulty,
    • Jimin Park,
    • Mikko Rautiainen,
    • Arang Rhie,
    • Dick Roelofs,
    • Harrie Schneiders,
    • Ilse Vrijenhoek,
    • Koen Nijbroek,
    • Olle Nordesjo,
    • Sergey Nurk,
    • Mike Vella,
    • Katherine R. Lawrence,
    • Doreen Ware,
    • Michael C. Schatz,
    • Erik Garrison,
    • Sanwen Huang,
    • William Richard McCombie,
    • Karen H. Miga,
    • Alexander H.J. Wittenberg,
    • and Adam M. Phillippy
    Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
    ...-to-fwd but not fwd-to-rev transitions) (Supplemental Fig. 3).Since ONT UL data require high-molecular-weight (HMW) DNA, which can be difficult to extract for certain sample types (Jain et al. 2018b), we also generated assemblies of only Duplex data. The scaffold statistics, hamming error, and QV are similar between...
  5. Method: Measuring X-Chromosome inactivation skew for X-linked diseases with adaptive nanopore sequencing
    • Sena A. Gocuk,
    • James Lancaster,
    • Shian Su,
    • Jasleen K. Jolly,
    • Thomas L. Edwards,
    • Doron G. Hickey,
    • Matthew E. Ritchie,
    • Marnie E. Blewitt,
    • Lauren N. Ayton,
    • and Quentin Gouil
    Genome Res. November 2024 34: 1954-1965; Published in Advance September 16, 2024, doi:10.1101/gr.279396.124
    ...precipitation (v2; https://nanoporetech.com/document/extraction-method/size-selection2) based on a method previously described (Jones et al. 2021); if <3 µg were available, we used a 0.82× high-molecular-weight bead clean-up (Promega ProNex). One microgram of DNA for each sample was then sheared to a 10–20 kb...
  6. Method: A new compression strategy to reduce the size of nanopore sequencing data
    • Kavindu Jayasooriya,
    • Sasha P. Jenner,
    • Pasindu Marasinghe,
    • Udith Senanayake,
    • Hassaan Saadat,
    • David Taubman,
    • Roshan Ragel,
    • Hasindu Gamaarachchi,
    • and Ira W. Deveson
    Genome Res. July 2025 35: 1574-1582; Published in Advance May 15, 2025, doi:10.1101/gr.280090.124
    ...by half without impacting downstream analyses, including basecalling and detection of modified DNA or RNA bases. Ex-zd compression saves hundreds of gigabytes on a single ONT sequencing experiment, thereby increasing the scalability, portability, and accessibility of nanopore sequencing.Nanopore...
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  7. 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...
  8. Research: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
    • Rylee Genner,
    • Stuart Akeson,
    • Melissa Meredith,
    • Pilar Alvarez Jerez,
    • Laksh Malik,
    • Breeana Baker,
    • Abigail Miano-Burkhardt,
    • CARD-long-read Team,
    • Benedict Paten,
    • Kimberley J. Billingsley,
    • Cornelis Blauwendraat,
    • and Miten Jain
    Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
    ...-molecule sequencing technologies (Oxford Nanopore Technologies [ONT] and Pacific Biosciences [PacBio]) have enabled readouts of long, native DNA molecules, including cytosine methylation. ONT recently upgraded their Nanopore sequencing chemistry and kits from the R9 to the R10 version, which yielded increased...
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  9. Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
    • Li-Ting Chen,
    • Myrthe Jager,
    • Dàmi Rebergen,
    • Geertruid J. Brink,
    • Tom van den Ende,
    • Willem Vanderlinden,
    • Pauline Kolbeck,
    • Marc Pagès-Gallego,
    • Ymke van der Pol,
    • Nicolle Besselink,
    • Norbert Moldovan,
    • Nizar Hami,
    • Wigard P. Kloosterman,
    • Hanneke van Laarhoven,
    • Florent Mouliere,
    • Ronald Zweemer,
    • Jan Lipfert,
    • Sarah Derks,
    • Alessio Marcozzi,
    • and Jeroen de Ridder
    Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
    ...of sequencing platforms are used for -wide cfDNA sequencing, including Illumina sequencing, Oxford Nanopore Technologies (nanopore) sequencing, and PacBio sequencing (Cristiano et al. 2019; Choy et al. 2022; Lau et al. 2023), with Illumina sequencing being the predominant platform owing to its low-cost per base...
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  10. Method: An optimized protocol for quality control of gene therapy vectors using nanopore direct RNA sequencing
    • Kathleen Zeglinski,
    • Christian Montellese,
    • Matthew E. Ritchie,
    • Monther Alhamdoosh,
    • Cédric Vonarburg,
    • Rory Bowden,
    • Monika Jordi,
    • Quentin Gouil,
    • Florian Aeschimann,
    • and Arthur Hsu
    Genome Res. November 2024 34: 1966-1975; Published in Advance October 28, 2024, doi:10.1101/gr.279405.124
    ...on which sequencing technology is most effective for quality control (QC) of LVs, and current cDNA sequencing approaches which rely on reverse transcription (RT) of the lentiviral RNA can introduce bias (Schulz et al. 2021).Nanopore direct RNA sequencing is a relatively new technology that enables...
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