Oxford Nanopore sequencing at large cohort scale: new insights from the NIHR BioResource

In the study of human health, identifying the many variants that contribute to the risk of complex diseases can prove challenging. With legacy short-read sequencing technology offering an incomplete picture, the need for comprehensive identification of variants across the genome is increasingly evident. At the London Calling 2025 conference, Dr Nathalie Kingston and Dr Kathy Stirrups of the NIHR BioResource (Cambridge, UK) described how they are utilising Oxford Nanopore sequencing to address this challenge in the first project to use the technology on such a large scale across multiple research areas.

The NIHR BioResource is a national platform for health research, with over 350,000 recallable participants from diverse backgrounds, including healthy individuals and those with a range of conditions. Their goal is to better understand the genetic and epigenetic landscape of some of the UK’s most urgent health challenges — and potentially redefine the future of population genomics in the process.

Complexity beyond the short-read horizon

The team decided to integrate large cohort Oxford Nanopore sequencing into three flagship studies. Unlike short-read sequencing technology, which fragments DNA and can miss large or complex changes, nanopore sequencing generates reads of any length, from short to ultra long. Nanopore reads of unrestricted length facilitate the detection of structural variants (SVs) and repetitive sequences, revealing regions of the genome that are challenging to resolve with short reads.

The NIHR BioResource team recognised that nanopore technology could be transformative — not just for variant detection, but for understanding biology at a much deeper level than before. Crucially, the approach would allow them to work with native DNA, preserving epigenetic signals and avoiding DNA damage associated with bisulfite conversion. This matters because DNA methylation patterns are increasingly recognised as key regulators in health and disease. While a complete analysis of the datasets is ongoing, early findings have already validated their approach.

The tool: PromethION

The researchers opted for the high-output PromethION device for large cohort sequencing due to its scalability. In their workflow, DNA was extracted from blood and saliva samples using a variety of methods due to sample age. The researchers used the EPI2ME human variation workflow, wf-human-variation¹, to examine SVs, single nucleotide variants, copy number variants, short tandem repeats, and CpG methylation with a single pipeline.

Kathy stated that ‘we’ve demonstrated that we have a workflow that can scale to 48 human genomes per week per PromethION with 30x coverage’. Across their eight devices, this enables the sequencing of up to 384 genomes per week — 1,500 every month.

Striking insights so far

In one project, the team sequenced research samples from participants in the UK Eating Disorders Genetics Initiative. They chose individuals with extreme phenotypes — a body mass index of either below 14 or above 60. Using Oxford Nanopore reads, they hope to uncover novel repeat expansions and structural changes that contribute to disease risk. Kathy emphasised that ‘there are no real drugs to treat these kinds of diseases’, so these variants may represent potential leads for new therapeutic targets in the future.

In another project, the team sequenced samples from the Genes and Cognition Study. This cohort of over 36,000 participants had undergone cognitive profiling in 2021 and again in 2023–2024. With heritability estimates for dementia ranging from 58–79%², and current polygenic scores falling short, the team suspected that currently undetected SVs and epigenetic changes could reveal novel information. In addition to these variants, age-related methylation patterns may influence disease onset. Through Oxford Nanopore sequencing, they were able to detect haplotype-level methylation which should enable the discovery of new functions at scale.

The researchers also applied high-output nanopore sequencing to the study of rare diseases to unveil more genetic information than with legacy techniques. In 2020, the NIHR BioResource launched its Rare Disease Project using short-read technology, which involved over 8,000 participants³. However, Kathy noted that they ‘only got a diagnosis for 20% of the patients that were part of the programme’. In this study, short-read technology failed to capture complex SVs, repetitive sequences, and methylation patterns — features that often underpin disease mechanisms.

Clearly, a new approach was needed. Kathy explained that they ‘want to do better for these patients, and that’s where our journey into long-read sequencing has started’.

By reanalysing research samples from known rare disease cases, they confirmed that nanopore technology can detect known variants, including de novo SNVs, compound heterozygotes, and SVs. Furthermore, epigenetic data was available in the same sequencing run, which allowed haplotype-specific methylation patterns to also be identified. With Oxford Nanopore reads, the researchers were able to phase without the need for parental samples — a major advantage over short-read sequencing technologies.

A new era for large cohort research

These projects from the NIHR BioResource are some of the first to apply Oxford Nanopore sequencing across multiple disease areas in a large population cohort — and the technique is already showing its value.

The pioneering work of NIHR BioResource highlights how Oxford Nanopore sequencing is not simply an upgrade, but a paradigm shift. From improved variant detection to rich methylation insights, the technology is helping researchers move beyond the limits of short-read data to see the full genomic picture. In doing so, they are bringing clinical research one step closer to the answers that matter for the future of precision health.

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