Science unlocked: publication picks from February 2025

In this monthly series, we share a selection of recent publications in which Oxford Nanopore sequencing was used to unlock novel insights. Spanning from cancer research, to gene therapy, to genome sequencing in the classroom, these studies showcase the advances in scientific research made possible by Oxford Nanopore sequencing.

Featured in this edition:

1. Identifying pathogenic variants in an intensive care setting

2. Unlocking insights into genetic diversity, disease risk, and human evolution

3. Improving the safety of gene therapy vectors

4. Restoring chemotherapy sensitivity in colon cancer organoids

5. Highlighting the need for personalised cervical cancer treatments

6. Overcoming adaptive sampling bottlenecks in large-scale genomic studies

7. Students assembling an endangered horse genome in the classroom

Human genetics

1. Singleton rapid long-read genome sequencing as first-tier genetic test for critically ill children with suspected genetic diseases (European Journal of Human Genetics)

Shotelersuk et al. explored the use of Oxford Nanopore sequencing as a first-tier genetic test for critically ill children in intensive care. Oxford Nanopore technology enabled the researchers to identify more causative variants than short-read sequencing, by better detecting structural variants (SVs) and offering phasing information. These advantages could lead to faster diagnoses and improved patient management in critical care settings in the future.

Key points:

• The researchers identified causative pathogenic variants in 11/18 children with suspected genetic disorders

• Oxford Nanopore sequencing uncovered three large deletions that short-read sequencing failed to detect

• Phasing provided insights into autosomal recessive disorders without needing parental samples, increasing accessibility to genetic testing

• The turnaround time for Oxford Nanopore sequencing was a median of 9 days — 3 days faster than the median time required for short-read sequencing

Read more from lead author Prof. Vorasuk Shotelersuk in our blog

2. Long-read sequencing of 945 Han individuals identifies structural variants associated with phenotypic diversity and disease susceptibility (Nature Communications)

Using Oxford Nanopore sequencing, Gong, Sun and Wang et al. identified 111,288 SVs in 945 Han Chinese individuals. Oxford Nanopore technology allowed for precise breakpoint mapping and haplotype resolution, enabling the detection of large, complex SVs. This study provides valuable insights into human genetic diversity and how this connects to disease risk, genetic traits, and ancient human ancestry.

Key points:

• Oxford Nanopore sequencing surpassed the capabilities of short-read sequencing in detecting complex variants — over 87,000 novel SVs were identified in this study that were missed in the gnomAD project (a high-coverage short-read dataset from nearly 15,000 individuals)

• 24.56% of the SVs discovered here had not been documented in previous long- or short-read datasets

• Oxford Nanopore sequencing captured large, complex SVs affecting gene function, enhancers, and regulatory elements

• The authors identified a variant in GSDMD linked to bone mineral density and kidney injury risk, and another in WWP2 associated with height, fat distribution, and immunity

• The authors used multiple long- and short-read datasets to study the Han diversity in a global and evolutionary context. Approximately 2% of their SVs are ancient polymorphisms shared with chimpanzees, and 5% are shared with Neanderthals and Denisovans, shedding light on evolutionary history

Explore our human variation workflow overview

Biopharma

3. Recombinant AAV batch profiling by nanopore sequencing elucidates product-related DNA impurities and vector genome length distribution (Molecular Therapy: Methods and Clinical Development)

Recombinant adeno-associated virus (rAAV) vectors can contain unintended DNA impurities that could pose safety risks. Current methods to assess purity either overlook unknown contaminants, require large input amounts, or cannot accurately resolve the highly structured inverted terminal repeats in rAAV genomes. Dunker-Seidler and Breunig et al. employed Oxford Nanopore sequencing for full-length vector genome analysis, achieving real-time comprehensive profiling that outperformed other methods.

Key points:

• Oxford Nanopore sequencing successfully identified impurities in rAAV vector genomes, including plasmid-derived DNA, helper plasmid DNA, and host-cell DNA impurities

• The authors detected a considerably improved read quality with Oxford Nanopore V14 compared with V9 chemistry, reducing false indels from 1.42% to 0.55%

• Compared with PacBio long-read sequencing, Oxford Nanopore sequencing provided comparable or superior results, especially for detecting vector genome truncations and impurities within the viral capsid

• Oxford Nanopore technology requires lower sample input compared with other sequencing platforms, making it feasible for early-stage gene therapy research

Read our AAV sequencing workflow overview

Cancer research

4. Overcoming cisplatin resistance in TP53-null colon cancer organoids (bioRxiv)

Cisplatin chemotherapy in colorectal cancer (CRC) often fails due to drug resistance, particularly in TP53-deficient tumours as TP53 mutations impair apoptotic responses. By leveraging Oxford Nanopore sequencing and CRISPR-based functional genomics, Khalili et al. uncovered new therapeutic targets for TP53-null CRC. While still in the early stages, this research has the potential to improve patient outcomes through targeted treatment strategies in the future.

