Diagnosing a particular strain of flu is normally a complicated business, requiring high-tech equipment and days of work. In a paper to be released today in the Journal of Molecular Diagnostics, researchers at Brown University describe a new biochip that promises to make that process much easier and faster.
The researchers hope to eventually design a chip that could be used by public health officials to quickly track new outbreaks, and by health-care workers in the developing world to cheaply detect drug-resistant strains of HIV and tuberculosis.
“This is the kind of test that could tell you you’re dealing with something new and unexpected,” says Andrew Artenstein, who contributed to the work. Artenstein is director of the Center for Biodefense and Emerging Pathogens at Memorial Hospital of Rhode Island, and a professor at Brown University.
The new biochip simplifies genetic amplification—a process in the middle of a series of steps needed to identify the makeup of a sample of blood or tissue.
Currently, to determine what strain of flu a patient has, a sample’s genetic material has to be amplified using either a polymerase chain reaction (PCR), which replicates DNA, or a nucleic acid sequence-based amplification, which copies the single-stranded RNA. Both of these processes can take hours to complete and require temperature modulations or need specialized conditions that are impossible to control outside a lab.
In their new assay, Artenstein and his colleagues have developed a way to quickly amplify RNA on a chip the size of a driver’s license without the need for temperature changes. On the biochip, the target stretches of RNA are marked with magnetic beads. Magnets draw these marked strands through a narrow channel, separating them from the unattached strands.
“In each disease, there is a specific sequence which identifies that RNA. We attack that sequence,” says Anubhav Tripathi, the probe’s designer, codirector of Brown’s Center for Biomedical Engineering, and corresponding author on the Journal of Molecular Diagnostics paper.
Once isolated, just the target strands can be replicated, instead of the entire sample, allowing the process to take place in a handheld device, far from a lab. This can also happen in a matter of minutes, rather than hours, as current systems require, says Tripathi, who named his new test SMART, an acronym for “a simple method for amplifying RNA targets.”
“With our method, we don’t want to amplify RNA or converted DNA. We want to amplify our own probe, which is very short—just 25 to 26 nucleotides,” Tripathi says.
Victor Ugaz, associate professor of chemical engineering at Texas A&M, praises Tripathi’s approach to a problem scientists have been trying to solve for at least a decade.
“This is really a much simpler, cleaner approach that is really well-suited for portable or portable-type applications,” Ugaz says. “In this case, the beauty, I think, is in the simplicity, which is not trivial.”
Samuel Sia, associate professor of biomedical engineering at Columbia University, says the paper “makes a valuable contribution to improving the methods for nucleic acid amplifications.” Any improvements in the amplification step “can be widely applied to a number of different targets,” Sia says, “because the need to amplify is quite universal.”
Ideally, he says, researchers will eventually incorporate other steps in the detection process onto the same microfluidic chip.
Tripathi hopes to raise money from industry so he can do more testing of his prototype assay. So far, he’s mainly looked for the influenza virus, including swine flu, in samples collected at Memorial Hospital in Rhode Island. He hopes soon to apply his SMART method to test HIV samples collected from a hospital in Kenya. The process of detecting HIV is already simple and easy, but his probe could make a big difference in detection of HIV’s viral load, a measure of the patient’s illness and the effectiveness of medication.