Developing a Smarter, Portable, and More Affordable Flu Diagnosis System with LabVIEW and NI CompactDAQ

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"By using NI CompactDAQ for our solution as well as LabVIEW graphical system design software for control and data analysis, we created a compact and portable system."

- Hsieh Tseng Ming James, Institute of Bioengineering and Nanotechnology, A-Star

The Challenge:
Developing a compact thermal cycler that is easier to use, portable, and more affordable than traditional systems.

The Solution:
Building a mini thermal cycler with NI CompactDAQ and LabVIEW to perform real-time polymerase chain reactions with the advantages of USB plug and play.

Author(s):
Hsieh Tseng Ming James - Institute of Bioengineering and Nanotechnology, A-Star

Polymerase chain reaction (PCR) thermal cycling is the gold standard of molecular diagnosis. However, a key challenge in the area of pandemic flu preparedness is that only specialized personnel can conduct available diagnostic tests. In addition, commercially available thermal cyclers are intended for laboratory use and, as a result, are difficult to operate, bulky, and expensive, which are barriers to expanding their application to emergency cases and public checkpoints, such as airports. Therefore, there is a pressing need to develop a cheap, portable, and disposable molecular diagnostic kit.

To provide flexible and affordable diagnosis, our team at the Institute of Bioengineering and Nanotechnology in Singapore developed a mini diagnostic system that detects infectious diseases through PCR recommended by the Center for Disease Control and Prevention (CDC). Our system integrates and automates the entire diagnostic process from real-time PCR to the detection of target strands of viral genes to performing data analysis.

By using NI CompactDAQ for our solution as well as LabVIEW graphical system design software for control and data analysis, we created a compact and portable system. It consists of a small peltier (thermal unit), a power supply (power unit), and a light detector (optical unit) with USB plug and play.

Our thermal cycler is portable, fully automated, and can be used for mass health screenings at strategic locations such as airports to contain the spread of infectious diseases at checkpoints. The system’s automation is a key benefit for a reliable diagnosis because pandemic flu may occur in remote areas where trained personnel are not available to handle test samples. In addition, automation greatly reduces man power and training costs.

The sample-to-answer process takes less than one hour to run simultaneously in three polymer chambers that contain preloaded PCR reagents, and allows for a wide range of biological versatility. An internal proportional-integral derivative (PID) chip with real-time temperature feedback from a thermistor handles temperature control. The controller consists of a compensator, output unit, and a feedback signal from a sensor, which are necessary to control the heater output power and maintain the temperature. Using LabVIEW, we programmed a graphical user interface displaying real-time temperature, set temperature, and real-time PCR results from the three channels (Figure 1A).

System Configuration

The configuration of the integrated system is complete with thermal cycling for PCR operation and reaction, fixtures for three blue LED light sources, and attachments that line up the optical paths of the LEDs into a photomultiplier tube (PMT) with associated lenses and filters for real-time optical detection. The system includes a set of heating chambers made of copper or brass, which integrate with the polymer chambers containing the sample.

LabVIEW is at the center of the system architecture. The central processing unit has been specifically designed to execute commands that are preprogrammed through LabVIEW to control the system start-up and health check, thermal cycling control for PCR operation, and optical detection for multiplexed fluorescence signals.

Upon thermal cycling of the PCR process, the system performs optical detection in the last seconds of the annealing cycle. The three LEDs are “fired” simultaneously, turning on for a period of 200 ms each by applying current from the NI 9265 analog output module and turning off before the next LED is activated.

A specially designed fixture to concentrate and direct the light source transmits the LED optical light path. This passes through a filter before illuminating the chamber containing the DNA sample. Then the light is transmitted through a series of lenses and filters into a PMT, and the NI 9206 analog input module reads the signal.

Using LabVIEW for signal processing to perform the averaging of the data set, the signal from the PMT is amplified and processed. Then the data is displayed and continuously updated through the main user menu as three independent graphs (see Figure 2).

The PCR mixture is placed in the polycarbonate PCR chamber and oil is added to avoid evaporation. PCR is performed with the following thermal profile: 95 °C for 20 seconds (activation of Taq polymerase) and 50 cycles of amplification (denaturation at 95 °C for 5 seconds, annealing and extension at 60 °C for 60 seconds). The LabVIEW program records fluorescence arising from DNA replication for each cycle number.

Stability and Repeatability

For molecular diagnosis, PCR is a common method to amplify the specific fragments of DNA into billions of molecules. It requires 40 to 50 cycles at a temperature of 94 °C for denaturation, 60 °C for annealing, and 60 °C for extension. It is critical that we precisely control temperature stability and achieve a heating rate of at least 2 °C/s to avoid generating and amplifying error DNA sequences.

Using LabVIEW to control independent high- and low-side referenced output channels, and with a circuit with high-speed power metal–oxide–semiconductor field-effect transistor (MOSFET), we designed and manufactured a solution for on-chip heating with real-time control of PWM. The temperature measurement shows that the obtained heating and cooling rates are about 2.5 °C/s and 2.2 °C/s, respectively. The overshoot is less than 1 °C for each temperature setting, and thermal stability is maintained within ±0.1 °C.

Results and Conclusion

We confirmed the performance of the real-time PCR detection with serial diluted Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) complementary DNA (cDNA) using a TaqMan probe from 1 to 104. The results demonstrate that the sensitivity determined from the Ct curve is comparable to the commercially available real-time thermal cyclers (Figure 1B).

Compared to other commercially available thermal cyclers, our system is more compact and portable and is superior in temperature stability (Table 1). The portability of our system is especially advantageous at the early stages of a pandemic flu outbreak. This diagnostic system is highly suitable for use in clinics, emergency rooms, and public checkpoints. In addition, the thermal cycler offers potential benefits for food safety because it is portable, inexpensive, small, and easy to operate.

References
1. J. Felbel, I. Bieber, J. M. Kohler, Chemical Surface Management for Micro PCR in Silicon Chip Thermocyclers, Proc. SPIE, 4937, 34-40, 2002.
2. S. Poser, T. Schulz, U. Dillner, V. Baier, J. M. Kohler, G. Mayer, A. Siebert, D. Schimkat, Temperature Controlled Chip Reactor for Rapid PCR, 2002.

Author Information:
Hsieh Tseng Ming James
Institute of Bioengineering and Nanotechnology, A-Star
31 Biopolis Way, The Nanos, #04-01
Singapore
Singapore
Tel: +65-68247229
Fax: +65-64789080
tmhsieh@ibn.a-star.edu.sg

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