Certain types of cancer are identified using DNA fragments that tumour cells “release” into the blood. A team of Vietnamese researchers has found a way to more reliably “read” these traces.
The so-called liquid biopsy is a particular and complex blood test—still largely experimental—which, in a variety of ways, makes it possible to determine if there is an early-stage tumour in the body or a tumour with active metastases, as well as to assess whether a therapy is having an effect. This innovation could lead to a great leap forward in quality, if the outcomes achieved by the oncologists at the Gene Solutions research institute and the Medical Genetics Institute in Ho Chi Minh City, in Vietnam, which have just been published in eLife, are confirmed.
This recently developed technique is based on the detection, in the blood or in other bodily fluids, of fragments of DNA lost from tumour cells, either naturally or as a result of cancer treatments (in technical terms, ctDNA, or circulating tumour DNA). However, due to the very limited amounts of ctDNA present and the extreme variability of genes, gene expression and other parameters, it is not easy to determine the type of cancer that is the source of these fragments. The tests used today thus often lack accuracy when it comes to classifying the source of tumour DNA and, in many cases, require additional exams, combined with in-depth “gene sequencing”, which is costly and cannot be performed on large numbers of patients.
The Vietnamese oncologists therefore developed a new version of the liquid biopsy, called SPOT-MAS (Screening for the Presence of Tumour by DNA Methylation and Size), which appears to be a distinctly more powerful diagnostic tool in comparison to the methods currently employed. Notably, the researchers implemented a system based on the simultaneous analysis of a range of variables, through the use of artificial intelligence. These parameters consist of: ctDNA fragment size, number of copies present, the methylation situation (in other words, if there is a specific type of chemical modification in the ctDNA), the sequence of the bases (the constituent elements of the genetic code) at the end of the fragments, and any repeated sequences. Taken together, these parameters differentiate tumour DNA from that of healthy cells, as well as making it possible to learn the origin of ctDNA, in other words, the type of primary tumour from which it was “lost” and what stage it is in.
Once the protocol was created, the researchers tested it on 730 patients with colorectal, lung, liver, stomach or breast cancer, as well as on 1,550 healthy individuals, by way of comparison, in order to determine a sort of specific genetic signature (in other words, a characteristic composition of the ctDNA) for each different type of tumour. They then used these “signatures” to analyse the blood of an additional 239 patients, all suffering from one of the five types of cancer involved in the study, in order to verify the reliability of the SPOT-MAS test.
In so doing, the researchers found that the test was able to detect 73% of cancers with 97% accuracy. Furthermore, in addition to detecting the “generic” presence of tumours, the new test—according to the researchers—allowed them, in 70% of cases, to detect the tumours’ tissue of origin, with the most accurate results found in cases of liver cancer (identified in 90% of cases) and the least accurate in cases of breast cancer, of which only about one out of every two cases was detected.
Naturally, the potential of the new SPOT-MAS liquid biopsy will now need to be verified through trials on larger sample groups (the Vietnamese oncologists themselves have already given advance notice of a new series of tests), whose results will have to be compared to data collected through traditional testing. Lastly, financial assessments will also need to be made, to make certain that the new test is actually cost-effective.
The hope is to make available to physicians tests which can increasingly become a part of routine clinical practice, especially in cases where they suspect the presence of a tumour of unknown origin, or to confirm the results of other types of exams.