Performance Comparison of Gel Imaging Devices Jong-Dae Kim1,2, Chan-Young Park1,2 , Sang-Cheol Shin2,3, Yu-Seop Kim1,2, Hye- Jeong Song1,2, 1Department of Ubiquitous Computing, Hallym University, Chuncheon, Korea 2Bio-IT Research Center, Hallym University, Chuncheon, South Korea 3Department of Computer Engineering, Hallym University, Chuncheon, Korea {jdkim, cypark, sangcheolshin, yskim01, hjsong}@hallym.ac.kr Abstract. This paper presents a method for gel imaging device comparison. Fully amplified DNA product was diluted to have six different concentrations. They were loaded into separate wells of a gel and electrophoresed. The images of the prepared gel were captured with the chosen cameras by installing them in turn on the mount of a gel documentation system. Two industrial video cameras, a compact digital camera, and a DSLR digital camera were selected for the comparison. Visual inspection of the images showed that the gel images from the industrial video cameras did not present the bands contrast to the digital cameras. Both digital cameras having similarly superior performance than the industrial ones were compared quantitatively using software packages for gel image analysis. The linearity between the band intensity and DNA density was compared for them, and results showed that the two cameras have similar performance. Keywords: Gel documentation system, digital cameras, industrial video cameras, gel image analysis 1 Introduction DNA detection is paramount for clinical diagnosis and pathogen detection for both humans and animals, environmental test, and forensic inspections [1-3]. Analysis of the DNA properties can be separated into 4 steps: DNA extraction, DNA amplification, electrophoresis, and the analysis of the gel image. Each step requires a high-cost and specific equipment according to the process [4-6]. In order to analyze the gel image, the agarose gel containing the DNA amplicons mixed with a substance that reacts with UV in its well must be electrophoresed. Gel documentation system (gel doc) then captures the image of the electrophoresed agarose gel by illuminating it with UV [7]. The properties of the DNA can be gained by analyzing the image captured from the gel doc. The camera of the gel doc takes up a large portion in the cost of the equipment. Therefore by reducing the cost of the camera, it is possible to realize a low-cost gel doc, which will encourage the wide spread of the equipment [7]. The camera performance is even crucial in the real-time PCR which is becoming common in the modern technology, since it detects the DNA during amplifying process reducing the processing time greatly. If the low-cost camera has a similar 81

2 Experiments and results performance to that of the high-cost camera, the supply of the real-time PCR system can be accelerated by integrating the low-cost camera to the equipment [9- 12]. To demonstrate the possibility of realizing the low-cost camera, the comparison of performances in camera according to the cost is necessary. Such research will become more important since the demand for DNA diagnosis and point-of-care- testing (POCT) is rapidly increasing [8]. However, there rarely have been reports on the issue. This paper presents a method to compare the performance of cameras that varies in their costs. The four different cameras in different price ranges were compared, and the irrelevance of the price and performance was demonstrated. 2 Experiments and results For the comparison of the camera performance, the HPV DNA (Biomedlab Co.) was amplified and diluted with distilled water (DW) to have the relative concentrations of 1, 1/2, 1/5, 1/10, 1/20, 1/50, 1/100, where the 1 indicates the concentration of the amplified DNA through PCR before dilution. Each sample of different concentration was inserted into separate wells in one agarose gel, and was electrophoresed. The image captured from this gel will then have bands with different DNA concentration for each lane. The images of the prepared gel were taken with the chosen four cameras by installing them alternately to the camera mount of the gel doc. It is convenient to analyze the gel image if the gel doc system is connected to a PC in order to control and take the image remotely. Without such remote management, the image has to be taken manually, and the captured image has to be transmitted to the computer with an additional manual step. Therefore the cameras were chosen from those that could be remotely controlled by the PC. Two commercial USB video cameras that provided PC control and two digital cameras having a different price range were selected. Since the price of the commercial video camera is commonly determined by its imaging device, two cameras from the same company, CMLN-13S2C with a CCD sensor ICX445 and FMVU-13S2C with a CMOS sensor IMX035, were chosen (Point Grey Research, Inc.). For the digital cameras, PowerShot S2 and a DSLR Nikon D80, both of which were able to be controlled by a PC, were selected. Each of CMLN-13S2C, FMVU-13S2C, PowerShot S2, and Nikon D80 will be abbreviated as CM, FM, PS, and NK respectively, throughout the rest of the paper. Since the image size from each camera was different, the sizes were equalized and cut at the same position, then put into one image as shown in figure 1. Figure shows the gel image parts of CM, FM, PS, NK starting from the left, and each part shows the DNA bands for the dilution of 1, 1/2, 1/5, 1/10, 1/20, 1/50, 1/100 from the left (The left most lane of each part is for the ladder marker). For the qualitative comparison, the image was inspected how lower concentrations could be detected with the bare eye. The three brighter bands in all four parts were distinguishable. For the close visual inspection of the lower density bands, the images were cut again to only contain the lower DNA concentration bands. Their backgrounds were eliminated by the minimum filter with 15×15 square structuring element, whose size was approximately similar to the thickness of the thickest band for fairer comparison. And 82

