Valerie Taly, Research Director & Group Lead, at Université Paris Cité, highlighted the implementation of digital PCR for monitoring cancer patients. Liquid biopsies are more patient-friendly than tissue biopsies because they are less invasive. For early-stage cancers, the level of ctDNA could be as low as 0.01%.
Taly and her group developed a qPCR assay with an approximate sensitivity of between 10% and 20%. It consists of two probes: one targeting the wild-type sequences with red fluorophores and the other targeting mutant sequences with green fluorophores. This is then used to create millions of droplets, and Taly explained that their assay was so sensitive that it could detect one mutant DNA among 200,000 wild-type DNA.
The team previously developed several assays for different mutations of colorectal cancer but with these assays, they could only screen 55% of patients. So, they wanted a single assay that could examine all of their patients. to improve the sensitivity of NGS and develop their own method called BPER which uses statistics and maths. Taly developed a more universal approach using methylation markers like NPY, ALB and WIF1 to detect ctDNA across all patients.
A comparative study demonstrated that digital PCR performed better than BPER in terms of sensitivity and predicting relapse. So, Taly decided to apply this method to the clinic. Taly wanted to determine whether patients would respond after surgery, identify minimal residual disease, analyse response to treatment, and detect early relapse.
Early data showed that the more ctDNA present, the worse the prognostic. In a colorectal cancer study, if a patient is undergoing chemotherapy treatment if one looks at the ctDNA after the second or third round of chemotherapy there are three key behaviours. Patients with increasing levels of DNA have worse survival compared to those with decreasing or normal levels of ctDNA. Patients with detectable levels of DNA benefit from extended chemotherapy, for example, Taly said that ctDNA-positive patients have much greater benefits from being treated for six months rather than three in comparison to ctDNA-negative patients. This is even more evident for patients with later-stage cancer. Finally, ctDNA levels post-surgery predict recurrence.
A study on pancreatic cancer combined ctDNA with CA 19.9 which led to improved patient stratification. Furthermore, Taly conducted a large validation study to confirm the prognostic value of ctDNA. The digital PCR and NGS displayed a good concordance of 96.7%. Developing methylation markers with high sensitivity and specificity was also stressed.
In a nutshell, liquid biopsy using digital PCR is a powerful, non-invasive tool for cancer monitoring. These tools provide a vital role in supporting early detection, treatment monitoring, and relapse prediction across multiple cancer types.
