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London Calling 2023: Technology update

Record-breaking performance and rapid sequencing, across the nanopore sequencing platform

Following the early access rollout of “Q20+” chemistry in 2022, Oxford Nanopore sequencing technology has now broken records in performance, providing more biological information than traditional platforms, rapidly and at any scale. The platform now enables the characterisation of telomere-to-telomere genomes, the sequencing of single nucleotide variants (SNVs) as well as, or better, than traditional technologies, in addition to the characterisation of structural variation, complex copy number variants and real-time gold standard methylation.  This year “Q20+ chemistry moved from early access to released stage.  

  • Improved performance: While the latest “Q20+” sequencing performance using the Simplex method continues to consistently deliver high performance for most genomic applications, the technology update included record-breaking performance data for more challenging projects using Duplex. Duplex exceeds Q30+/99.9% single molecule accuracy irrespective of read length and will become more widely available in a controlled commercial launch.  

  • Richer data: The Company highlighted an expanded machine learning model to enable real-time, high-accuracy epigenetic insights in all contexts, including plants and bacteria, delivering on the promise to sequence any DNA modification in any genome. 

  • Adaptive sampling: The software-controlled technique that enables real-time enrichment or targeting, built into MinKNOW, is available for the PromethION, including the P2 Solo, allowing researchers to rapidly answer specific biological questions from larger datasets on small and accessible devices.   

  • Improved basecalling: Continual improvements were announced for the latest, most high-performance basecaller, Dorado, simplifying and accelerating primary data processing to expedite research and discovery. Dorado will keep up with 24 flow cells on PromethION A100 towers and run CpG methylation and alignment with minimal slowdown, adding base modifications to standard sequencing with no extra cost.  It will be folded into MinKNOW by July.  

  • Full device integration of PromethION and NVIDIA A100 GPUs harnesses their computational power for faster basecalling. 

Pipeline: enabling accessible, distributed sequencing for anyone, anywhere 

Oxford Nanopore continues to innovate towards a new future of near-sample, real-time, low-cost technology that can characterise biological samples in any environments from clinics to factories to classrooms.   

  • High-output, small format: The PromethION 2 Solo rollout continues, opening up new high-output sequencing possibilities with compact form factor. Developer access to the PromethION 2i, with integrated compute and screen, starts now and will continue through the year.   

  • New MinION – with iPad1 connectivity: The MinION sequencer has been revamped for the first time since 2015 and will continue to enable a broad scientific community to take control of their high-performance experiments, rapidly and in any environment. Features include better thermal control and an updated connection to USB-C for user convenience. 

  • The new MinION MkID will also offer easy seamless connection to an iPad Pro, enabling it to use all the latest features including long battery life, accelerated processing, 5G mobile connectivity and more. Developer access starts later this year.  

  • Smaller formats: In development and now showing Q20+ sequencing, a new, small and low-power chip (application specific integrated circuit - ASIC) will further drive the ability to analyse anything, anywhere. This new ASIC will underpin a new family of lower-cost, lower-power devices, including the MinION MkII while the standard MinION ASIC is also being revamped to deliver data more quickly. 

  • These small form factor, single flow cell devices are equipped with vertical loading for ease of use. A new device, a multiple flow cell MinION MkII is in design and will enable up to eight flow cells on a low-power, USB-C interface, with a total output of 40-80 Gb per run. 

Direct RNA sequencing launch, available in Q3 2023 

RNA, the messenger molecule that carries genetic information from DNA and directs the synthesis of proteins, has traditionally been sequenced by conversion to cDNA.  New understanding of RNA’s functional significance – and related emergence in RNA-based therapies including vaccines – has underscored the importance of RNA-related research. Oxford Nanopore is the first to enable direct sequencing of the native molecule, and in doing so reveals more biology including RNA base modifications. 

  • New RNA chemistry: Oxford Nanopore has introduced a new kit and flow cell for direct RNA sequencing for increased accuracy and output, with the potential to unlock a new field of biological analysis. This update will enable significant advancements in the RNA research market alongside novel applications of direct single molecule sensing such as mRNA vaccine research, where non-natural RNA bases used in their development need to be sequenced. Single molecule raw-read accuracy has increased significantly, while output has improved 3-4x compared to existing Oxford Nanopore RNA sequencing chemistry. This new chemistry is even more accurate at detecting RNA modifications. 

Simplifying products and workflows to support broader usage 

To support different users taking advantage of nanopore sequencing, innovations are being introduced to simplify and make more accessible the end-to-end sequencing process. These includes provision of easy-to-use data analysis tools in EPI2ME, the analytics tool set provided by Oxford Nanopore. 

  • Easier interface to support more applications: EPI2ME supports increasingly broad applications, from infectious disease, biopharma quality control testing, human variations and single cell. This enhanced interface equips users at all levels of expertise with the information they need, wherever they are. New features also include the ability to run on local hardware or seamlessly integrate with cloud compute. The interface will allow users to run workflows and interact directly with results. It will be compatible with Windows, macOS and Linux. 

Pipeline: enabling ultra-high output, high-quality nanopore sequencing  

The PromethION 48 is already capable of delivering nearly 10,000 genomes per year, at two human genomes per flow cell, from $345 per genome.  Oxford Nanopore highlighted improvements to high-output sequencing with the PromethION line to support users with larger programmes, large sample numbers, or service providers in high-output applications.   

  • Increased output: The Company highlighted the immense headroom still available in the platform that will be delivered overtime utilising new pipeline enzymes (that pass DNA through a nanopore faster), for increased output and improvements to run buffers. With greater speeds there is the potential to deliver as many as four human genomes from a single PromethION Flow Cell and up to 20,000 genomes per year. 

Notes 

Release phases: 

1 Developer access: Trial release of new innovations to a small group of developers to confirm functionality and explore early use cases. Available by request only. 

2 Early access: All customers have access to the latest innovation. Products are available to order in the main or private store. Products are subject to availability and regular changes. 

3 Released: Products are stocked, available to all customers. Iterations can still be expected but are more controlled with one to three months change notifications. 

4 Fully released: These products are mature with users receiving change notifications three to six months in advance. 

Footnote:

1. iPad and iPad Pro are trademarks of Apple Inc.