Science unlocked: publication picks from May 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 pharmacogenomics, to mRNA modifications, to antimicrobial stewardship, these studies showcase the advances in scientific research made possible by Oxford Nanopore sequencing.

Featured in this edition:

1. Prescriptions informed by your genome

2. RNA decoded: revealing methylation, splicing, and tail length in a single run

3. Could Oxford Nanopore sequencing be the future of genetic testing?

4. Ultra-sensitive viral screening for safer gene therapies

5. Direct RNA sequencing maps hidden biomarkers in sepsis

6. Faster pathogen ID to tackle antimicrobial resistance

Human genetics

1. Targeted adaptive sampling enables clinical pharmacogenomics testing and genome-wide genotyping (medRxiv)

Over 90% of people carry variants that could impact drug efficacy or safety. Here, Peng and Lin et al. validated Oxford Nanopore sequencing for accurate, haplotype-resolved testing of 35 pharmacogenomic targets, achieving high accuracy and enabling genome-wide genotyping — a scalable, cost-effective step towards truly personalised medicine.

Key points:

• Pharmacogenomic (PGx) testing improves medication safety and efficacy by identifying genetic variants that affect drug response

• The authors validated targeted Oxford Nanopore sequencing for accurate PGx testing in 17 samples across 35 genes

• Oxford Nanopore sequencing delivered >99% accuracy for small variants and >95% for structural variants (SVs), outperforming Illumina microarray

• The method successfully resolved complex haplotypes in key genes such as CYP2D6 and NAT2

• Off-target reads enabled reliable genome-wide genotyping, with strong performance for rare variants

• Through multiplexed three-sample runs, Oxford Nanopore sequencing achieved 25x depth of coverage per sample in under four days, showing potential for scalable clinical use

Watch Pamela Gan’s talk at London Calling 2025

2. Nanopore direct RNA sequencing of human transcriptomes reveals the complexity of mRNA modifications and crosstalk between regulatory features (Cell Genomics)

Understanding the interactions between various mRNA features remains largely elusive due to the limitations of short-read sequencing technology. Kim and Saville et al. used Oxford Nanopore direct RNA sequencing to simultaneously analyse native mRNA modifications, splicing, and poly-A tail length in leukaemia cells, revealing their complex interactions. This high-resolution view offers new insights into transcript regulation and highlights the therapeutic relevance of targeting RNA modifiers like METTL3 in cancer.

Key points:

• By preserving native RNA, Oxford Nanopore direct RNA sequencing enabled simultaneous interrogation of the transcriptome and epitranscriptome at the single-nucleotide, isoform level — information that would not be possible to obtain with short-read methods

• Kim and Saville et al. identified over 12,000 high-confidence m⁶A RNA modification sites across 3,825 genes

• Most m⁶A-rich mRNAs exhibited reduced stability and translation

• The authors found a negative correlation between poly-A tail length and mRNA abundance

• METTL3 knockdown reduced m⁶A globally and influenced gene expression, poly-A tail length, and alternative splicing patterns

• These findings offer a powerful resource for understanding RNA regulation and advancing RNA-based therapies

Explore our direct RNA workflow overview

3. Validation of a comprehensive long-read sequencing platform for broad clinical genetic diagnosis (Frontiers in Genetics)

Short-read sequencing (SRS) technology struggles to resolve large or complex SVs, and repetitive or GC-rich regions, meaning multiple types of testing are required, increasing time and costs. In this study, Oxford Nanopore sequencing enabled accurate whole-genome detection of diverse variant types in a single test — resolving cases that short-read methods could not. This approach could offer clinicians a faster, more streamlined testing, and ultimately improve patient outcomes in the future.

Key points:

• Sen and Handler et al. used Oxford Nanopore sequencing followed by a bioinformatics pipeline comprising eight publicly available variant callers

• When applied to buffy coat samples, the method achieved 100% sensitivity for clinically relevant single nucleotide variants (SNVs), SVs, repeat expansions, and pseudogenes, and 96.15% sensitivity for indels

• Oxford Nanopore sequencing outperformed SRS for variant phasing, repeat sizing, and pseudogene discrimination

• The pipeline resolved variants in complex regions, including PMS2, PKD1, and RFC1, without the need for supplementary tests

• Oxford Nanopore sequencing demonstrated future potential as a diagnostic tool by resolving four cases that were previously ambiguous with SRS

Figure: variants detected using the Oxford Nanopore pipeline from 72 clinical samples. Variants assessed using Oxford Nanopore were grouped into four categories: SNVs, indels, SVs and repeats. For each variant category, the number of variants accurately detected by the pipeline are shown in blue and the number of variants that were not accurately detected by the pipeline are shown in red. Image redistributed from Sen and Handler et al. 2025 under Creative Commons Attribution License CC BY 4.0.

