Genomics England expands use of Oxford Nanopore sequencing in cancer

04 April 2022

Oxford Nanopore technology will be used by Genomics England to investigate and validate at increasing scale the benefits of sequencing for improving patient care and advancing research to develop new treatments. Genomics England’s “Long-Read Sequencing Programme” takes advantage of Oxford Nanopore’s ability to sequence any-length fragments of DNA, including long and ultra-long

Oxford Nanopore has announced today the next steps in its collaboration with Genomics England, which is using nanopore technology in an ongoing proof-of-concept project to evaluate the clinical and research applications of comprehensive genomic analysis of cancer tumours.

Following successful completion of an initial phase of the project, where Genomics England generated and analysed nanopore sequence data on several hundred tumour samples from across its cancer programme. The next phase will focus in more depth and at larger scale on haemato-oncology, sarcoma and brain tumours.

Genomics England researchers will use Oxford Nanopore technology to investigate methylation (5mC,5hmC), SV calling, copy number variant analysis and single nucleotide polymorphism (SNP) detection in the samples. The work is expected to be performed on PromethION 48 devices, the highest-output nanopore sequencers, capable of running up to 48 flow cells at once and performing all these types of variant analyses simultaneously.

Genomics England has one of the world’s largest collections of short-read sequence data from matched patient germline and tumour samples, and one key aim of this project is to resolve structural variants (SVs) and other features and regions of the genome that can be missed by short-read sequencing. The team are also able to simultaneously analyse base modifications in the same data set, potentially enabling faster turnaround times critical in clinical care.

More complete cancer data

Oxford Nanopore’s technology is well suited to serve Genomics England’s aim of developing cancer genome analyses that rapidly and accurately identify the full range of the challenging variants known to cause cancer. The ability to sequence any-length fragments of DNA – as long as 4 million bases – has exciting potential to provide clinicians and researchers a more complete and actionable picture of an evolving cancer genome.

Methylation is also known to be important in cancer, and nanopore sequencing is now able to characterise methylation in real time. Broader access to sequencing technology, with easier-to use, smaller but powerful devices, will potentially be a significant advantage in future applications, especially in some cancer types where turnaround time and fast results are crucial.

Gordon Sanghera, Chief Executive Officer, Oxford Nanopore Technologies, commented:

“Oxford Nanopore’s technology has been used successfully by Genomics England in initial proof-of-concept work and is continuing to deliver rich insights across the entirety of the human genome. This is so important as we work towards much more comprehensive genomic data for cancer research.

We are now delighted to be embarking on the next phase and supporting Genomics England to sequence many more cancer genomes and to extend the application of our technology to more programmes to drive pioneering science and better clinical and health outcomes for patients in the UK and around the world.”

Parker Moss, Chief Commercial Officer, Genomics England, said:

“Oxford Nanopore sequencing and methylation analysis continues to show great promise in cancer. Genomics England is partnering with the company, and the wider academic community, to validate potential clinical, operational and research benefits of their technology. We are really pleased to extend our collaboration programme, which we hope will demonstrate the potential clinical readiness of the technology for the NHS.”

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Genomics England’s Cancer 2.0 Initiative. Since the launch of the 100,000 Genomes Project, Genomics England has brought together patients, clinicians, researchers and industry to collect and analyse genomic and long-term clinical data to gain insight into the nature of genetic changes that drive cancer evolution. In the next step of our cancer programme we are exploring new technologies including long-read sequencing, multimodal data and machine learning, and always with the same goals in mind: to improve outcomes for patients, help clinicians deliver more personalised treatments, and provide world-leading research capabilities in the UK to develop the next generation of precision medicine. Learn more about our Cancer 2.0 initiative here.

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