QIAGEN Reveals a Sensitive Side

Volume 16 | Issue 13 | 37 | Jun. 24, 2002 Previous | Next QIAGEN Reveals a Sensitive Side Highly sensitive microarrays provide a true expression profile | By Hillary E. Sussman Photo: Courtesy of Qiagen SensiChip DNA microarray bar Since their inception, DNA microarrays have been valuable in fields ranging from drug discovery to agricultural engineering. But the high-density chips suited for large-scale screening of differential gene expression patterns lack the sensitivity necessary for in-depth, secondary analysis of the resultant target genes. Netherlands-based QIAGEN saw this gap in the DNA microarray market and decided to close it with the SensiChip™ DNA Microarray System, an amplification-free technology that provides the true expression profile of a cell. The company recently unveiled SensiChip at Analytica 2002 in Munich, Germany. Developed in collaboration with Zeptosens, SensiChip is based on planar waveguide (PWG) technology that enables highly sensitive microarray analysis with as little as 1 µg total RNA. SensiChip microarrays are coated with a thin film of tantalum pentoxide (Ta2O5), which has a higher refractive index than the glass slide. A laser beam, directed into the thin PWG layer by a coupling grating, propagates within the PWG layer and generates a strong electromagnetic field. This evanescent field decays rapidly as it penetrates the PWG layer, limiting its depth to approximately 300 nm. Detection of fluorescent molecules is re-stricted to the sensing surface, so capture probes and their bound target molecules are observed without background noise. Thus, SensiChip detection technology increases signal-to-noise ratios for highly sensitive detection. Photo: Courtesy of Qiagen SensiChip Reader QIAGEN expects the SensiChip system will prove important in understanding disease processes such as cancer. Martin Potgeter, QIAGEN's global product manager for microarrays, explains that traditional DNA microarray technology requires approximately 20 µg total RNA for analysis. "With dissected material containing different cell types, you are not able to profile the true expression pattern of the target cancer cell," he says. In contrast, fine-needle aspirates (FNA) contain pure cancer cells and are therefore ideal for analysis. "But since you can only isolate 2 to 4 µg total RNA from FNAs, you can't use FNAs with traditional microarrays," he concludes. SensiChip is sensitive enough that 100,000 cells (equivalent to 1 µg total RNA) are sufficient for analysis. "You can get an expression profile which you could not get before," says Potgeter. With SensiChip, scientists can quantify the differential expression pattern of genes that are expressed at very low levels. Regulatory genes involved in signal transduction, such as those encoding protein kinases and phosphatases, often produce transcripts in low abundance even though many play major roles in diseases such as diabetes and cancer. In collaboration with Axxima Pharmaceuticals, QIAGEN provides ready-made arrays consisting of oligonucleotide probes corresponding to all known human serine/threonine and tyrosine kinases and phosphatases. But QIAGEN mainly provides customized SensiChip DNA microarrays. Customers simply provide the GenBank accession numbers for the genes of interest, and QIAGEN designs optimal 70-mer oligos as capture probes and spots them onto a SensiChip DNA microarray. These oligos are long enough to be highly selective but shorter than cDNA to allow the discrimination of splicing variants and gene families. Each SensiChip DNA microarray carries its own microfluidic cell, which functions as a hybridization chamber. The arrays are preassembled under clean-room conditions, eliminating the error-prone handling of cover slips and contributing to highly reproducible results. Hybridization is conveniently carried out on the SensiChip HybStation using the optimized buffers in the SensiChip Buffer Set. The system's modularity renders it suitable for low, medium, or high throughput. SensiChip DNA Microarray Bars contain six separate microarrays, and the SensiChip DNA Microarray Bar Carrier is designed in a microplate format for use with multichannel pipettes. The SensiChip Reader has an integrated stacker with a 10-plate capacity for up to 300 arrays per run. QIAGEN also offers SensiChip Control Software for image acquisition and control of the reader and SensiChip View Software for image analysis. --Hillary E. Sussman ©2002, The Scientist Inc. Comment E-mail article For More Information: QIAGEN Inc.(800) 426-8157www.qiagen.com

QIAGEN Reveals a Sensitive Side

QIAGEN Reveals a Sensitive Side

Highly sensitive microarrays provide a true expression profile | By Hillary E. Sussman

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