Software that speeds up the process of creating new diagnostic tests could help fight future pandemics, say bioengineers and chemists in Scotland and China.
The team has developed a system that suggests new response pathways to accelerate the design and development of new diagnostic tests.
The system – freely available for researchers to research, adapt and use – could also be used to identify the early stages of non-infectious diseases such as cancer.
In a new article published in nature communication† researchers from Glasgow University and Shanghai Jiao Tong University, China describe how they developed the system and demonstrated its effectiveness.
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They set out to develop response graphs – representations of the biomechanical processes that enable rapid diagnostic testing, including cross-priming amplification (CPA) and loop-mediated DNA amplification (LAMP).
Unlike PCR testing, which requires access to labs and trained personnel, isothermal tests like LAMP can provide fast, accurate results by creating interactions between chemicals and the DNA strands in patient samples and delivering rapid results at the point of care.
However, in many cases, those rapid tests are designed and developed for a specific purpose, which can add unnecessary complexity and make it difficult to easily adapt one test for use in a different diagnosis.
The researchers developed a more generalizable approach to creating new tests, by building a software tool that can convert the reaction graphs into suggestions on how chemical primers and reactions can be used to create the desired diagnostic results.
In the paper, the research team describes how they explored the effectiveness of the software by using it to design the chemical primers and reactions for four different diagnostic tests — three for infectious diseases and one for cancer, a non-communicable disease.
They created a multiplex test for a form of HIV with high levels of sequence variations, a highly sensitive test for tuberculosis, and a study to analyze clinical samples from patients for the presence of hepatitis B. They also developed a test to detect short miRNA sequences. relevant in the diagnosis and prognosis of cancers, including squamous cell carcinoma of the mouth, breast cancer and glioma.
They used their diagnostic tests to test patient samples from labs in China. They then confirmed their results using separate PCR tests. They tested their results against LAMP diagnostics for the same diseases and found that their results were more specific and reproducible than the LAMP tests.
In a statement, lead author Professor Jon Cooper of Glasgow University’s James Watt School of Engineering said: “We have been working for a number of years to develop isothermal tests for diseases such as malaria and hepatitis C for use in parts of the world where reliable access is available. is limited to PCR testing.
“As we built those diagnostic systems, it became clear that we were also building an understanding of how to create a more generalizable approach to testing for specific biomarkers.
“Our programmable system automates much of the early trial-and-error work required to develop new tests, and we have shown that it can be used to reliably diagnose a useful cross-section of transmissible and non-communicable diseases. † It is an exciting discovery and suggests many potential applications in medicine.”
The research was supported by funding from the Innovation Research Plan from the Shanghai Municipal Education Commission, the Natural Science Foundation of Shanghai, the Engineering and Physical Sciences Research Council (EPSRC) and the European Research Council.
