Revealing more to transform human health

Out with the old. In with the future

At the booth, we demonstrated both our wet and dry lab best practice workflows (check them out on our Resource Centre), and showcased our automated, sample-to-answer device, TurBOT. This benchtop system is designed to generate libraries and perform sequencing, including basecalling and data analysis, in a fully automated fashion – find out more and register your interest now.

At our ever-popular Data for Breakfast sessions, our experienced bioinformaticians discussed advances in the analysis of repeat expansions, and the workflow for targeted analysis of pharmacogenes using adaptive sampling (see the poster).

Answers to questions you didn’t even know you had

We were honoured to be joined by Pilar Alvarez Jerez (NIH Intramural Center for Alzheimer’s and Related Dementias (CARD), US), who presented to the gathering crowd on how nanopore sequencing could be used to view haplotype-resolved variation and methylation in the human genome. We thoroughly enjoyed hearing about the cutting-edge research being undertaken using Oxford Nanopore devices, and had the opportunity to chat to Christos Proukakis (University College London, UK), who shared his research on single-cell whole-genome sequencing of human brain tissue to identify somatic mutations which may have a role in neurodegenerative disorders. He discussed the reliability of using long nanopore reads to resolve complex gene regions:

We also caught up with Stephanie Yan (Johns Hopkins University, US) about her research into gene expression and splicing diversity in samples from the 1000 Genomes Project. She highlighted the importance of obtaining long sequencing reads from human samples representing a wide geographic profile for improving our understanding of human genetic diversity:

Finally, we talked to Kofi Opoku (University of North Carolina at Chapel Hill, US) who is investigating the potential of whole-transcriptome sequencing on the Oxford Nanopore platform as an alternative approach for solid tumour diagnosis in resource limited settings. He highlighted how affordability and portability were crucial for sequencing device selection:

If you're interested in hearing how nanopore transcriptome sequencing could be applied to address cancer outcome disparities in low-resource settings, you can watch more here.

Ultra-rich data for answers with impact

In the CoLab Theater, we demonstrated the capacity of nanopore sequencing technology to capture single nucleotide variants (SNVs), structural variation (SVs), repetitive regions, haplotype phasing, RNA splice variants, isoforms, fusion transcripts, oligonucleotide base modifications, and more. We explored how a multi-omics view into biology is providing insight into genetic and genomic medicine, and that tumour development can be elucidated using an end-to-end native tumour-normal sequencing workflow with long nanopore reads. You can learn more by viewing our tumour-normal sequencing workflow or listening to our Knowledge Exchange on characterising variants in tumour-normal research samples.

Meanwhile, at the poster hall, the Oxford Nanopore Applications team presented the following posters:

• Targeting and comprehensive characterisation of pharmacogenes using Oxford Nanopore Technologies’ adaptive sampling
• Nanopore adaptive sampling combines both targeted and low-pass whole-genome sequencing in a single assay
• Haplotype-resolved multi-modal analysis of cancer genomes using Oxford Nanopore sequencing
• Comparison of structural variant calls from Oxford Nanopore haplotype resolved and telomere-to-telomere genome assemblies

What you're missing matters

Finally, at our Industry Education session, we were delighted to host Lucy Kaplun (Variantyx Inc., US), and Kimberley Billingsley (NIH Intramural Center for Alzheimer’s and Related Dementias (CARD), US), alongside Cora Vacher (Market Segment Manager — Human Genetics, Oxford Nanopore Technologies), and Rosemary Sinclair Dokos (VP of Product Management, Oxford Nanopore Technologies), to discover how researchers are asking bolder questions with Oxford Nanopore.

Lucy Kaplun shared how Variantyx are using low-pass nanopore sequencing to corroborate and provide contextual information on variants detected, but not fully characterised, by short reads, in a clinical research setting. Research examples were shared demonstrating how long repeats could be captured in a single nanopore read, elucidating whether the variant is pathogenic. Beyond repetitive regions, nanopore sequencing was also used to clarify research cases with mobile element insertions, SVs, variant phasing, and mitochondrial heteroplasmy. Overall, with visual inspection, Variantyx achieved variant detection sensitivity of 0.99394 for SNVs, 0.97857 for small insertions/deletions, and 0.95833 for SVs, whilst avoiding the time-consuming steps and logistical complications associated with using multiple, variable technologies. Lucy will be presenting at the Nanopore Community Meeting: 2023, Houston — see the full agenda and register.

Kimberley Billingsley walked us through how CARD is establishing their long-read initiative, with the goal of generating a genetic resource from thousands of human brain samples, in order to accelerate research into Alzheimer’s disease and related dementias. Long sequencing reads are key for this initiative as they capture important, disease-relevant forms of genetic variation, such as repeat expansions and SVs; these are currently poorly understood but could provide new targets for future clinical research. Kimberley described the steps taken to develop the wet-lab protocol, computational pipeline, and accessible data storage solution, all of which needed to be optimised to establish this ambitious high-throughput project¹. The team are now exploring the data to characterise SVs, gene expression, differential methylation, and somatic/mosaic variation, across brain regions. Both genetic variants and methylation patterns can be analysed from the same sample when using nanopore technology, maximising data retrieval and removing the sample and time limitations that need to be considered when performing multiple, independent analyses.

We hope that all who attended ASHG enjoyed the event as much as we did. If you’d like to find out more about the exciting insights being discovered by researchers using nanopore technology, we will be hosting our next Nanopore Community Meeting as a hybrid event in Houston in December. Discover the scientific agenda and register now – don't miss out!