United Kingdom

In less than 30 years, NHS genetic diagnostic capability has progressed from low resolution chromosome analysis and sequencing of a very small number of rare diseases associated genes, to the introduction of the routine use of whole genome sequencing at scale, for the first time in any national healthcare system. The primary focus to date, has been the diagnosis of rare heritable diseases including rare cancer predisposition syndromes, with limited therapeutic implications in all but a few examples. The advent of high throughput sequencing technologies and improved bioinformatics along with the reorganisation of existing regional genetic laboratories into a smaller number of Genomic Laboratory Hubs delivering the National Genomic Test Directory supported by Genomic Medicine Service Alliances, will form the National Genomic Medicine Service in the UK. These developments along with progress in other spheres of laboratory diagnostics create exciting possibilities in the advance of truly integrated and personalised diagnostics to support the development of personalised medicine. Collaboration between academic, clinical and industrial partners is essential if these potential developments are to be maximised. This session will explore ways in which these potential opportunities can be realised in the NHS with particular emphasis on the North East and Yorkshire.

Diagnostics North East

From genes to genomes and beyond: developing genomic medicine in the NHS, Dr Michael Wright

### **Precision Diagnostics for Precision Medicine** 
 
Our work continues in [Diagnostics North East](https://diagnosticsnortheast.org.uk/) to provide a unique and integrated diagnostics infrastructure for industry and academia.


Learn more about the resources and expertise available to support researchers, clinicians, and industry in developing and deploying new and innovative diagnostic technologies across the discovery, development, evaluation and adoption pathway.

Speakers are: 

* Dr Michael Wright, Clinical Geneticist, Deputy Medical Director for Newcastle upon Tyne Hospitals
* Professor Sir John Burn, Chair of Newcastle upon Tyne Hospitals
* Professor Nick Reynolds, Consultant Dermatologist and Stratified Medicine Lead for the NIHR Newcastle MIC
* Professor Alastair Burt, Professor of Precision Medicine and Director of NovoPath
* Dr Seamus O'Neill, CEO of Northern Health Science Alliance<br><br>




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Join us in October to learn more about the resources and expertise available to support researchers, clinicians, and industry in developing and deploying new and innovative diagnostic technologies across the discovery, development, evaluation and adoption pathway.


keynote

Converting diagnostic developments into practice involves a complex process of invention, validation and promotion, often in the face of determined opposition from established, if inferior, approaches. I have been involved in two clinically relevant developments which offer approaches of potential broader relevance.

Both developments have had their origins at the Centre for Life where our funding to develop the complex involved a commitment to promote commercial development. I had previously been involved in “spinning out” identity testing into a company called Northgene which we moved into the Centre for Life Bioscience Incubator in 1999 as the first “occupant” on site. This company is now wholly independent and continues to trade. I proposed a technology company called Life Diagnostics which eventually became a wholly owned subsidiary of the University and Newcastle Hospitals called Newgene ltd and traded successfully until it was made quiescent by the effective nationalisation of genomic diagnostics with the creation of the Genome Laboratory Hubs. The staff, all based at the Centre for Life, were transferred into the Yorkshire North East GLH.

1. In the early 2000’s, while head of Institute at the Centre for Life, I offered lab space to a start-up biotech company I had been advising, exploring the concept of point of care genomic diagnosis. When this “spin in” was ready to launch in 2008 as QuantuMDx Ltd, I was allowed to become a shareholder and Chair by the University. The concept originally rested on use of nanowires as the primary sensor but subsequently moved to a more traditional fluorescent marker detection following a rapid “shuttle” thermal PCR. The decision to stick with thermal PCR rather than the now widely recognised isothermal technique, LAMP, was its simplicity and the option of extensive multiplexing. The general focus was infectious disease such as drug resistant tuberculosis where a molecular approach could offer identification of the organism and its drug sensitivity in a single test. A version of the device was put into trial in Peru in 2018 focused on the 14 carcinogenic forms of Human Papilloma Virus underlying cervical cancer. While reasonably successful, it exposed limitations in the resilience of the device and prompted a structural redesign to allow effective use in a wide range of settings.

The Covid19 pandemic caused a rapid realignment of assay development; a triple target SARS-CoV2 assay was developed as both a lab assay and as a new cassette. The single use disposable cassette was refined and put into manufacture while the new version of the QPoc was manufactured and completed CE-IVD testing in July 2021 in our fully accredited laboratory in central Newcastle and first sales were achieved. With a reliable PCR result in around 30 minutes, the newly established sales team are now seeking to secure a market foothold while the assay team are working on a broader respiratory panel assay including Flu A and B and a multiplex Sexually Transmitted Disease panel and the digital team are developing the interface to link directly to laboratory informatics systems.

