Liquid biopsy tests detecting cancer-derived DNA

For cancer earlier detection, researchers are seeking to develop methods that are less invasive than current tests, which would allow them to be performed on more people and at a higher frequency. Liquid biopsies, taking advantage of cancer-specific biomarkers such as tumour-derived DNA in the blood, urine or saliva, are an attractive opportunity for a minimally invasive detection or screening assay. The challenge for the field is to make these detection methods sensitive and specific enough. To be used as a reliable cancer test, assays need to be able to detect the very low levels of circulating tumour DNA (ctDNA) in the blood and differentiate this from DNA shed into the blood from normal cells. 

TAPS DNA methylation detection technology

Modifications of DNA by methylation and hydroxymethylation have important roles in gene silencing and other cellular regulatory processes but are frequently altered in cancer cells and maintained in tumour DNA that is released into the blood. An advantage of methylation profiling is that the usable information is spread across hundreds of sites, potentially increasing the chances of detecting evaluable profiles at even low ctDNA concentration. DNA methylation signals may also provide cancer type-specific information, as Dr Chunxiao Song has shown in lung, pancreatic and liver cancer, important in an early detection screening programme.

However, the clinical application of DNA methylation profiling with low-input circulating DNA was limited by the previous dependency on bisulphite sequencing. Bisulphite is a harsh chemical that causes severe degradation of the DNA sample, lowering sensitivity. To overcome this issue, Drs Chunxiao Song and Benjamin Schuster-Böckler developed a bisulphite-free and base-resolution sequencing method, TET-assisted pyridine borane sequencing (TAPS), for detection of 5mC and 5hmC. TAPS biochemistry uses a mild reaction that preserves DNA integrity and is effective at very low DNA concentrations. Due to its unique direct mechanism, TAPS generates fewer errors and is cheaper than bisulphite sequencing.

TAPS is now being tested in a variety of cancers, including oesophageal, pancreatic and liver cancers with the support of the NIHR Oxford Biomedical Research Centre, Ludwig Cancer Research (Oxford Branch), and Ellie Barnes' DeLIVER programme.

Spinning out TAPS technology

In June 2020, the biotechnology company Base Genomics was launched based on the TAPS technology with an oversubscribed seed funding round of $11 million USD (£9 million GBP), led by Oxford Sciences Enterprises alongside investors with industry expertise in genomics and oncology. Four months later, Base Genomics was acquired in a $410 million deal by Exact Sciences to accelerate their work towards developing a blood test for early-stage cancer.

TriOx multi-cancer detection test

TriOx is an innovative test that analyses multiple features of DNA in the blood to identify subtle signs of cancer, which could offer a fast, sensitive and minimally invasive alternative to current detection methods. The test, developed in Professor Anna Schuh’s laboratory (Department of Oncology), combines TAPS with machine learning to integrate various signals from the DNA circulating in the blood.

The TriOx test was evaluated on blood samples from patients with and without cancer who had been referred by their GP with symptoms that might be due to cancer, as well as on asymptomatic individuals without cancer. It demonstrated the ability to detect cancers of six types (including early-stage cancers) and distinguish between people who had cancer and those that did not with 94.9% sensitivity and 88.8% specificity.

The team are now validating TriOx across more cancer types and larger patient groups. They are also adapting TriOx to allow its application in resource-limited clinical settings such as the NHS or lower- and middle-income countries.

Liquid biopsy test for detection of Burkitt lymphoma in sub-Saharan Africa

In collaboration with the Muhimbili University of Health and Allied Sciences (MUHAS) in Dar es salaam, Tanzania, as part of the National Institute for Health and Care Research (NIHR)-funded AI-REAL consortium, Professor Anna Schuh and her team have developed a minimally invasive liquid biopsy test for the rapid and precise detection of Burkitt lymphoma.

Despite its aggressive nature, Burkitt lymphoma is often curable when treated quickly, with survival rates over 90%. Treatment is widely available and free-of-charge in most sub-Saharan countries, however current diagnostic tests demand specialist expertise and laboratory equipment that are often unavailable in resource-limited settings. Due to this, most children either remain undiagnosed or are diagnosed too late. In much of the region, survival rates can fall below 50%.

The new blood test demonstrates strong ability to distinguish Burkitt lymphoma from other conditions, achieving an overall accuracy of 98%. Importantly, the blood test dramatically reduces the time needed to reach a diagnosis. In a study published in Nature Medicine, the liquid biopsy diagnosis was 40.3 days faster on average, compared to tissue biopsy diagnosis, cutting diagnosis time to just 6.5 days.

Further work is now being carried out to understand how to scale the test for clinical use so that more children can benefit from this advance.

Using platelets as tumour DNA sponges

Research led by Professor Beth Psaila (MRC Weatherall Institute of Molecular Medicine) and in collaboration with the Universities of Edinburgh and Swansea has uncovered an unexpected and powerful new function for platelets - the tiny blood cells primarily known for their role in blood clotting. The Cancer Research UK-funded study, published in Science, demonstrated that platelets also act as scavengers, capturing and storing fragments of DNA that are circulating in the blood, including foetal DNA and mutated DNA from cancer cells. Analysis of platelet DNA via a simple blood test was found to reveal the presence of even “pre-cancerous” changes - indicating this may be a powerful technique for the early detection and prevention of cancer. This finding may mean that the sensitivity of cancer screening tests could be improved, enabling cancers to be detected much earlier than previously possible.

Further research is underway to assess which parts of platelet DNA provide the most useful information about cancer and how blood tests can look for them accurately.