Automated Gene-expression Profiling
Xceed Molecular (www.xceedmolecular.com) says it increases the productivity of microarray experiments by processing up to eight arrays in about four hours.
“We saw an emerging need for an automated platform for gene-expression profiling,” said Susan Bromley, Ph.D. vp, diagnostic product development. “The microarray space is transitioning from discovery applications using whole-genome arrays to validation of focused sets of candidate genes. Such experiments require analysis of a subset of genes using multiple experimental conditions or large sample sets.”
Ziplex™ Automated Workstation performs all steps of microarray processing, including data collection and analysis, in an automated format. Each workstation is able to simultaneously process eight proprietary chips.
The 6.5-mm square Flow-Thru Chips® are made out of porous silicon. This unique substrate contains more than 700,000 uniform microchannels per square centimeter. Each microchannel has a diameter of 10 mm and a length of 450 mm. When oligonucleotide probes are printed on the chips, each resulting spot covers and fills about 70 of the individual microchannels, with a total surface area for probe binding a hundred times greater than that achieved on an impermeable, 2-D surface, reports the company. The porous structure allows reagents to cycle through the chip during incubations, reducing hybridization times.
“Many laboratories currently outsource microarray processing and analysis,” says Dr. Bromley. “Our system will allow researchers and, in the future, reference labs and hospitals to bring microarray technology in-house.” The Ziplex™ Workstation will be available for research use later this year. Currently, the company is trying to obtain FDA clearance for its instrument and diagnostic kits.
“Many infectious diseases present similar symptoms. Doctors commonly prescribe a broad spectrum antibiotic without an exact diagnosis. A rapid test is available only for Streptococcus, and typical lab analysis for other infections may take up to five days,” said Charles Daitch, Ph.D., president of Akonni Biosystems (www.akonni.com). “Ideally, a doctor would screen a patient’s sample for multiple infectious diseases using a rapid, simple-to-use, low-cost test.”
Akonni developed TruArray™, arrays of 3-D microdrops consisting of a proprietary hydrogel. The diameter of each drop is 100 microns. DNA or antibodies are anchored to the gel, creating a micro test tube. The arrays are embedded into microfluidic devices.
“We have developed a simple and straightforward microarray production method,” added Michael Farmer, chairman of Akonni’s Board. “All components of the micro test tube are mixed together, spotted on solid support, and UV-polymerized. As a result, we could decrease the cost to less than $10 per array for identifying multiple pathogens. It takes us only 30 days to produce and validate a test for a new microorganism.”
The company plans to initially market the arrays via public health disease surveillance labs. The Akonni system may be useful for early identification of pathogens where symptomology by itself is insufficient. The system, due to be released at the end of 2008, will include a portable reader device and credit card-sized disposable microfluidic card with embedded TruArray. The card, loaded with a small sample of blood, urine, or saliva, is placed in the reader, which automatically processes the sample.
“We are also developing on-chip PCR to increase sensitivity of detection to about 100 colony-forming units per milliliter,” added Dr. Daitch. “Each microdrop would contain a covalently tethered pair of specific primers. Since primers are spatially isolated, we would eliminate primer interference and achieve specificity of detection of five standard deviations above background. We can achieve highly multiplexed amplification impossible in solution-phase PCR.”
In a recently completed two-site trial, Akonni compared TruArray technology for identification of drug-resistant tuberculosis with a standard eight-week culturing procedure. Eighty-eight SNPs from six genes associated with multidrug resistant tuberculosis were anchored in the gel drops. DNA was obtained from sputum samples, amplified, and hybridized to the arrays. The TruArray procedure demonstrated similar sensitivity and specificity as culturing, but completed the process within several hours.