By Benjamin Ross
April 10, 2019 | During the Molecular Medicine Tri-Conference, dozens of early-career scientists presented their solutions to real-world clinical, scientific, and organizational problems at the event's poster viewing sessions.
Among these young scientists, university students presented their work for a Student Fellowship opportunity.
Several entries stood out, including work from Navjot Kaur at the Indian Institute of Science, Eric Liaw at the California Institute of Technology, and Venkat Subramaniam Rathinakannan at the University of Turku.
Navjot Kaur's work focuses on improving diagnostics for Tuberculosis (TB). According to Kaur, a PhD student in chemical engineering, the disease affects approximately 10 million people every year and is one of the top ten causes of death worldwide. And though the disease has existed for over 1,000 years, access to proper diagnostics for the disease is limited in impoverished areas.
"The current methods for TB diagnostics are out of reach for people living in low-resource settings, both in terms of affordability and accessibility," Kaur wrote in her poster description. "But it is these people who are most prone to being victims of this horrifying disease owing to the low hygiene levels of their surroundings and their weak immune systems. TB patients not only suffer severe physical ailments, they also face a lot of psychological pressure due to social detachment and loss of employment."
Kaur and her collaborators developed a diagnostic tool that works on an isothermal DNA amplification assay and does not require a high-end thermal cycler. The fluorescence-based detection for this assay is based on the interaction of DNA with a DNA intercalating dye, which Kaur says is inexpensive compared to molecular beacon probes.
The device is made of paper and plastic, and there is no requirement for any expensive ancillary equipment to operate it. Kaur says this diagnostic solution has the potential to place modern diagnostics into the hands of underprivileged people, providing an affordable and accessible solution for TB diagnostics.
"This diagnostic solution has the potential to take the power of modern diagnostics to the hands of underprivileged people, providing an affordable and accessible solution for TB diagnostics," Kaur wrote.
Eric Liaw and his co-researchers are tackling the problem of rapid antibiotic susceptibility testing (AST) for bacteria. According to Liaw, the slow speed of current diagnostics necessitates broad-spectrum empiric antimicrobial treatments in the treatment of most infectious diseases.
"A breakthrough in this problem was the advent of genotypic AST," Liaw wrote in his entry form. "These methods use nucleic acid amplification (NAA), such as a Polymerase Chain Reaction (PCR), to detect the qualitative presence of a genetic marker known (through prior research) to be correlated with antibiotic resistance."
While NAA is useful, Liaw says genotypic NAA tests have failed to replace culture-based phenotypic AST tests in clinical scenarios because genetic markers and antibiotic resistance have a low correlation, making the design of rapid phenotypic AST test a high priority.
Liaw and the lab at the Claifornia Institute of Technology developed a solution that uses nucleic acid amplification to measure phenotypic properties of bacterial cells. Liaw says this approach benefits from the speed, robustness, high sensitivity, and high specificity of nucleic acid amplification, yet also bypasses the shortcomings of genotypic AST methods.
According to Liaw, the test has so far worked consistently, and the lab are preparing to test their method on clinical samples.
Venkat Subramaniam Rathinakannan's work applies to the programming challenges of annotating Variant Call Format (VCF) files. Rathinakannan's solution provides an application-based method for annotating VCF files by a non-programming user. According to Rathinakannan, this would allow the user to work independently without the involvement of a bioinformatician for smaller datasets with preset parameters.
"This solution is an improvement as it doesn't require the researcher to understand and learn programming for using the PERL based annotation tool ANNOVAR," Rathinakannan wrote. "The developed application as it can be hosted on to a server can be updated and doesn't have the hassle of installation and constant updates on the local system. It also allows the user to view the results instantly and allows an option for download if the output files are desirable."
The solution makes ANNOVAR more interactive with the application of the R Shiny framework. Rathinakannan says the application is freely available and can be hosted on to a server and the link can be used through a web browser.
So far the application has been tested in a lab with the help of clinicians and wet lab researchers, with upgrades including options available within the tool but not in the application. The end goal, Rathinakannan says, would be to integrate a DNAseq analysis pipeline, thereby automating the entire process.