A single blood or stool sample could spare thousands of people from unnecessary colonoscopies each year. The UK’s bowel cancer screening programme relies on a faecal test that often gives false positives, sending many cancer-free patients for an expensive and unpleasant colonoscopy that the NHS already struggles to provide enough of. This project tests ATOM-Seq, a new DNA sequencing method that can detect tumour DNA from tiny, fragmented samples in blood or faeces—something standard sequencing cannot do. If the assay reliably picks up colorectal cancer from these samples, patients who test negative could skip the colonoscopy altogether, freeing up appointments for those who genuinely need them. The same test would also provide immediate genetic information about any tumour found, removing the need for a separate biopsy. Because ATOM-Seq uses standard lab equipment, it could slot into existing NHS pathology labs without major new infrastructure. A health economics analysis will calculate exactly how much money and waiting time the NHS could save.
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Colonoscopies are the current gold-standard method for detecting Colorectal Cancer (CRC), but demand for these tests already exceeds capacity. Many of these expensive, unpleasant examinations result from false-positive Faecal Immunochemical Tests—the test utilised in the national CRC screening program. There is therefore a great need for smarter patient stratification prior to colonoscopy. Detection of tumours through Next Generation Sequencing (NGS) testing of cell free/circulating tumour DNA (cf/ctDNA) is a promising potential solution, but this approach has yet to be put into clinical practise. Traditional NGS methods struggle to process cf/ctDNA because it too highly fragmented for PCR-based approaches and of too low concentration for ligation-based approaches. We therefore present ATOM-Seq, a novel library preparation technology that avoids these limitations and is uniquely suited to use in liquid-biopsy testing. Internal testing on reference standards and limited clinical samples has shown our assay to be a highly powerful method for low-frequency mutation detection and we now seek to clinically validate our approach. In this 36-month project, we will develop a CRC-specific ATOM-Seq assay and variant calling software and use this to determine whether an ATOM-Seq-based assay could reliably detect CRC from typical clinical samples: Formalin preserved (FFPE) tumour samples or blood/faecal derived cf/ctDNA. We will also perform a health economics analysis to determine what benefit the implementation of our assay would provide to existing healthcare systems. If ATOM-Seq can reliably detect CRC from such samples, cancer-free patients could be spared unnecessary colonoscopies. This would greatly reduce NHS costs and waiting times by allowing colonoscopies to be provided to those with genuine need. The mutational information we generate would allow for immediate stratification of genuine cancer patients without the need for further testing. Our assay uses standard molecular biology laboratory equipment and skillsets and so can be readily incorporated into existing healthcare infrastructure.
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