Sequencing Technologies in Clinical Research

Nanopore-based sequencing has become a highly effective next generation sequencing tool for biological research. Nanopore sequencing converts the electrical signals generated by a nucleotide strand (either DNA or RNA) passing through the nanopore into the base sequence.

This methodology was exclusively commercialized by Oxford Nanopore Technologies, allowing sequencing of long reads with real-time sequence detection and analysis. It can also provide base modification detection. The technique has short sample preparation times with low instrument costs.

The technology is a relatively new, rapidly expanding and groundbreaking, with ~79% of nanopore-related literature published within the last 5 years (determined from PUBMED publication stats).

The design of nanopore devices has given this technology greater versatility/flexibility than other sequencing platforms. Allowing work to occur out in the field (using a portable sequencing device) or within a traditional lab research setting. A portable version of Nanopore have been used in randomised clinical trial to produce real-time near-complete genome sequencing of viruses isolated from clinical samples. This study suggests a future role of this portable technique in virus infection monitoring for early detection in diverse populations. As well as analysis of human samples and long-read sequencing of bacterial genomes.

Prof Beggs research group has been as the forefront of the optimisation and deployment of Nanopore sequencing technologies in clinical research. This work that has been disseminated in multiple peer-reviewed publications (in 2018, 2020, 2021 and 2023). Beggs group have used this unique technology to address existing clinical questions such as "how we can improve HLA typing, by potentially reducing process time and cost", aiming to generate a rapid single-tube assay?

Nanopore dependent-research (within Cancer and Genomic Sciences) and service support (from Genomics Birmingham) are essential for our work and supporting the sequencing of internal and external clients, now and moving forward.

Illumina and Nanopore sequencing are currently used routinely within our labs. Both rapidly sequence DNA or RNA and produced rapid and highly accurate genomic, transcriptomic and epigenomic data.