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Innovative UK SME GeneFirst and University of Leeds win £1.4M NIHR grant to clinically validate the use of a novel NGS based technology in bowel cancer screening

GeneFirst has teamed up with the Division of Pathology and Data Analytics at the University of Leeds to investigate the clinical utility of a novel NGS technology, Adaptor Temple Oligo-Mediated Sequencing (ATOM-Seq™), in bowel cancer screening and diagnostics. As the recipient of the highly competitive Invention for Innovation (i4i) funding from the National Institute of Health (NIHR), the aim of the project is to determine whether a sequencing-based assay for bowel cancer, testing either faecal tumour DNA or blood-derived cf/ctDNA (cell free/circulating tumour DNA), would be suited for the implementation into clinical use. In this 36-month project jointly led by Professor Philip Quirke, the ultimate goal is to improve patient experience and outcomes in screening using an innovative technology in addressing current bottlenecks in the screening pathway.

Bowel cancer occurrence is frequent, with 1.85 million cases annually worldwide, and the second deadliest UK cancer, killing 16,571 patients annually In the UK and 850,000 worldwide. Five-year survival ranges from greater than 90% if diagnosed early to less than 10% at advanced stages. The NHS introduced a UK-wide Colorectal Cancer screening program using the guaiac Faecal Occult Blood Test (gFOBT) to detect blood in the stool, offered every two years to people aged 60-69. Now, gFOBT is being replaced by the more accurate Faecal Immunochemical Test (FIT) – both tests are inexpensive and use samples collected at home, ideal for population screening programmes. If blood is detected, the result is confirmed by colonoscopy. NHS England performs typically in excess of 450,000 colonoscopies on average, at a cost of £451 each (more than £200 million annually). Unfortunately, greater than 50% of positive gFOBT and approximately 25% of positive FIT tests are false positives, with no neoplasia identified in subsequent colonoscopy, meaning many patients undergo this expensive, unpleasant procedure unnecessarily. Conversely, these tests also have significant cancer miss-rates. There is a clear healthcare need for more sensitive, specific and cost-effective bowel cancer assays, to support or complement faecal-testing and to reduce unnecessary colonoscopies and false-negatives.

Testing of released tumour DNA extracted from bodily substances, such as blood (circulating DNA or from tumour cells present in blood - cf/ctDNA)) or faeces, can potentially reduce the number of colonoscopies performed and cancers missed. Current market solutions either struggle to detect early-stage cancer and precancerous lesions or have limitations for use in screening and patient stratifications. These limitations are compounded by the highly fragmented cf/ctDNA, often too low in concentration to be captured appropriately using standard methods. Addressing these specific challenges is paramount to evolve bowel cancer diagnostics; GeneFirst proprietary technology, ATOM-Seq, presents a unique opportunity to improve standard practices for cancer screening and diagnosis.

Widely used NGS technologies utilise one of two broad approaches for DNA capture, PCR and ligation. These technologies have drawbacks which can limit their ultimate effectiveness when used in conjunction with testing highly damaged or challenging clinical material, such as that found in cfDNA extracted from liquid biopsies. GeneFirst has developed a novel NGS library preparation chemistry which was designed from the ground up with cell-free material in mind, to maximise the ultimate utility of liquid/faecal biopsy testing. This chemistry, ATOM-Seq, has strengths and is highly versatile which imparts advantages over both PCR- and ligation-based approaches. This technology is ligation free, simple, efficient, flexible, and streamlined, and offers novel advantages that make it perfectly suited for use on highly challenging clinical material.

NGS Team Lead, Dr Thomas Dunwell, said, “The ATOM-Seq chemistry we have developed is an elegant approach to NGS library preparation and the protocols underpinned by this technology are very quick and simple to complete. Huge effort has gone into optimising the efficiency and specificity of the technology without sacrificing sensitivity. This technology has substantial promise, and I am excited to see the quality of data which is produced during this study and how it may improve bowel cancer screening.”

This project considers the wider patient and public perspectives, with expected economic and societal impacts to arise from effective patient triage in the care pathway. Importantly, the health economic evidence of the proposed product will be evaluated, identifying the areas of highest population health and population benefits. This demonstration in improved service delivery and patient care is crucial in supporting informed decision making for healthcare providers and for innovative technology adoption into the clinical pathway.

Chief Operations Officer, Dr Winnie Wu, said, “We are immensely proud to have been recognised by the NIHR and we could not have found a better partner in Professor Quirke and his team to collaborate together and address this vital healthcare challenge. We believe that ATOM-Seq can make a significant impact in bowel cancer diagnosis and complement existing state-of-the art to improve the overall patient experience in screening for this disease.”

Professor Quirke, Yorkshire Cancer Research Centenary Professor of Pathology at the University of Leeds, adds, “This is an exciting opportunity to evaluate a new approach to the earlier diagnosis of bowel cancer. We can treat early disease much more effectively than in its later stages so we hope that if this works for our patients then we can spare them many of the side effects that current patients experience and hopefully reduce the death rate of this horrible disease.

About GeneFirst:

GeneFirst, based in Oxford, UK, is a molecular diagnostics company specialised in developing innovative solutions for infectious diseases and cancer testing using its suite of patented and proprietary breakthrough technologies. The GeneFirst mission is to provide simple, reliable and effective molecular solutions to aid the accurate diagnosis of diseases and improvement of patient management.

For more information please contact:

Dr Winnie Wu

Chief Operations Officer

+44 (0) 1865 407400

About University of Leeds:

The Division of Pathology and Data Analytics at the University of Leeds is one of the largest academic departments in the UK with an international reputation with major interests in pathology, molecular pathology, microbiome and digital pathology. The department has received funding from various sources including MRC, CRUK, Yorkshire Cancer Research, NIHR and Wellcome Trust and has a track record of successful industrial collaborations, including the delivery of products into the market and licensing of novel digital pathology technology.

For more information please contact:

Professor P Quirke

Pathology and Data Analytics,

Leeds Institute of Medical Research at St James,

Wellcome Trust Brenner Building,

St James University Hospital,

Beckett Street,



About the National Institute of Health Research:

The National Institute for Health Research funds health and care research and translate discoveries into practical products, treatments, devices and procedures, involving patients and the public in all our work. We ensure the NHS is able to support the research of other funders to encourage broader investment in, and economic growth from, health research.

For more information please contact:

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