1 Species, 3 Slides, 30,000 Genes

Ebersberg, Germany-based MWG-Biotech AG has officially entered the human genome microarray market. The company's Pan® Human Array, scheduled for release this month, consists of three slides containing a total of 30,000 known or described human genes; MWG began offering the first slide in the set last December. Santa Clara, Calif.-based Affymetrix Inc. also recently launched a human genome microarray product, the GeneChip® Human Genome U133 set.1 However, the two products differ in three key areas. One difference involves the strategy each company adopts to maximize sensitivity and specificity. MWG, an oligo-synthesis company, places a single 50-nucleotide-long probe species per gene. In contrast, according to an Affymetrix Technical Note,2 Affymetrix places several pairs of 25-nucleotide-long probes per gene—11 pairs, in the case of the Human Genome U133 set—each consisting of a perfectly matched oligo and an oligo containing a mismatch at nucleotide 13. Also, while Affymetrix synthesizes its probes directly on the chips using a photolithographic process, MWG's oligos are synthesized separately. Then, prior to arraying, the company purifies these oligos, rather than spotting crude mixtures, and tests them for quality control using matrix-assisted laser desorption ionization (MALDI) mass spectrometry. Finally, MWG's chips can be read using any scanner or reader capable of accepting standard 1 x 3-inch slides, in contrast to Affymetrix's chips, which are analyzed using the company's GeneChip hardware platform. Because these two platforms adopt such different strategies, direct comparison of the data they produce is often difficult, says John Ambroziak, director, genomic services and discovery for MWG-Biotech Inc., MWG's High Point, NC-based US subsidiary. One additional feature that distinguishes the Pan arrays from other company's products is the bioinformatics software used to pick the probe sequences. "We have an incredible bioinformatics infrastructure, which we're glad to compare with any of our competitors in terms of the number of people, the hardware that we've invested in, [and] the software that we've invested in," says Ambroziak. Key to that infrastructure is the GeneMatcher 2 supercomputer, from Paracel Inc. of Pasadena Calif., which allows MWG Biotech to run the required software without limiting database analysis or any other bioinformatics algorithm. The probe sequences arrayed on the chips are proprietary information, though MWG can provide the sequences of a subset of the probes to purchasers under a non-disclosure agreement. Users can, however, obtain information that describes how the probes were designed, to which genes they will hybridize, and to which genes they are specifically designed not to hybridize using the Compact Gene Index database, available at the MWG-Biotech Web site. For those scientists who wish to make their own arrays, MWG Biotech sells the Pan Human 10K/30K oligo sets separately, in 96- and 384-well plate formats. Ambroziak notes that, since these are the same oligos that are found on the arrays, researchers should have no trouble comparing data generated using homemade chips with data produced using MWG's premade Pan arrays: "You can easily go back and forth from one part of the platform to another, and all of our products and oligo sets will give comparable results," he says. MWG is now working to develop hardware and protocols to automate and standardize the use of the company's arrays. "Our future is very much looking towards more standardized array applications, including diagnostics," says Ambroziak. For example, the company is developing an automated system for sample processing, labeling, and hybridization. These accessories, developed by MWG and its corporate partners, will soon be in beta testing, and should be released by mid-year. The Pan Human 10K array costs $950 (US) / €950. —Jeffrey M. Perkel References 1. A. Constans, "Arraying the genome," The Scientist, 16[5]:41, March 4, 2002. 2. Affymetrix Inc., "GeneChip arrays provide optimal sensitivity and specificity for microarray expression analysis," www.affymetrix.com/products/25mer_content.html, 2001. For More Information MWG-Biotech AG +49 (0) 8092-8289-0 www.mwg-biotech.com

1 Species, 3 Slides, 30,000 Genes

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