Methylation in action: two stories in every read

On an Oxford Nanopore device, you can choose to generate modification data alongside your genetic or transcriptomic dataset.

Epigenetics and epitranscriptomics play a key role in regulating gene expression, so can provide another layer of insight to your nanopore research without any additional lab steps or sequencing runs.

In this Tech Talk with Researchers blog, we hear from scientists investigating the role of methylation across diverse research areas, from wildlife conservation and human development to cancer and rare diseases. Along the way, we’ll share more case studies that showcase what’s possible with nanopore methylation analysis. Plus, at the end, you’ll find our suggested resources to help you get started.

Non-invasive biomarkers for wildlife conservation

Eugenie ‘Charley’ Yen (University of Massachusetts Amherst, USA & Queen Mary University of London, UK)

Sea turtles are threatened by climate change due to their temperature-dependent sex determination system, but changes in sex ratios of hatchlings can’t be tracked without lethal or invasive procedures. At London Calling 2026, Eugenie discussed her work on identifying sex-related methylation biomarkers to tackle this problem.

The researchers identified differentially methylated sites across 24 genes that could robustly identify sex in turtles using non-lethal skin biopsies. This data provides a basis for developing a scalable method for sexing sea turtles that could inform real-world conservation management practices.

Download our plant, animal, and environmental sequencing white paper for a deeper dive into how nanopore sequencing could help you study the far-reaching impacts of climate change.

Decoding human development through RNA modifications

Ailsa MacCalman (University of Exeter, UK)

RNA modifications are crucial for understanding human development and disease, but historically, analysis has been limited to one modification type per experiment. Ailsa and her team are using direct RNA sequencing of human pancreatic samples to generate a comprehensive modification dataset.

Using samples representing different stages of pancreatic development, Ailsa simultaneously tracked the enrichment and loss of eight distinct modification types in genes linked to pancreatic development or disease, or insulin production. Novel datasets like this could guide targeted therapies and rare disease diagnosis in the future.

RNA modifications also underpin brain function. Read our transcriptomic case study to find out more about the role of methylation in neurological development and disease.

Real-time insights: methylation tools in oncology

Lennart Kester (Princess Maxima Center for Pediatric Oncology, The Netherlands)

Faster tumour classification could enable quicker access to the right treatment. Real-time methylation-based tumour classifiers could produce rapid answers, so Lennart and his team are working on these tools.

Classification tools have been developed for central nervous system tumours, other solid tumours, and for haematological malignancies. With high accuracy and rapid turnaround, these tools could deliver clinically actionable results for cancer patients faster than current classification methods.

Learn how other research teams are using nanopore sequencing for leukaemia or brain tumour classification, with the ultimate goal of reducing the time to treatment for patients.

Building epigenetic knowledge at population scale

Danny E. Miller (University of Washington, USA)

Methylation influences many diseases, and epigenetic data has the potential to support diagnosis or help determine whether variants of uncertain significance are pathogenic. However, population-scale datasets and analysis tools are currently lacking. This is where Danny and his team step in.

Their work focuses on EpiSignaLR, a tool to identify or evaluate epigenetic signatures associated with rare diseases. This is designed for Oxford Nanopore data, providing an alternative to array-based tools. By incorporating data from the wider research community, EpiSignaLR could become a powerful tool to tackle the diagnostic odyssey.

Brynja Sigurpálsdóttir (Amgen deCODE genetics, Iceland)

Generating population-wide data is a big investment, and if genetic and epigenetic data requires two separate sequencing runs, then time and costs add up. So, for Brynja and the deCODE team, who undertake large-scale studies, nanopore sequencing is the answer.

The team are resequencing 50,000 UK Biobank samples using Oxford Nanopore technology to analyse structural variants and methylation data in one go. Initial insights suggest that rich datasets like this will provide new understanding on traits linked to health, such as smoking, and what drives gene expression.

Hear more from Danny and Brynja in our studio interview following their London Calling talks. You can also find out how scientists are developing large-scale datasets to better understand neurodegenerative diseases.

Finding the right resources

If these examples have inspired you to use nanopore sequencing for your own methylation project, we have a range of resources to help you get started.

New to epigenetic analysis with Oxford Nanopore sequencing? Get a rapid low-down with our epigenetic demo, or for more in-depth information on the kits you may need and questions you may have, check out our methylation getting started guide. Alternatively, watch our knowledge exchange to better understand how nanopore sequencing detects methylation patterns, and the benefits of using our platform for your research.

Familiar with nanopore sequencing but want a better understanding of the data you can expect? You can find an overview of how Oxford Nanopore compares to other detection methods in our methylation flyer, while our methylation poster provides comprehensive benchmarking data.

Whether you are looking to undertake human variant analysis, tumour-normal sequencing, or transcriptomic analysis, to guide your research we have a range of workflows that incorporate methylation analysis. Finally, if you want to understand best practice for our methylation detection bioinformatic tool Modkit, watch our Oxford Nanopore led training session.

If you’ve enjoyed this Tech Talk with Researchers blog, why not try our Real Talk with Researchers series, where we hear from our community on topics such as accuracy, scalability, and the robustness of nanopore data.

Oxford Nanopore Technologies products are not intended for use for health assessment or to diagnose, treat, mitigate, cure, or prevent any disease or condition.