Today’s genomics laboratories require high throughput, cost-effectiveness, detection sensitivity, and high resolution. However, many of these laboratories are using traditional methods that require hours or days of tedious procedures that are subject to human errors to produce results. In addition, these systems are not as cost-effective as they appear to be.
Microfluidic, miniaturized digital genetic analyzer systems, software, and consumables for biological materials testing applications from eGene Inc. (Irvine, CA) detect, quantify, identify, and characterize DNA and RNA at high rates of specificity and sensitivity while automating routine and nonroutine laboratory and industrial procedures critical to product safety, development, quality, and productivity. The HDA-GT12™ genetic analyzer is a cost-effective, multichannel capillary electrophoresis system for high-sensitivity and high-resolution detection. The bench-type system uses a fluorescence mechanism for nucleic acid detection. A consumable multichannel capillary gel cartridge used with the system can automatically inject and analyze 12 strip samples simultaneously in less than 10 min or a 96-well plate in 1 hr. The system can be operated easily in research or industrial laboratories for various kinds of genomic analysis.
Driven by an electric field, capillary electrophoresis analysis is performed in narrow-bore fused-silica capillaries and enables the rapid separation of many hundreds of different compounds. Almost all large and small molecules and even whole organisms can be separated in this manner. The technique can be optimized for numerous types of separations, especially in situations where other liquid phase separation techniques are limited or impractical.
High electric field strengths separate the molecules based on differences in charge, size, and hydrophobicity. The end of the capillary is immersed in a sample vial, and pressure, vacuum, or voltage is applied. Capillary electrophoresis has very high efficiencies, enabling hundreds of components to be separated at the same time. It requires minute amounts of sample, is easily automated, can be used quantitatively, and consumes limited amounts of reagents.
However, some currently available capillary electrophoresis systems rely on expensive and inefficient light sources that limit the miniaturization of the optical detection system. Other systems have only one capillary, while still others have multicapillary capabilities that are costly and complex to operate.
Table 1 - Workflow time comparison chart
By reducing the mechanical/optical alignment complexity, gel/buffer consumption, separation time, and cost per run, eGene has made the manufacturing process of its capillary electrophoresis system simpler, faster, and more cost-effective. Based on a novel and proprietary multiplexed fluorescence detection system with solid-state light sources and microoptical collectors, a cartridge that contains individual separation channels with a built-in chemical reagent, and software that controls the instrument and checks the quality of the results, the system provides high-resolution analyses with short run times and minimal sample and reagent consumption.
The HDA-GT12 system reduces separation time from 2 or 3 hr to 10 min. It eliminates the labor-intensive procedures of manual sample loading, visual examination, data analysis, photo-taking, and record-keeping. The system enables minimal human intervention, thus reducing the possibilities of human error (see Table 1).
The system provides multiple applications in one instrument platform. It integrates sample loading, electrophoresis, and data analysis in one step. Automated sample handling keeps hands free for sample loading. The system reduces labor costs and increases laboratory productivity. It also reduces manual handling errors.
The system’s replaceable gel cartridge eliminates the need for gel preparation. The cartridge-based system is easy to use and efficient. It saves time and increases productivity.
Detection sensitivity is as low as 0.1 ng/μL. The HDA-GT12 system offers fast analysis with an average 7- to 10-min time period required to analyze 12 samples. Users can obtain a high-resolution electrophoresis pattern for 96 samples within 0.5–1.3 hr, increasing laboratory productivity. Resolution with the system is up to 1- to 5-base pair DNA fragments. This provides confidence in data interpretation.
Electropherogram and gel view formats are available. Multiple data viewing options enable flexibility with both types of data. Powerful, user-friendly analysis tools collect digital data for qualitative and quantitative analysis. Data are easy to use and present, and the tools simplify analysis.
High throughput is a major benefit of the system, which offers 4-, 8-, and 12-channel capillary cartridges to handle different sample capacities. The result is flexibility in throughput. The compact system fits on a laboratory bench, saving a great deal of space.
Cost analyses have been performed to compare the HDA-GT12 system with other types of electrophoresis systems. In a conventional agarose gel electrophoresis of 12 samples, the total time required to prepare the gel, load the samples, separate, stain, and document ranges from 101 to 191 min, not counting the time needed to prepare the buffers. Performing the same 12-sample separation with the HDA-GT12 system takes 10.2 min, as seen in Table 1.
Instrument costs for slab gel electrophoresis are similar to the instrument cost of the HDA-GT12 system, but the difference is in the efficiency. When the costs of an electronic precision balance, microwave, electrophoresis unit, power supply, horizontal shaker, gel documentation system, personal computer, and automatic pipettor are calculated for 12 samples, the cost is $25,636. For a 96-sample electrophoresis unit, the total is even higher. The cost for a completely automated HDA-GT12 system is comparable (see Table 2).
Table 2 - Cost of conventional gel electrophoresis of 12 samples*
Labor costs for agarose gel systems far exceed those for the HDA-GT12 system because the time required for the analysis is much greater (101–191 min for agarose gel versus 10.2 min for the HDAGT12 system). Numerous consumables have to be purchased to use the agarose gel system. Although the unit cost per sample is only a few dollars, there are about a dozen individual items to purchase. Thus, the cost per sample with agarose gel is $3.12–$5.62 for 12 samples and $1.56–$2.81 for 24 samples. The HDA-GT12 system, which requires only a cartridge, can separate 12 or 24 samples for $0.55 per sample, including the cost of labor.
In summary, the HDA-GT12 system demonstrates cost-effectiveness when compared with other electrophoresis systems. It is preferable to slab gel systems that are similar in price but far less efficient and accurate in terms of cost and reagent consumption. It also compares favorably with expensive automated systems that cost more than three times as much while delivering less efficiency.
Dr. Amirkhanian is Executive Vice President, and Dr. Liu is Chief Executive Officer, eGene Inc., 17841 Fitch, Irvine, CA 92614, U.S.A.; tel.: 949-250-8686; fax: 949-250-8833; e-mail: [email protected]. Dr. Guttman is Head, and Dr. Szantai is postdoctoral associate, Horvath Laboratory of Bioseparation Sciences, Institute of Innsbruck, Austria. The Horvath Laboratory provided a detailed analysis of the comparative electrophoresis procedures.