Oxford Nanopore User Group Meeting, Sydney

Genomic sequencing is today well established as standard of care in rare disease diagnostics, enabling analysis from single genes to most of the genome. Yet challenges remain, largely stemming from the predominant use of short read data, including missed diagnosis in inaccessible genomic regions, inability to ascertain more complex variations, and or the need to resolve ambiguous variants using orthogonal methods. Oxford Nanopore long-read sequencing promises to overcome many of these challenges, from enabling diagnosis in previously unsolved cases using whole genome sequencing to streamlining laboratory processes using the vast potential application space of adaptive sampling. Here we will share our wins and challenges in implementing various ONT based assays into routine diagnostic service delivery, including challenges encountered on the path to clinical accreditation, recommendations for future improvements, examples of cases solved, and a vision for the future use of ONT technology in our laboratory.

Clinical metagenomics aims to sequence bacterial, viral, fungal and parasitic microbes in clinical samples to generate a comprehensive profile of all relevant pathogens in a single rapid test. In theory, this provides all the information clinical, infection control and public health teams need for decision-making in their different domains; however, although theoretically plausible and an attractive proposition, there are many implementation barriers that need addressing to realise this vision. In 2025, the UK NHS and UKHSA jointly embarked on a 3-year national programme to implement and evaluate a same-day respiratory metagenomic service for intensive care unit patients with severe infection on 30 hospital sites. The service has been established at 6 sites so far with a further 10 sites planned for 2026. Metagenomics has identified a range of culturable, fastidious and unculturable pathogens, most of which are common and expected but some more unusual or missed by standard testing. Initial treatment is being reproducibly optimised in around a quarter of patients across the different sites and about 2000 metagenomic datasets have been transferred to UKHSA for deeper analysis of potential emerging pathogens and antimicrobial resistance genes through the mSCAPE programme. Alongside implementation, the network has been tasked with generating clinical and health economic evidence and progressing an accreditation and quality assurance framework to inform a commissioning decision in 2028. The talk will provide a broad update on progress and challenges, along with a personal perspective on what is needed to make linked clinical-public health metagenomic networks a practical global proposition.

Oxford Nanopore Technologies (ONT) has shown us that what you’re missing matters. Now, managing the data matters too.

For labs to turn ONT sequence data, and the new insights it reveals, into clinical reports, they need data management solutions that work in regulated settings and save them time getting there.

In research it’s acceptable to wait for pipelines to run;it’s ok for scientists to manually pore over the output files, and it’s reasonable for the data to live on various servers across an institution. But in a clinical environment, the workflows must be fast, automated, reliable, standardised and secure.

At Genomical, we specialise in genomic data management for clinical labs, helping them achieve accreditation, automate pipelines, integrate different genomic software tools and store the data – all within a single secure cloud platform. And now Genomical can do this for ONT workflows too.

Genomical comes pre-integrated with ONT-compatible tools, meaning, labs inherit all the sophistication, cybersecurity and compliance of a mature Genomic Information Management System (GIMS).

In this presentation I will cover how Genomical runs Epi2Me at scale, connects with an ONT-compatible tertiary tool, and stores the data for future re-analysis. For labs looking to take their research to real-world clinical use, Genomical provides the infrastructure to make it operational.

Our laboratory has been working with Oxford Nanopore long-read sequencing for over three years, evaluating a range of applications and experimental approaches. Through this process, we have translated long-read sequencing to establish it as a reliable diagnostic tool. This presentation will outline how we selected and validated our first clinical assays within a diagnostic framework, the operational requirements addressed to enable routine implementation, and representative cases demonstrating diagnostic value. It will also highlight our future directions, including expansion of long-read applications, assay development, and integration into broader clinical genomics workflows.

Title: Oxford Nanopore technical update Synopsis: Over the past year, Oxford Nanopore Technologies has delivered a range of technical advances updates its sequencing platform. This presentation will highlight key updates in basecalling, innovations in adaptive sampling for targeted sequencing, and newly released and enhanced protocols. With a particular focus on human genomics applications, we will explore how these developments are expanding genomics in Australia, while also offering a forward look at what’s on the horizon.