May 15, 2006 (Vol. 26, No. 10)

Digital Genotyping to Replace Time-Consuming Slab Gel Electrophoresis Methods

While working as an applications scientist in the bio-instrument industry, molecular geneticist Ming Liu, Ph.D., came to appreciate the potential of capillary electrophoresis and decided to develop the technology into a routine tool for the molecular biology laboratory. In 2000, he and systems engineer Varouj Amirkhanian started BioCal Technology to simplify the design of capillary electrophoresis instruments to make them as common as pH meters on every scientist&#8217s benchtop, says Dr. Liu, now CEO at eGene ( in Irvine, CA.

In 2004, BioCal Technology merged with Centroid Consolidated Mines to form eGene, which manufactures and sells the HDA-GT12 analyzer, a low-cost, automated digital genotyping system.

Just as e-mail and eBay changed the way people think about communications and retailing, the name eGene represents a paradigm shift in the way that scientists think about genetic analysis. The automatic, affordable, user-friendly capillary electrophoresis genotyping system, offered by eGene, represents the future of DNA analysis, explains Dr. Liu.

He was inspired to create the new system by Leroy Hood, a professor when Dr. Liu attended Caltech, who advised students to learn how to use their brains, not their hands. So Dr. Liu, who detested running slab gels, teamed up with Amirkhanian to invent an easier and faster automated system for the scientific community.

Overcoming Disadvantages

The HDA-GT12, short for high-performance DNA analyzer for genotyping on 12 channels, replaces time-consuming slab gel electrophoresis methods, used to separate segments of DNA.

Slab gel electrophoresis, a technology that was developed more than 20 years ago and has not undergone a major facelift since its inception, requires extensive manual manipulation and hours or days of tedious procedures that are prone to human errors. These methods also lack high-throughput capabilities, detection sensitivity, and resolution.

In contrast, capillary electrophoresis technology produces accurate results in minutes. Capillary electrophoresis systems use a strong electric field to separate molecules within narrow capillaries, making them suitable for DNA sequencing, mutation/polymorphism analysis, genetic profiling screening, and bacterial/virus DNA testing. Most commercial capillary electrophoresis instruments, however, are large and expensive. The operation and reagents needed to run them are costly.

The HDA-GT12 was designed to overcome the disadvantages of current capillary electrophoresis instruments. The new system contains a low-cost, high-throughput, 12-channel replaceable gel-cartridge for rapid DNA separation and detection that can handle up to 2,400 samples. Furthermore, the disposable cartridge contains 12 short separation channels with a built-in consumable chemical reagent to simplify analysis. The reagents are stable at room temperature.

The HDA-GT12 is based on real-time multiplexed fluorescent detection with low-cost, solid-state light sources, or light emitting diodes, and micro-optical collectors. Simplifying the design of the optical detection system reduces the manufacturing cost and improves the reliability of the instrument. The cost of chemicals for each analysis is less than half that of slab gel systems. The instrument provides 12 test results in 5&#821110 minutes or 96 results in 60&#821190 minutes, compared to 3&#82114 hours with slab gel methods.

By getting data in hours instead of days, you can do more experiments and progress faster, says Amirkhanian, director of R&D.

To operate the system, the user simply inserts a cartridge, loads a sample tray, and pushes the start button. The BioCalculator software controls the operation of the instrument and data analysis. Operators can choose electropherogram and gel-view formats for genetic identification and characterization analysis.

In addition, the HDA-GT12 can accommodate 96 samples. This allows microarray users to check the quality and quantity of their amplified multiplex DNA fragments before advancing to microchip detection. The rapid and reproducible quantitative DNA analysis is especially suitable for PCR-amplified DNA products. We advertise ourselves as a post-PCR analysis tool, says Dr. Liu.

The company also offers a GCK-RNA QC (Quality Control) Gel Cartridge Kit for the HDA-GT12 system to perform RNA sample quality checks prior to gene expression analyses. The kit checks the quality of total RNA, poly A, RNA, cRNA, cDNA, fragmented RNA, or cDNA prior to performing Northern blots, real-time PCR, microarray and microchip hybridization assays, or cDNA library constructions. The integrity of RNA samples is crucial for gene expression analysis, since it has a tremendous effect on downstream analysis, says Dr. Liu.


The Center for Disease Control (CDC) in Taiwan ( recently purchased the HDA-GT12 system to integrate into its infectious disease detection process. The Center for Research and Diagnostics at Taiwan&#8217s CDC is currently using the system to detect the Dengue virus, the Japanese encephalitis virus, and Rickettsia. The CDC selected the HDA-GT12 system because of its ease of operation, fast results, and affordable test costs.

At the New York State Institute for Basic Research in Developmental Disabilities in Staten Island, NY, researchers used the HDA-GT12 system to screen for trisomy in a mouse model for down syndrome. The Ds65Dn segmentally trisomic mouse, widely used to study down syndrome, possesses an extra copy of a piece of chromosome 16, translocated to chromosome 17. This segment includes the mouse homolog of human chromosome 21, critical in down syndrome.

The targeted DNA fragments were resolved and quantified by the HDA-GT12 genetic analyzer in less than three minutes and compared to the results obtained by agarose gel electrophoresis, stained with ethidium bromide. Both data sets came within 10&#37 of the expected results. The experiment, reported in the journal Analytical Biochemistry, demonstrates the precise and efficient identification of trisomic and disomic animals at any developmental stage.

Comparison Studies

Researchers at the Center for Molecular and Mitochondrial Medicine and Genetics at the University of California, Irvine (, under the direction of Douglas Wallace, compared traditional slab gel electrophoresis to the automated HDA-GT12 analyzer in performing their routine procedures. They concluded that the automated method reduces the work load from hours down to five minutes, while increasing the number of samples that can be run concurrently and decreasing the cost per test. In addition, all the information can be stored on the automated system for comparison and further analysis.

When eGene representatives demonstrate the HDA-GT12 system, people really open their eyes, because no one has seen this type of machine, says Dr. Liu. Since launching the HDA-GT12 system in 2004, eGene has shipped more than 130 units to research laboratories worldwide, where they are used for a variety of applications.

We have more customers in agricultural research than in medical research, says Dr. Liu. The experts at eGene are consulting with companies who want to use the HDA-GT12 to develop PCR diagnostic kits. The company is seeking distributors to get the machines into the hands of customers, says Dr. Liu.

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