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UK Research and Innovation, Cancer Research UK and industry are investing more than £11 million in an Oxford-led artificial intelligence (AI) research programme to improve the diagnosis of lung cancer and other thoracic diseases.
Professor Fergus Gleeson at the University of Oxford will lead on a programme of research focusing on accelerating pathways for the earlier diagnosis of lung cancer. Lung cancer is the biggest cause of cancer death in the UK and worldwide, with £307 million/year cost to the NHS in England. The earlier that lung cancer is diagnosed, the more likely that treatment will be successful but currently only 16% patients are diagnosed with the earliest stage of the disease. To address this clinical problem, NHS England is launching a £70 million lung cancer screening pilot programme at 10 sites*.
To improve patient care beyond the current screening guidelines, a team of academics from Oxford University, Nottingham University, and Imperial College London; NHS clinicians from Oxford University Hospitals NHS Trust, Nottingham University Hospitals NHS Trust, the Royal Marsden Hospital, the Royal Brompton Hospital, and University College London Hospitals NHS Foundation Trust; and the Roy Castle Lung Cancer Foundation will join forces with three leading industrial partners (Roche Diagnostics, GE Healthcare, Optellum).
Working with the NHS England Lung Health Check programme, clinical, imaging and molecular data will be combined for the first time using AI algorithms with the aim of more accurately and quickly diagnosing and characterising lung cancer with fewer invasive clinical procedures. Algorithms will also be developed to better evaluate risks from comorbidities such as chronic obstructive pulmonary disease (COPD). In addition, this programme will link to data from primary care to better assess risk in the general population to refine the right at-risk individuals to be selected for screening. It is hoped that this research will define a new set of standards for lung cancer screening to increase the number of lung cancers diagnosed at an earlier stage, when treatment is more likely to be successful.
Professor Fergus Gleeson, Chief Investigator for the programme, said
“The novel linking of diagnostic technologies, patient outcomes and biomarkers using AI has the potential to make a real difference to how people with suspected lung cancer are investigated. By differentiating between cancers and non-cancers more accurately based on the initial CT scan and blood tests, we hope to remove the delay and possible harm caused by repeat scans and further invasive tests. If successful, this has the potential to reduce patient anxiety and diagnose cancers earlier to improve survival and save the NHS money.”
This programme builds on the National Consortium of Intelligent Medical Imaging (NCIMI) at the Big Data Institute in Oxford, one of five UK AI Centres of Excellence. The funding, delivered through UK Research and Innovation’s (UKRI’s) Industrial Strategy Challenge Fund, is part of over £13m government investment in ‘data to early diagnosis and precision medicine’ for the research, development and evaluation of integrated diagnostic solutions. UKRI is also partnering with Cancer Research UK, which is making up to a £3m contribution to the cancer-focused projects. The Oxford-led project is one of six awarded from this competition.
Science Minister, Amanda Solloway MP, said:
“Our brilliant scientists and researchers in Oxford are harnessing world-leading technologies, like AI, to tackle some of the most complex and chronic diseases that we face. Tragically, we know that one in two people in the UK will be diagnosed with some form of cancer during their lifetime. The University of Oxford project we are backing today will help ensure more lives are saved and improved by using state of the art technology to identify cancerous tumours in the lung earlier and more accurately.”
Dr Timor Kadir, Chief Science & Technology Officer at Optellum Ltd, commented:
“Three industry leaders – Roche, Optellum and GE – have joined their expertise in molecular diagnostics, imaging and AI to help diagnose and treat lung cancer patients at the earliest possible stage. The programme results will be integrated into Optellum’s AI-driven Clinical Decision Support platform that supports physicians in choosing the optimal diagnostic and treatment procedures for the right patient at the right time.”
Ben Newton, General Manager, Oncology, at GE Healthcare, said:
“We are very pleased to be working with the University of Oxford via the NCIMI project on this important lung cancer research. By extending our existing NCIMI data infrastructure and creating innovative AI solutions to spot comorbid pathologies, we aim to help identify lung diseases earlier in the UK.”
Geoff Twist, Managing Director UK and Ireland and Management Centre European Agents at Roche Diagnostics Ltd, said:
“We are thrilled with this funding award, because it gives us the opportunity to work towards ground-breaking innovation in early diagnosis and because working in partnership is vital to achieve success in the health system. By bringing together the collective knowledge and expertise of these academic, medical and industry partners, this project has the potential to impact patient care globally through new diagnostic solutions in lung cancer.”
