The Nanopore Community Meeting 2024 in Boston unveils 'a new frontier of genomics — multiomic single-molecule sensing’

This year, the Nanopore Community Meeting (NCM) was held in Boston, USA, welcoming a host of speakers that ‘represent the crucible of this multiomic genomic revolution’, including Nobel Laureates, professors — and even a high school student — to discuss the impact of their research using nanopore technology. The talks are available to watch via the online NCM platform — sign up for free to view posters and products, talk to nanopore experts, and watch talks on demand.

Over the past two days, researchers have presented how they use nanopore sequencing across a wide range of applications, from sequencing water of a local natural swimming spot to investigating genes that drive kidney disease at the isoform level. Here are some highlights of the compelling research presented.

The power of high-quality, closed microbial genome assemblies

Opening the event, Dr Samuel Shelburne (The University of Texas MD Anderson Cancer Center, USA) discussed the power of whole-genome sequencing (WGS) to study healthcare-associated infections (HAIs) and determine how they are transmitted. Samuel presented the nanopore workflow he and his team developed ‘to efficiently and accurately assess genetic relatedness amongst major antimicrobial-resistant pathogens’, ultimately providing data that could inform preventative measures and protect public health.

Dr Julie Haendiges (U.S. Food and Drug Administration, USA) further highlighted the importance of WGS with nanopore technology to generate closed genome assemblies of foodborne pathogens. Julie introduced the Center for Food Safety and Applied Nutrition (CFSAN), a branch of the FDA that uses nanopore sequencing to generate reference-quality genome assemblies from microbial isolates for research into functional genomics and phylogenetic analysis. Watch Julie’s talk to hear how the CFSAN outreach programme is providing domestic and international laboratories with ‘the tools and knowledge to close their own genomes’, bringing the power of long nanopore reads to the future of food safety.

For the first time ever, a high schooler took to the stage at NCM. Noah Bryan (Bayview Secondary School, Canada) took the challenge of presenting to a large audience of scientists in his stride to demonstrate how he used nanopore technology to develop a field-based water test. Find out why ‘the MinION is the perfect tool for this test', and how a 16-year old student is using it to tackle water contamination.

Simplifying methylation detection with direct nanopore sequencing

As part of the opening session on day two, Brynja Sigurpálsdóttir (deCODE genetics, Iceland) presented her large-scale methylation research using nanopore technology. She found that CpG methylation detection using nanopore sequencing was consistent with laborious oxidative bisulfite sequencing and ‘identified about 190,000 methylation-depleted sequences covering about 83 Mb of the genome’. Watch her talk online to find out what previously hidden associations she discovered, and how nanopore sequencing has given her ‘the potential, finally, to do a lot of these studies that we didn’t have before’.

Methylation, along with causing imprinting diseases, may act as a molecular marker of disease severity and progression in conditions that are not triggered by methylation. Dr Matthew Bainbridge (Rady Children's Institute for Genomic Medicine, USA) took centre stage and announced: ‘I love these mics — they make me feel like Madonna’ before presenting his research in undiagnosed paediatric diseases. He explained how he is utilising long nanopore reads to characterise repeat regions in research samples from undiagnosed disease cases because ‘short-read sequencing is only telling us that this is expanded, but we don’t know how it’s expanded’. Watch Matthew’s engaging talk to find out how he is also using nanopore technology to characterise methylation patterns to uncover potential biomarkers for a range of diseases, not just imprinting disorders.

Revealing novel genomic information in human diseases

Not only can nanopore sequencing directly detect methylation, but it also provides a comprehensive solution for resolving complex genomic regions associated with rare diseases. Dr Paula Saffie (Clinica Santa Maria, Chile) presented a low-cost extraction and nanopore sequencing workflow that generates high-quality, whole-genome sequences to investigate hereditary ataxias. This single pipeline paves the way for characterisation and potential diagnosis of rare diseases, as well as to increase global access to genomic sequencing because the workflow is so simple 'anyone could do it'.

As well as hearing how nanopore sequencing is being used to investigate the genomic aetiology of complex neurological disorders, we found out how Dr Benjamin C. Reiner (University of Pennsylvania, USA) is using the technology to investigate the effects of neurological treatments at the single-cell level 'with long-read data alone'. Watch the presentation to find out how Benjamin used RNA nanopore sequencing to investigate molecular changes in prefrontal cortex tissue research samples after either ketamine or electroconvulsive therapy.

Speeding up characterisation of cancerous tumours

Finally, Mathilde Filser (Curie Institute, France), presented how she uses nanopore sequencing across an array of cancer research applications, including detecting structural variants in predisposition genes and identifying methylation, fusions, and copy number profiles simultaneously — all in a single assay. Watch the talk online to find out about the potential of nanopore sequencing as ‘a really robust three-in-one tool for the classification of brain tumours and sarcomas’.

Missed any of the live talks? Catch them online!

This rounds up the Nanopore Community Meeting for 2024. To hear about the Post-Community Meeting Biopharma Day, stay tuned for a blog from Veronica Fowler (Commercial Development [Applied Markets], Oxford Nanopore Technologies) discussing how nanopore sequencing is transforming the biopharmaceutical landscape.

If you have missed any of the talks from the past two days, they are now available to watch on demand on the NCM platform until Tuesday 24 September, and then they will be on the Resource Centre.

We look forward to seeing you next at London Calling in May 2025! Abstract submissions are now open, and tickets will be available in January.

Submit your abstract for London Calling 2025 here.