Dolapo Adeyemo
Dolapo, a rising senior studying cognitive and behavioral neuroscience at Loyola University Chicago, optimized and validated qPCR assays for infectious diseases endemic to West Africa.
Infectious diseases pose a threat to our public health. To aid early detection of these diseases, we need reliable quantitative Polymerase Chain Reaction (qPCR) based assays. qPCR is a gold-standard technique used to detect viral DNA and RNA. However, a lot of qPCR based assays have not been optimized for performance and sensitivity. Optimization of assays are dependent on primer concentrations which determine the cycle threshold (CT) and ultimately, qPCR efficiency.
An overthinker—the role I took on during my first week at the Ó³»´«Ã½. I nearly convinced myself that I could not fully grasp my research project or work independently in a lab. But I was very wrong. BSRP pushed me to grow in ways that I did not expect. I’m extremely grateful for my mentors and the incredible BSRP team who were there to support us every step of the way. In the span of these eight weeks, I found confidence, clarity and community. This program transforms how you see not just science—but also yourself.In this study, we test various primer concentrations—ranging from 200nM to 600nM while keeping the probe concentration of 200nM constant. We aim to produce validated qPCR assays within the context of pathogens endemic to West Africa; where the Sabeti Lab has many collaborators aiming to provide pathogen surveillance. Using the Luna Script RT-qPCR kit, we evaluated qPCR assays for eighteen target pathogens including Ebola virus, Lassa fever and others. We conducted 10-fold serial dilutions of synthetic viral DNA or RNA gene fragments, which enabled us to create standard curves for each primer/probe concentration. Our results indicate that some assays, such as Hepatitis B, have shown that the 400nM primer concentration has yielded the best R squared and qPCR efficiency values, in line with manufacturer recommendations. Some pathogen assays such as Orthopoxvirus have yielded the best efficiency with a higher primer concentration of 600nM. Other assays such as HIV-1 have shown a better qPCR efficiency with a lower primer concentration of 200nM. By optimizing these assays, we increase global access to more accurate, sensitive, and reliable diagnostics.
Project: Optimization of qPCR-based Infectious Disease Assays
Mentors: Kyle McMahon and Elyse Stachler, Sabeti Lab, Infectious Diseases and Microbiome Program
