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Scientists at the National University of Singapore (NUS) have developed a unique low-cost way of cancer testing. This novel test, known as the Heatrich-BS assay, sequences clinical samples that have been heated in order to identify cancer-specific signals contained in a patient’s blood.
The innovative technique offers a non-invasive alternative to tissue biopsies. It costs around S$50 (approximately US$35) from start to finish, compared to other sequencing technologies, which can cost up to S$1,000 (approximately US$740).
The team, led by Assistant Professor Cheow Lih Feng, consists of researchers from the NUS Department of Biomedical Engineering in the College of Design and Engineering as well as the NUS Institute for Health Innovation & Technology. They are now looking for industry partnerships to bring their technology to market.
Current cancer testing technologies may be insensitive or too costly to be utilized for routine screening. Different organs in our body create the DNA in our blood, which is the genetic information that directs our cells how to synthesize proteins and other critical biological building blocks. Cancer cells also leak DNA into the circulation, which can be discovered via liquid biopsies, which analyze blood samples. However, combing through all of the genetic material in a sample – a procedure known as whole-genome sequencing – may be costly and time consuming.
Instead of checking every single person, some physicians look for cancer-specific signs in cell-free DNA, rather like looking for certain faces in a vast crowd of individuals. Even yet, Asst Professor Cheow emphasized, such approaches are not without flaws. “Some patients may have cancer signs that are slightly different, allowing them to pass through the screening procedure,” he explained.
A more sensitive test at a quarter of the cost
The Heatrich-BS assay has been tested on patients with colorectal cancer at the National Cancer Centre in Singapore. The scientists discovered a strong association between how much cancer-specific DNA was detected in a patient’s blood sample and the size of their tumors over time by comparing the findings of their blood analysis with CT scans that depicted the size of patients’ tumors.
Asst Professor Cheow’s team established a method to eliminate non-informative regions of a patient’s DNA in order to pinpoint where the majority of cancer-specific biomarkers are located.
Our DNA is made up of nucleotide components such as adenine (A), thymine (T), guanine (G), and cytosine (C). Cancer-specific signals are often localized in sections of the genome with high repetitions of C and G nucleotides, known as CpG islands, which account for just around 1% of our genome.
“We were doing some unrelated tests when one of our researchers heated a sample,” Asst Professor Cheow explained, recalling the team’s unintentional finding that heat damaged non-informative parts of the genome while leaving the CpG island substantially intact. This enabled them to sequence the remaining genome and diagnose malignancies at a tiny fraction of the market price.
“We achieve a significantly more sensitive assay at virtually the same cost as simple protein biomarker testing,” he explained, “because our technology really focuses on sequencing these areas that matter the most.”
On September 9, 2022, the NUS team published their findings in the scholarly journal Science Advances, and a patent for their work was also submitted.
Article Reference: National University of Singapore Journal Reference: Cheruba, Elsie, et al. "Heat selection enables highly scalable methylome profiling in cell-free DNA for noninvasive monitoring of cancer patients." Science Advances 8.36 (2022): eabn4030. Journal Impact Factor - 14.4 (2021)