2. My research focus has been on hereditary cancers for over 30 years with a particular interest in the most common disorder, Lynch syndrome, though to be carried by more than 1 in 300 people and amenable to preventive use of low dose aspirin based on our CAPP2 trial. Sequencing the four mismatch repair genes is expensive and limited but a key feature is the accumulation of multiple “spelling mistakes” in tumour DNA called microsatellite instability. Over more than a decade our academic consortium at the Centre for Life has developed a new form of the assay suitable for large scale analysis using high depth next generation sequencing. This has the advantage of almost unlimited scalability with minimal input from clinical scientists and pathologists and inclusion of other molecular markers such as the driver mutation BRAF V600E which helps to differentiate sporadic MSI high cancers from those likely to be the result of an inherited predisposition. We are now working to embed the new assay across the national Genomic Laboratory Hubs and commercialise with the help of Cancer Research UK the patents owned by the university. Newcastle Hospitals adopted the Newcastle MSI Plus assay in 2020 and it has been accepted as the standard of care for tumour screening in the North East. If current funding applications are successful, we will seek to commercialise through the newly created Buisness, Development and Enterprise Directorate at Newcastle Hospitals and will explore reactivating Newgene ltd to drive international sales and broaden the use of the assay to include urine screening for cancers in the renal tract for which we currently have no simple screening approach.

Despite clear progress, these two success stories are not yet complete. Diagnostics is challenging due to long lead times in research, costs of winning and defending patents, rapid technological advance, institutional preference for existing methods, international competition and short term investment decisions. The NHS and British government could do more to incorporate “social value” into procurement and strengthen policies to protect research investment. Our academic institutions and hospitals need to embrace entrepreneurship, give due credit to achievement of secure intellectual property and help promote its development.


Two journeys across the Valley of Death: QPoc and the Newcastle MSI Plus assay, Professor Sir John Burn

Precision and P4 medicine are contemporary models of healthcare that aim to deliver structured, stratified and relevant approaches to disease and well-being. It is enabled by the availability of large, rich data sets from genomics and multi-omics and a range of cell-free diagnostics (liquid biopsies). Some have predicted that with such developments in these methodologies, the role of histopathology in precision diagnostics may decline in future. Nonetheless, morphological assessment of tissue sections has contributed to a form of precision diagnostics for many decades. The development of high throughput whole slide scanners is now taking tissue-based diagnostics to the next level. Digital pathology offers advantages in workflow for histopathologists and some large departments in the UK have now converted to this platform. In addition, digitisation allows the application of adjunct techniques that enhance diagnostic capabilities for example more accurate measurements than the human eye such as cell proliferation indices. More excitingly, the application of artificial intelligence (AI) algorithms will provide further advances in precision tissue-based diagnostics. At its simplest level, machine learning approaches have been developed by which computers can essentially replicate the morphological assessment of histopathologists and with some applications can do so more accurately and reproducibly. Two such approaches for the diagnosis of breast and prostate cancer have recently been approved by the FDA for use in clinical practice in the US. Deep learning approaches offer potentially much greater information for precision diagnostics with recent studies demonstrating that scanned images of routinely stained sections can be analysed by computer to predict mutational alterations, prognosis, and response to therapy. It appears that “the demise of histopathology has been greatly exaggerated”!

Digital technologies – the coming of Age of Diagnostics, Professor Alastair Burt

In a time of enormous upheaval in the Health and Life Sciences sector, I will attempt to describe the main political and policy drivers that are immediately relevant to the field of Diagnostics in the UK. The presentation will include a brief introduction to the NHSA and our role as advocates for the North and a consideration of the recent Life Sciences vision published by government as well as noting some other relevant policy areas. The implications and likely impact for the north and diagnostics in particular will be explored.

Opportunities under the Levelling-up Agenda, Seamus O’Neill

The study of immune mediated inflammatory diseases (IMIDs), has been revolutionised by the new Omic technologies which are generating a high dimensional picture of the complex and confounding processes that occur during the initiation and progression of IMIDs. Faced with the ability to generate bewilderingly large datasets, researchers are now faced with a unique interpretation challenge. Our understanding of the systems biology of IMIDs are potentially confounded by heterogeneous phenotype data, particularly composite disease scores used to measure disease activity. Machine Learning and Artificial Intelligence methods are garnering considerable interest as novel tools to support Omics and precision medicine, enabling a synthesis of biologically meaningful signals from a background of data noise. Omics and AI are bringing new insights into the molecular landscape of IMIDs, such as rheumatoid arthritis and psoriasis, the impact of these insights on precision medicine will be discussed.

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