Provision of Sequencing Equipment and Consumables

Guys and St Thomas’s NHS Foundation Trust (GSTT) has been awarded Funding from NHS England (NHSE) and the Department of Science, Innovation and Technology (the “Funders”) for the financial years 2023/24 and 2024/25 as the lead provider for the delivery of the Respiratory Metagenomic Clinical Service Development Programme (the ‘Project’), from Oxford Nanopore Technologies PLC.<br/> <br/>The Project is a pilot based on patented nanopore based sequencing technology and therefore this contract notice is issued under Regulation 32 (a) of the PCR 2015.<br/> <br/>The Project aims to deliver a national respiratory metagenomics (RMg) pilot clinical service with an integrated biosecurity surveillance purpose, as a world-first programme to combine effective infectious disease management with rapid emerging pathogen detection and notification.<br/> <br/>Oxford Nanopore sequencing is unique, in that it is the only sequencing technology available on the market that enables direct, real-time analysis of short to ultra-long fragments of DNA/RNA, in fully scalable formats. All Oxford Nanopore sequencing devices use flow cells which contain an array of “nanopores” embedded in an electro-resistant polymer membrane. Oxford Nanopore devices are based around a core sensing unit - a nanopore set in an arrayed sensor chip - used alongside a bespoke Application-Specific Integrated Circuit (ASIC), which controls and measures the experiments. Each nanopore corresponds to its own electrode connected to a channel and sensor chip, which measures the electric current that flows through the nanopore. When a molecule passes through a nanopore, the current is disrupted to produce a characteristic ‘squiggle’. The squiggle is then decoded using base-calling algorithms to determine the DNA or RNA sequence in real time. A strand of DNA or RNA is made up of a sequence of different combinations of four nucleotide bases: A, T (or U for RNA), G and C and as each base passes through the nanopore it can be identified through the characteristic disruption it causes to the electrically current in real-time. Advantages of “real-time” sequencing include rapid access to time critical sequencing information (e.g. pathogen identification) and the generation of early sample insights.<br/>

• Oxford Nanopore sequencing is unique, in that it is the only sequencing technology available on the market that enables direct, real-time analysis of short to ultra-long fragments of DNA/RNA.<br/>
• Direct, real-time nanopore based sequencing and data analysis allows rapid turnaround of results and enabling sample to answer within 6-7hrs.<br/>
• Rapid library preparation solutions (from 10 minutes) as well as automatable, high-throughput library preparation that can be performed on various liquid handlers from as little as 3.5 hours for 96 samples.<br/>
• Possibility to perform a sequencing run, recover the library from the flow cell, and re-sequence on another flow cell to increase output.<br/>
• Real-time sequencing, with integrated compute enabling real-time base calling including epigenetic modifications (5mC and 5hmC, high accuracy base calling model).<br/>
• The GridION device can sequence native DNA and RNA from fragment sizes of 20 bp to millions of bases for up to 5 independent MinION Flow Cells.<br/>
• Scalable, benchtop and easily portable devices allowing multiple placements and sites to be set up cost efficiently in a decentralised model.<br/> <br/>The Project has been jointly funded by NHS England and the Department of Science, Innovation and Technology (DSIT) until March 2025 to support the development of a networked respiratory metagenomics clinical service for acutely unwell patients in ICUs across England. The pilot will generate pathogen sequence and patient metadata with the potential to inform national surveillance systems in partnership with UK Health Security Agency.<br/> <br/>As part of the Project, GSTT will disseminate the Funding to the Partner Trust to fund its participation in the Project (the “Work”).<br/> <br/>The Partner Trusts included in the Work are:<br/> <br/>Great Ormand Street Hospital NHS Foundation Trust<br/>University College London Hospitals NHS Foundation Trust / HSL (Pathology supplier to UCLH)<br/>Oxford University Hospitals NHS Foundation Trust<br/>University Hospital Southampton NHS Trust<br/>University Hospitals Birmingham NHS Foundation Trust<br/>Manchester University NHS Foundation Trust<br/>Cambridge University Hospitals NHS Foundation Trust<br/>Newcastle upon Tyne Hospitals NHS Foundation Trust<br/>Guy’s and St Thomas’ NHS Foundation Trust