Science Unlocked: publication picks from June 2026
In this monthly series, we share a selection of recent publications that use Oxford Nanopore sequencing to unlock novel insights. Spanning gene therapy, cancer, and infectious disease, these studies showcase the advances in scientific research made possible by Oxford Nanopore sequencing.
Featured in this edition:
1. Comprehensive profiling of gene therapy vectors
2. Resolving structural variants linked to cancer risk
3. Tackling antibiotic resistance in the NHS with 16S sequencing
4. Spotting the asymptomatic spreaders of tuberculosis
Biopharma
1. AviNP-seq: a blindspot-free nanopore-based framework for unmasking AAV genome diversity and determining packaging limits (Human Gene Therapy)
Getting a complete picture of recombinant adeno-associated virus (rAAV) vectors isn't straightforward, but AviNP-seq helps remove the blind spots. Using nanopore sequencing, the workflow combines motor-anchored ligation with Cas9 linearisation to capture intact, truncated, and damaged genomes in a single low-input assay, avoiding the terminal bias of conventional library preparation.
The workflow enabled a comprehensive view of vector composition. It demonstrated greater sensitivity than PacBio HiFi sequencing for detecting tandem species, giving Li et al. deeper insights to support vector design and identify contaminants.
'By integrating integrity mapping, tandem detection, and impurity profiling into a rapid (<36 h), low-input workflow, AviNP-seq provides a robust analytical tool to guide vector design and de-risk early-stage process development'
Li, G-H. et al.1
Read our workflow overview for AAV sequencing.
Cancer Research
2. Identifying a novel intergenic deletion causing Lynch syndrome by nanopore sequencing (Journal of Medical Genetics)
Lynch syndrome is a cancer predisposition condition, sometimes caused by a known mechanism where a 3’-end deletion of EPCAM epigenetically silences MSH2. However, intergenic EPCAM-MSH2 deletions were previously classified as variants of unknown significance (VUS) due to short-read limitations in characterising structural variants.
In a family with Lynch syndrome-related cancers, Oxford Nanopore sequencing successfully defined the breakpoints of the intergenic deletion and showed epigenetic silencing, suggesting that the VUS behaves similarly to the 3’-end deletion. Steffens Reinhardt et al. have therefore reclassified the variant as likely pathogenic. Insights like this could inform hereditary cancer prevention strategies in the future.
'Long-read sequencing proved essential for resolving the breakpoints and mechanism of disease, particularly when MLPA yielded incomplete information'
Steffens Reinhardt, L. et al.2
Explore more applications of cancer research with Oxford Nanopore sequencing.
Microbiology and infectious disease
3. Implementing 16S sequencing in the healthcare sector could enhance antimicrobial stewardship (eBioMedicine)
Bacterial infections are time-critical, and every hour counts to accurately identify the pathogen. Researchers across seven NHS hospitals evaluated Oxford Nanopore 16S rRNA sequencing as a rapid approach for bacterial identification, delivering genus- or species-level insights within 24–72 hours. By providing actionable information faster than culture-based methods, our technology supported antimicrobial stewardship decisions in more than half of cases, with particular value in complex infections where diagnostic uncertainty can be high.
This study by Cunningham-Oakes and Carlisle et al. highlights the potential of nanopore sequencing to help bridge the gap between genomic innovation and future clinical workflows. By enabling rapid characterisation of bacterial communities, including challenging polymicrobial infections, our technology could support more informed antibiotic strategies in the future, and contribute to the global effort to tackle antimicrobial resistance.
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Figure 1. Reasons for requesting 16S sequencing and the resulting outcomes. A) The majority of requests for 16S sequencing originated from failure to grow with conventional culture methods. B) In most cases, the sequencing results supported the current treatment choice (26.6%) or resulted in no change (28%); however, the results contributed to antimicrobial stewardship in 56.2% of cases through either escalation (8.3%) or rationalisation (48.6%) of the antibiotic regimen, including stopping or narrowing of therapy. Figure redistributed from Cunningham-Oakes and Carlisle et al.3 under Creative Commons Attribution License CC BY 4.0.
'The integration of [Oxford Nanopore Technologies] 16S sequencing into routine NHS diagnostics has enabled antimicrobial stewardship by offering a faster method with improved taxonomic resolution'
Cunningham-Oakes, E. and Carlisle, D. et al.3
Read more about this research in our interview with Alistair Darby and Anna Smielewska, or watch Anna’s talk at the ESCMID conference.
4. Diagnostic potential of targeted nanopore sequencing for asymptomatic tuberculosis (BMC Microbiology)
Asymptomatic tuberculosis (TB) often slips under the radar of standard diagnostics like mycobacteria growth indicator tube (MGIT) culture and GeneXpert MTB/RIF assays due to long turnaround times or insufficient sensitivity. In this study, Zhu and Shao et al. put targeted Oxford Nanopore sequencing through its paces, with impressive results. They found our technology to have higher accuracy and sensitivity than standard methods, despite the low bacterial load in the samples.
Nanopore sequencing allowed them not only to detect Mycobacterium tuberculosis, but also to pinpoint drug resistance in the same workflow. Combined with the speed and portability of our technology, these results position nanopore sequencing as an ideal candidate to improve asymptomatic TB detection, which is essential for curbing community transmission of the disease.
'[Targeted nanopore sequencing] is ideal for high-burden, resource-limited scenarios due to its portability, speed, and cost'
Zhu, J. and Shao, S. et al.4
Want to use Oxford Nanopore for your microbial sequencing research? Here’s our getting started guide.
Apply Oxford Nanopore sequencing to your own research questions and you'll never see sequencing the same way again. Explore the nanopore sequencing solution.
Oxford Nanopore Technologies products are not intended for use for health assessment or to diagnose, treat, mitigate, cure, or prevent any disease or condition.
Li, G-H. et al. AviNP-seq: a blindspot-free single-molecule framework for unmasking AAV genome heterogeneity and determining packaging limits. Hum. Gene Ther. 0(0) (2026). DOI: https://doi.org/10.1177/10430342261454324
Steffens Reinhardt L. et al. Identification of a novel intergenic EPCAM-MSH2 deletion causing EPCAM-associated Lynch syndrome by long-read nanopore sequencing. J. Med. Genet. 0:1–5 (2026). DOI: https://doi.org/10.1136/jmg-2026-111541
Cunningham-Oakes, E. and Carlisle, D. et al. Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship. eBioMedicine 129, 106317 (2026). DOI: https://doi.org/10.1016/j.ebiom.2026.106317
Zhu, J., Shao, S., Zheng, W., Chen, L., Zhang, K. et al. Diagnostic value of nanopore-based targeted sequencing technology for subclinical tuberculosis. BMC Microbiol. (2026). DOI: https://doi.org/10.1186/s12866-026-05254-7