Biopharma

4. A sensitive sample preparation pipeline for adventitious virus detection using Oxford Nanopore sequencing (Molecular Therapy: Methods and Clinical Development)

Oxford Nanopore sequencing, paired with the new CoNS-seq sample prep workflow, enabled rapid and sensitive detection of viral contaminants during cell and gene therapy manufacturing. By enriching for viral genomes even at very low levels, this method could accelerate product releases and boost safety — helping critically ill patients access therapies sooner in the future.

Key points:

• Tsinda and Swofford et al. developed CoNS-seq, a sample prep pipeline using concentration, nuclease digestion, and sequence-independent single primer amplification (SISPA) to enhance virus detection

• CoNS-seq achieved a three-log improvement in virus detection sensitivity compared to standard sample preparation, detecting viruses at 0.001 vg per cell

• The method outperformed standard workflows, with up to 1,420-fold enrichment of viral reads despite background host DNA

• Oxford Nanopore technology generated long reads that spanned entire viral genomes, facilitating rapid, accurate identification

Microbiology and infectious diseases

5. Utilising nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers (BMC Infectious Diseases)

He and Ganesamoorthy et al. used Oxford Nanopore direct RNA sequencing to gain insights into transcriptional and post-transcriptional regulation in sepsis. They were able to capture full-length mRNA from blood samples, revealing gene expression, poly(A) tail length, and isoform-level changes. Oxford Nanopore sequencing provided insights beyond those possible with standard techniques, advancing understanding of infection biology and paving the way for RNA-based diagnostics in the future.

Key points:

• The authors compared Oxford Nanopore direct RNA sequencing and Illumina NextSeq cDNA sequencing on sepsis blood samples and found that gene-level expression was highly correlated across the quantification tools used

• The team mapped poly-A tail length patterns across GO and KEGG pathways in human blood mRNA using Oxford Nanopore direct RNA sequencing — a first to their knowledge

• They identified significant variations in poly-A tail length that are closely related to molecular functions

• Oxford Nanopore direct RNA sequencing enabled direct measurement of poly-A tail lengths, isoform-level resolution, and novel transcript discovery — features not accessible with Illumina cDNA-seq

6. Evaluating the diagnostic utility of 16S ONT sequencing in patients with central nervous system infections and its usefulness in antimicrobial stewardship (The Journal of Infectious Diseases)

Culture-based diagnostics for central nervous system (CNS) infections can be slow and unreliable, particularly for patients already treated with antibiotics. This study showed that Oxford Nanopore 16S rRNA sequencing could rapidly and sensitively identify pathogens missed by culture, potentially supporting faster diagnosis and more targeted antibiotic use in the future — a critical step forward for antimicrobial stewardship in low-resource settings.

Key points:

• CNS infections such as bacterial meningitis and encephalitis are a significant public health concern in low- to middle-income countries (e.g. Vietnam, where the samples were collected for this research)

• Misdiagnosis results in prolonged illness and contributes to antimicrobial resistance

• In this retrospective study, Van Dong et al. obtained 329 cerebrospinal fluid samples from patients with suspected CNS infections

• Oxford Nanopore sequencing identified 17 pathogens that were missed by culture, including in nine patients pre-treated with antibiotics

• The method detected bacteria of regional importance, such as Streptococcus suis, that are not always captured by other methods

• 'If 16S ONT sequencing results had been available to guide therapy decisions alongside CSF culture, 18 patients would have benefited from this additional diagnostic method. This would have included de-escalation of antibiotic therapy for 11 patients, escalation for 5, and a change in antibiotics for 2 patients'

Figure: bacterial pathogens detected using 16S ribosomal RNA Oxford Nanopore sequencing compared to cerebrospinal fluid (CSF) culture. Oxford Nanopore-negative results were anticipated in four patients, as C. neoformans and T. asahii are fungi so are not detectable by 16S rRNA sequencing. Image redistributed from Van Dong et al. 2025 under Creative Commons Attribution License CC BY 4.0.

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