Key points:

• Tumour cells with TP53 mutations compensate for DNA damage by relying on alternative repair pathways

• Using a genome-wide CRISPR knockout screen, researchers pinpointed DNA repair pathway genes, including FANCL, ERCC6, and BRIP1, as key mediators of drug resistance

• Oxford Nanopore sequencing validated CRISPR screening results, providing high-resolution confirmation of guide RNA depletion and structural changes in resistant tumour cells

• Inhibition of FANCL, ERCC6, and BRIP1 significantly increased cisplatin sensitivity, suggesting that blocking these pathways could potentially enhance chemotherapy effectiveness

• This research supports precision oncology, demonstrating how genetic profiling could guide personalised therapies in the future

5. The mutation and clonality profile of genomically unstable high-grade serous ovarian cancer is established early in tumour development and conserved throughout therapy resistance (bioRxiv)

The diversity of high-grade serous ovarian cancer (HGSOC) makes tracking tumour evolution challenging. Oxford Nanopore sequencing successfully phased ultra-long SVs, revealing that tumour evolution is driven by early clonal events rather than therapy-induced mutations. Despite shared mutational mechanisms, each person develops unique somatic mutations, supporting the need for a personalised medicine approach to cancer treatment.

Key points:

• Tumour heterogeneity is believed to be a key feature of recurrence and resistance in HGSOC tumours

• In matched primary and recurrent HGSOC tumours from 32 patients, Diaz and Gull et al. found that somatic mutation profiles remained largely conserved through disease progression

• Chemoresistance likely arises from pre-existing clones rather than new mutations

• Ultra-long reads generated by Oxford Nanopore sequencing validated SVs detected by short-read sequencing, but also uncovered novel SVs including large insertions, deletions, and complex rearrangements

• SV analysis identified three distinct tumour subtypes, providing potential biomarkers for targeted treatment strategies in the future

Discover the Oxford Nanopore Ultra-Long DNA Sequencing Kit and explore what ultra-long reads can do for your research

Bioinformatics

6. Enhancing nanopore adaptive sampling for PromethION using readfish at scale (Genome Research)

Adaptive sampling enables live targeted Oxford Nanopore sequencing without additional library preparation. Here, Munro et al. have improved readfish — a tool that supports live adaptive sampling — so that it can handle the high data output of a PromethION device. Combining adaptive sampling with high-throughput sequencing increases coverage over targeted sequences, enhances SV and copy number detection, and reduces costs, making Oxford Nanopore sequencing the ideal solution for large-scale genomics and personalised medicine in the future.

Key points:

• Readfish is now fully compatible with PromethION, offering both standard and barcode-aware adaptive sampling

• The introduction of mappy-rs (a multithread alignment tool) eliminates computational bottlenecks, keeping up with the high data output of the PromethION device

• Improved multiplexing efficiency allows researchers to sequence multiple human genomes on a single flow cell

Expand the capabilities of your targeted sequencing assays

Animal genetics

7. Sequencing and assembling the genome of Przewalski's horse in the classroom (Journal of Equine Veterinary Science)

In this review, Faulk describes his graduate course in which students used Oxford Nanopore sequencing to provide a high-quality, highly contiguous genome assembly, including the mitochondrial genome, and DNA methylation analysis for the endangered Przewalski’s horse, which previously lacked a complete reference genome. The review highlights the accessibility and affordability of Oxford Nanopore technology, with only $4,000 of materials required for this project.

Key points:

• With Oxford Nanopore technology, genome sequencing is now feasible in educational settings, allowing students to get hands-on experience whilst contributing to scientific knowledge

• The previous genome assembly for Przewalski’s horse was highly fragmented and incomplete, limiting its use in conservation and research

• The new EquPr2 assembly has 25-fold fewer scaffolds and a 166-fold increase in read length N50

• The students found that the mitochondrial genome was 99.63% identical to that of the domestic horse, aiding evolutionary research

• Oxford Nanopore sequencing enabled allele-specific epigenetic analysis, identifying 226 differentially methylated regions, including key imprinting genes

• Pseudohaplotype phasing allowed for precise analysis of heterozygosity and inbreeding, which could inform breeding strategies for endangered populations

Read more in the original publication

Inspired? 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.