Oxford Nanopore User Group Meeting, Sydney
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Join us on 5th of March in Sydney, for an exciting series of talks from local researchers using nanopore sequencing. The agenda also includes a technical update from the Oxford Nanopore team, as well as a Q&A with the presenters and a product display.
Space is limited! Please register early to secure your spot.
Time | Agenda | Speaker |
|---|---|---|
10:30 - 11:00 | Registration | |
11:00 - 11:10 | Welcome & Introduction to Oxford Nanopore | Ross Napoli, Oxford Nanopore Technologies |
11:10 - 11:40 | Coming soon | Sebastian Lunke, Victorian Clinical Genetics Services |
11:40 - 12:10 | Progress update from the UK NHS respiratory metagenomic network for clinical care and public health surveillance | Jonathan Edgeworth, Guy’s & St Thomas’ Hospital |
12:10 - 13:10 | Lunch & networking | |
13:10 - 13:40 | Developing a strategic pathway to clinical Nanopore sequencing: Validation and accreditation experience in a diagnostic laboratory | Jessica Wright, Genomic Diagnostics |
13:40 - 14:10 | Managing the data matters: How to get from sequence to report, fast | Natalie Thorne, Genomical |
14:10 - 14:50 | Coming soon | Tony Roscioli & Javad Jamshid, Randwick Genomics NSW Health Pathology |
14:50 - 15:20 | Coffee break & networking | |
15:20 - 15:50 | Coming soon | Dianne De Santis, PathWest |
15:50 - 16:20 | Oxford Nanopore technical update | Andre Sim, Oxford Nanopore Technologies |
16:20 - 16:30 | Closing remarks | Ross Napoli, Oxford Nanopore Technologies |
Speakers
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.
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.
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Jonathan Edgeworth, Consultant Microbiologist , Guy’s & St Thomas’ Hospital 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.
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.
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Natalie Thorne, Genomical)
Jessica Wright, Product Development Lead, Genomic DiagnosticsJessica Wright leads the product development group at Genomic Diagnostics, specialising in the development, validation, accreditation, and implementation of new technologies and assays within a diagnostic laboratory environment. Her work combines innovation, continuous improvement, and workflow optimisation with creative problem-solving, supporting teams to deliver reliable, timely and high-quality clinical results. Jess is also currently studying for RCPA fellowship in Molecular Genomics through the Faculty of Science.
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Dianne De Santis, PathWest, Fiona Stanley HospitalDr. Dianne De Santis is a Clinical Scientist at the Department of Clinical Immunology, PathWest, Fiona Stanley Hospital, Perth, Australia and a Fellow of the Faculty of Science, RCPA. She completed a PhD at the University of Western Australia investigating the role of Killer Immunoglobulin-like receptors in Haematopoietic Stem Cell Transplantation (HSCT). She currently oversees the Haematopoietic Stem Cell Transplantation donor search program in Perth, Australia and is responsible for developing new technologies to improve HLA typing methods used in solid organ and HSCT matching algorithms. Dianne and her team were the first to publish a novel high resolution HLA typing method utilising single molecule sequencing on the Oxford Nanopore platform for deceased organ donor allocation. She is currently the Vice President of the Asia-Pacific Histocompatibility and Immunogenetics Association (APHIA) and a councillor of the International Histocompatibility Workshop committee.
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Sebastian Lunke, Victorian Clinical Genetics ServicesA/Prof Sebastian Lunke is the Head of Division of Genetics and Genomics at the Victorian Clinical Genetics Services. His team at the Victorian Clinical Genetics Service constitutes one of the largest clinically accredited genetics and genomics laboratories in Australia, with a strong focus on translating novel technologies into clinical practise. He is also a co-lead of the Translational Genomics Research Group at the Murdoch Children’s Research Institute.
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Andre Sim, Field Applications Scientist, Oxford Nanopore TechnologiesAndre Sim is a Bioinformatics-Field Applications Scientist at Oxford Nanopore Technologies, supporting New South Wales and New Zealand. He has a background in transcriptomics, single-cell and long-read sequencing applications. Prior to joining ONT, earned his PhD in Germany through the Max Planck Graduate School and completed a postdoctoral fellowship at the Genome Institute of Singapore, where he focused on long-read RNA sequencing data analysis. He developed computational tools for transcript discovery and quantification across bulk, single-cell, and spatial transcriptomics datasets, including the development of Bambu. His research also leveraged nanopore sequencing to investigate polyadenylation dynamics, RNA modifications, and alternative splicing.
