Single Molecule Sequencing for Health in the North East

The North East is well-known for studying the molecular basis of disease, with Universities working in close partnership with the NHS and commercial partners. Traditional areas of expertise were focused on rare diseases such as mitochondrial and neuromuscular disease, rare childhood cancers and rare immune deficiencies. While rare disease remains a key area of expertise, we have expanded our research significantly into more common diseases including common cancer types, reproductive disorders, Type 2 diabetes, inflammatory bowel disease and sepsis, but also increasingly in antimicrobial resistance and wastewater studies. In all of these disease areas we have seen an increased uptake of genomic approaches, largely due to technological developments that now allow us to obtain a more complete picture of the molecular biology of these diseases or use genomics as a highly accurate tool to characterize bacteria. This is essential for prevention and early detection of disease, for rapidly and more precisely diagnosing patients and pointing them to increasingly more targeted/personalised therapies, and for the discovery of new drug targets. In addition, molecular approaches because of their increased specificity and sensitivity have found their way into wastewater monitoring and public health studies.
In this proposal, we are requesting funds to expand our genomic capabilities in the North East to allow us to provide the best opportunities for our biomedical research in all the above mentioned disease areas. Specifically, we would like to acquire equipment that will allow us to study extremely long DNA and RNA fragments, and do so in real-time with very high capacity. This enables us to read the human genome more accurately, as current equipment is unable to study large parts of the genome. The same equipment will also allow us to perform more detailed studies of the transcriptome, the RNA in our cells which is critical to understand the molecular basis of disease, and to study bacterial genomes and the mitochondrion.

Nanopore sequencing technology relies on a nanoscale protein pore that serves as a biosensor embedded in an electrically resistant polymer membrane. Negatively charged single-stranded DNA or RNA molecules can be driven through these molecular pores, creating a disruption of the ionic current from the membrane that is recorded and 'translated' into the base sequences in real-time. This single molecule long read sequencing technology enables the analysis of highly homologous, repeat-rich regions in the genome and sequencing of entire transcripts to study allele-specific expression and splicing defects, and simultaneously allows the study of DNA and RNA modifications. Researchers have performed small-scale pilot studies with this technology by using hand-held equipment (minION, Oxford Nanopore Technologies, released in 2014). Oxford Nanopore Technologies has now developed the significantly larger capacity PromethION machine to allow for applications such as long read whole genome sequencing and native DNA and RNA sequencing. Each PromethION flow cell can deliver around 290Gb of raw data per run with the capacity to sequence 24 different samples in parallel, substantially increasing the yield and speed of sequencing compared to other sequencers. Importantly, both the read length as well as the sequencing accuracy of the technology has markedly improved, with a recently released kit pushing raw read accuracy up to 99.92%. The accompanying NVIDIA DGX Station A100 will provide server grade compute capacity to facilitate and streamline basecalling. The GCF works closely with the Bioinformatics Support Unit and the Newcastle University IT (NUIT) services to transfer, store and process data for further analysis by users. Our high throughput genomics equipment is connected through 10 Gigabit switches for secure transfer of data. The High Performance Computer system has over 5000 cores and 500TB storage, with additional storage available upon purchase.