Punch card programmable modular molecular diagnostics platform for resource poor settings

Infectious diseases are a leading cause of death and disability especially in resource-limited settings. Diagnosing many infectious diseases, especially when patients have a similar clinical representation, often requires diagnostic tools that can reliably and correctly identify the cause in order to take the appropriate intervention. Currently, such tools are lacking in many rural areas and poor countries because of their high cost, infrastructure requirements such as reliable wall-plug power and the need for a cold-chain for reagents. Lack of these tools leads to an over-reliance of syndromic management of diseases. With rising antimicrobial resistance, there is an urgent need for robust diagnostic tools. Microfluidics has emerged as one way to address this challenge due to the capacity to run biochemical assays using low fluid volumes resulting in minimal use of expensive reagents. However, current systems are costly, a single pump costing several hundreds of dollars for example. To address this challenge, we invented a low-cost programmable microfluidic system that can be ran without electricity. The microfluidic module is composed of three main components: a microfluidic chip, punch card tape and a reader/actuator that acts on the microfluidic chip based on instructions encoded in the punch card tape. In our system are 30 independently addressable pumps, each pump costing less than 2 dollars for the basic hand-crank powered system and a flow rate of 100 microliters per minute per pump. In addition, we have 30 independently addressable valves, each valve costing less than a dollar, taking 100 milliseconds to close upon opening. We also implemented 30 on-demand droplet generators for each device, capable of generating 2.5 nanoliter droplets for digital biochemical assays. In addition we implemented a programmable enhanced mixer effectively tackling the challenge of mixing at low Reynolds numbers in the microfluidic channels. Programming of the microfluidic system is achieved through the presence or absence of holes in punched cards which are interpreted by reader/actuator system. Added to this module are additional ones for a completely integrated system for running molecular biochemical assays. The system can run all standard nucleic acid assay steps including DNA extraction, isolation, amplification and detection. DNA extraction is through a thermal lysis system capable to reaching 90 degrees Celsius from room temperature in less than 5 minutes. Nucleic acid isolation is achieved through an array of fusion-5 glass microfiber matrix discs embedded in the microfluidic chips. Isothermal amplification is implemented using a self-regulating heating element. The optical detection module is comprised of three light-sheet lasers and three cameras fitted with emission filters to enable three-channel real-time fluorescence imaging. The current detection system is designed for FAM, Cy5 and Cy3 fluorescence channels. All the modules are programmed and controlled using a raspberry pi computation module fitted with a 13,000 milliampere-hours rechargeable battery. With this system, we designed and implemented a recombinase polymerase amplification assay for detecting all five malaria species known to cause disease in humans (P. falciparum, P.vivax, P.knowlesi, P.malariae and P.ovale). With our modular molecular diagnostic platform, we hope to empower health practitioners glob- ally with tools that will enable timely and appropriate intervention for patients all over the world. In addition to the medical applications, we envision a general purpose platform with applications in education, agriculture, research and environmental monitoring.

Keywords: Bioengineering.
Advisor: Prakash Manu 
LaBeaud Desiree 
Pease R. (R. Fabian W.) 
Yock Paul G.