Fig. 1. The image parts of CM, FM, PS, and NK. their contrasts were stretched from zero to 5 times of the standard deviations of their image intensities. Figure 2 shows the resultant aggregated image. As can be seen on the two left image parts in figure 2 that are from the commercial video cameras, it is hard to distinguish the bands having the DNA concentration of less than 1/20. On the other hand, in the right two image parts that are from the digital camera, the bands up to 1/100 diluted samples can be detected at least even though they are very dim. Although the image part from the compact digital camera (PS) seems to have more noise in the background, it cannot be said that the DSLR camera (NK) has better performance. It is because the detection of the bands with the bare eye is the primary concern in the qualitative test. Therefore the quantitative analysis of the gel image is required for the more reliable comparison. Fig. 1. The image parts of CM, FM, PS, and NK. Fig. 2. Image parts only with the lower concentration The quantitative analysis for the digital cameras was done with a free analysis SW, GelAnalizer [13], and a trial version of a commercial SW, GelCompar II (Applied- math, USA). The latter was expected to be robust on the noise due to its sophisticate algorithm. Table 1 gives the analysis result. All the band intensities could be obtained with GelAnalyzer by additional manual peak detections for the lowest DNA densities, while only 5 higher-density bands were detected with GelCompar II for the images from both digital cameras. Even though lowest 2 bands could be detected with GelAnalyzer, they were ignored for the linearity investigation because they corrupted the linearity severely. Since the analysis was constructed with the assumption that the relative band intensity is proportional to the relative DNA concentration, comparing the linearity of the two quantities will have a significant meaning. Especially, the logarithmic relation of the two quantities will have the slope of ‘1’ as the following equations. ρ ∝ g , (1) 83

3 Conclusion log10g=log10p+k (2) where p , g and k are the relative DNA concentration, the relative band intensity, and a constant, respectively. Table 2 shows the slopes and the coefficients of determination of the digital cameras from both tools. The deviation from the unity of the slope for PS was slightly greater than that for NK with GelAnalyzer, while they were the same with GelCompar II. The coefficients of determination for PS were greater than that for NK with both tools. However, the relative differences of the slops were less than 8.8% regardless of the tools. The coefficients of determination were even closer from each other showing the relative difference less than 1.5%. The density-intensity relations were more linear with GelCompar II that was more robust tool. These results indicated that both cameras performed similar in quantifying the DNA densities. Despite that the linearity analysis results differed slightly, it can be interpreted as both cameras having similar performances considering the accuracy of the experiment, dilution of DNA, quantity of the fluorescent material, and the uniformity of the gel. 3 Conclusion This paper presented a method to compare the gel image analysis performance of cameras with different price ranges, and demonstrated the comparison with four selected cameras. The digital cameras showed better performance than the commercial video cameras, which might have resulted from the market supply rate. That is, since the digital cameras are widely spread and used, their performance is superior compared to the cost. Also the compact digital camera had similar performance to that of the high-cost DSLR camera. The results indicated that the camera price and DNA detection performance was not proportional. Thus, the cost reduction of the gel doc system was possible by applying the compact digital camera. As the necessity of POCT is increasing, the comparison of the imaging equipments suggested in this paper will become paramount. Especially, the importance of this method will become more crucial once the real-time PCR system becomes more common, since the imaging device is essential in the system 84

Table 1. Relative band intensity (%) relative density GelAnalyzer GelCompar II PS NK 100 50 43 53 48 56 20 21 34 22 32 10 8 14 5 3 4 6 2 1 Table 2. Linear relationship of the relative DNA concentration and the relative band intensity Tools PS NK Relative difference (%) slope 1.14 0.95 8.76 GelAnalyzer R2 0.99 0.96 1.43 1.08 0.92 8.15 GelCompar II 0.98 0.67 Acknowledgments. The research was supported by the Research &Business Development Program through the Ministry of Knowledge Economy, Science and Technology (N0000425) References Salm, E., et al.: Electrical Detection of dsDNA and Polymerase Chain Reaction Amplification. Biomedical Microdevices 13, 973--982 (2011) Kodziusa, R., et al.: Inhibitory Effect of Common Microfluidic Materials on PCR Outcome. Sensors and Actuators B 161, 349--358 (2012) Wu, J., et al.: Fast Detection of Genetic Information by an Optimized PCR in an Interchangeable Chip. Biomedical Microdevices 14, 176--186 (2012) Bajla, I., et al.: An Alternative Method for Electrophoretic Gel Image Analysis in the GelMaster Software. Computer Methods and Programs in Biomedicine 77, 209--231 (2005) Ye, X., Suen, C.Y. , Cheriet, M., and Wang. E.: A Recent Development in Image Analysis of Electrophoresis Gels. In: Vision Interface ‘99, Canada, pp. 19--21 (1999) 85

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