Dr Jesme Fox, Medical Director of the Roy Castle Lung Cancer Foundation, said:
“The majority of our lung cancer patients are diagnosed too late for the disease to be cured. We know that we need to be diagnosing lung cancer at an earlier stage, through screening. This innovative project has the potential to revolutionise lung cancer screening, making it more efficient and most importantly, saving lives. Roy Castle Lung Cancer Foundation is delighted to support this Programme”
Professor Xin Lu, co-Director of the CRUK Oxford Centre and Director of the Oxford Centre for Early Cancer Detection, commented:
“I am delighted that this national multi-site collaborative programme will be led from Oxford by Fergus Gleeson. Involving a world-class team of academics, clinicians, local and global industry, and patient representatives, this research is hugely important for accelerating lung cancer detection.”
* The 10 NHS England Lung Health Check sites are:
- North East and Cumbria Cancer Alliance – Newcastle Gateshead CCG
- Greater Manchester Cancer Alliance – Tameside and Glossop CCG
- Cheshire and Merseyside Cancer Alliance – Knowsley CCG and Halton CCG
- Lancashire and South Cumbria Cancer Alliance – Blackburn with Darwen CCG and Blackpool CCG
- West Yorkshire Cancer Alliance – North Kirklees CCG
- South Yorkshire Cancer Alliance – Doncaster CCG
- Humber, Coast and Vale Cancer Alliance – Hull CCG
- East of England Cancer Alliance – Thurrock CCG and Luton CCG
- East Midlands Cancer Alliance – Northamptonshire CCG and Mansfield and Ashfield CCG
- Wessex Cancer Alliance – Southampton CCG
About the technology
TET-assisted pyridine borane sequencing (TAPS) is a new method for measuring DNA methylation, a chemical modification on cytosine bases. DNA methylation has important regulatory roles in the cell but is frequently altered in cancer. These altered DNA methylation levels are preserved in DNA that is released into the blood from cancer cells and therefore DNA methylation has great potential as the basis for a multi-cancer blood test. However, a key limitation to achieving this aim, especially for detecting cancer at the earliest stages, is the low sensitivity of current DNA methylation technology.
One of the advantages of TAPS over the current standard methodology is the avoidance of the use of bisulphite, a harsh chemical that severely degrades DNA. TAPS is a mild reaction that preserves DNA integrity and is effective at very low DNA concentrations, which would increase the sensitivity of blood-based DNA methylation assays. TAPS also better retains sequence complexity, enabling simultaneous collection of DNA methylation and genetic data, and cutting sequencing costs in half. Read more about the potential of TAPS as the basis for a multi-cancer blood test here.
The company Base Genomics has been launched to set a new gold standard in DNA methylation detection using this TAPS technology.
“I am thrilled about the launch of Base Genomics and look forward to seeing the TAPS technology developed in my lab applied to new technologies for cancer detection and the advancement of a variety of fields of biomedical research,”
– Dr Chunxiao Song, assistant member of the Ludwig Institute Oxford Branch, co-founder of Base Genomics, chemistry advisor to the company.
“Genomic technologies with the power, simplicity and broad applicability of TAPS come along very infrequently,
“It has the potential to have an impact on epigenetics similar to that which Illumina’s SBS chemistry had on Next Generation Sequencing.”
– Base Genomics CTO Dr Vincent Smith.
About Base Genomics
Base Genomics has a team of leading scientists and clinicians, including Dr Vincent Smith, a world-leader in genomic product development and former Illumina VP; Professor Anna Schuh, Head of Molecular Diagnostics at the University of Oxford and Principal Investigator on over 30 clinical trials; Drs Chunxiao Song and Yibin Liu, co-inventors of TAPS at the Ludwig Institute for Cancer Research, Oxford; and Oliver Waterhouse, previously an Entrepreneur in Residence at Oxford Sciences Innovation and founding team member at Zinc VC.
The company has closed an oversubscribed seed funding round of $11 million USD (£9 million GBP), led by Oxford Sciences Innovation alongside investors with industry expertise in genomics and oncology. This funding will progress development of the TAPS technology, initially focusing on developing a blood test for early-stage cancer and minimal residual disease.
”The ability to sequence a large amount of high-quality epigenetic information from a simple blood test could unlock a new era of preventative medicine,
“In the future, individuals will not just be sequenced once to determine their largely static genetic code, but will be sequenced repeatedly over time to track dynamic epigenetic changes caused by age, lifestyle, and disease.”
– Base Genomics founder and CEO Oliver Waterhouse.
“In order to realise the potential of liquid biopsies for clinically meaningful diagnosis and monitoring, sensitive detection and precise quantification of circulating tumour DNA is paramount,
“Current approaches are not fit for purpose to achieve this, but Base Genomics has developed a game-changing technology which has the potential to make the sensitivity of liquid biopsies a problem of the past.”
– Base Genomics CMO Professor Anna Schuh
For more information, see the Base Genomics press release.
Dr Sharib Ali specialises in the applications of AI to early oesophageal cancer detection