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Spanish Researchers Developing POC Test for Detecting Risk SNPs for Osteoporosis, Other Diseases


NEW YORK – A Spain-based group of researchers has developed a cheap, point-of-care test technology that can detect single-nucleotide polymorphisms and, they said, be applied to a range of diseases.

The use of the test in determining a patient's genetic risk of osteoporosis, described in a paper published in July in ACS Central Science, is the team's most recent application, but it has done previous work to detect genetic variants associated with cardiomyopathy and antimicrobial resistance for tuberculosis.

To build the osteoporosis risk test, the team utilized previous genome-wide association studies that identified which SNPs were associated with osteoporosis, said Ciara O'Sullivan, a professor in the department of chemical engineering at Universitat Rovira i Virgili in Tarragona, Spain, and one of the developers of the test.

Once the team knew which SNPs to look for, it built primers to detect the SNPs in DNA from a patient's finger-prick blood sample. The platform uses isothermal solid-phase primer elongation with ferrocene-labeled nucleoside triphosphates, where four primers specific to each SNP are placed on individual electrodes in a microfluidic cell. After combining a thermally lysed blood sample with recombinase polymerase amplification reagents and injecting it into the cell, the primers get elongated as long as they are 100 percent complementary to the SNP. The elongation reaction produces an electrochemical signal that indicates the presence of a specific SNP, and that data is fed into an algorithm that determines a risk score for osteoporosis, O'Sullivan said.

The ACS paper tested for five SNPs, with the results validated by Thermo Fisher Scientific TaqMan SNP genotyping assays and Sanger sequencing, although O'Sullivan noted that many more SNPs can be detected in one test if necessary. The test does not require DNA extraction or purification, and the time to result doesn't change based on the number of markers, she said — key benefits for ease of use in multiple settings, including at the point of care. The blood sample only needs to be diluted and thermally lysed before running the test, which returns results in about 15 minutes.

The arrays and overall concept of the test were designed by O'Sullivan's team, but she said that UK-based laboratory automation company Labman Automation created the electronic device used to run the test. The researchers noted in the ACS paper that the maximum number of SNPs that could be simultaneously detected with the device is 16, but that developmental work is ongoing to produce a device with more channels that could increase the number of SNPs detected in one test.

In its first proof-of-concept paper from 2021 detailing the testing method, the team detected a single SNP associated with resistance to rifampicin in sputum samples with Mycobacterium tuberculosis.

In that paper, the authors said that the electrochemical detection method they developed could facilitate the multiplexed detection of SNPs "closer to the point-of-need," and while many microarray platforms are for use in whole-genome analysis, their method "can find applications where a subset of application-specific SNPs need to be analyzed in a rapid, cost-effective, and facile manner."

The method and device are both "generic," meaning they are not limited to one disease or condition. To adapt it for other diseases, O'Sullivan said the user would only need to switch the probes to be specific for whichever condition is being detected. Her research group is starting a project to determine the genetic risk of developing cardiovascular disease using SNPs, and there are other groups investigating the use of SNPs in determining patients' response to medication.

O'Sullivan's group is also working on an assay to identify 14 high-risk human papillomavirus genotypes from cervical swab samples that could serve as a screening tool for patients at higher risk of developing cervical cancer, as well as a tool to detect infection. O'Sullivan did not specify the exact genotypes her team aims to identify, but the National Cancer Institute said the 14 high-risk HPV types are HPV 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68.

Hans Peter Dimai, a professor at the Medical University of Graz who was not involved in the development of the test, said via email that one of the strengths of the technology developed by O'Sullivan's team is that it can be adapted to measure and quantify genetic markers of any disease. 

Dimai noted that, in addition to the speed of the results, another benefit is that genetic loci, "which usually require access to highly specialized and costly laboratory equipment in tertiary settings can be measured in low-threshold healthcare institutions," such as a general practitioner's office. 

The team aims to eventually commercialize the technique it has developed, and O'Sullivan said they have seen particular interest from groups in Europe that would like to apply the platform to metabolic disorders. The researchers are also working with institutions for tropical medicine in the UK and Portugal to determine how the device could be applied in low- and middle-income countries, particularly to determine antibiotic resistance. According to O'Sullivan, the price per SNP — which includes the array, reagents, and primers — is about €1.00 ($1.07), making it cheap enough to implement in most countries. She noted that Labman Automation has commercialization rights to the device itself.

As for the osteoporosis test, the next step is a "much larger-scale clinical validation," as the most recent ACS study only used 15 samples, she said.