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Scanning the Horizon - HP Gene Array Scanner

Photo: Courtesy of Affymetrix Affymatrix Hybridization Pattern, the human p53 Gene Affymetrix, the Santa Clara-based DNA chip company, has partnered with Hewlett Packard in the development of the HP GeneArray Scanner, a high resolution, high throughput scanner for use with GeneChip¨ probe arrays. The GeneChip Probe Array, a technology pioneered by scientists at Affymetrix, is a marriage between the computer and biotechnology industries which provides access to genetic information on minia

August 18, 1997

Photo: Courtesy of Affymetrix

Affymatrix Hybridization Pattern, the human p53 Gene
Affymetrix, the Santa Clara-based DNA chip company, has partnered with Hewlett Packard in the development of the HP GeneArray Scanner, a high resolution, high throughput scanner for use with GeneChip¨ probe arrays. The GeneChip Probe Array, a technology pioneered by scientists at Affymetrix, is a marriage between the computer and biotechnology industries which provides access to genetic information on miniaturized, high density DNA arrays. On each 1.28 cm x 1.28 cm glass chip are tens to hundreds of thousands of different oligonucleotide probes, laid out in precise locations and available for hybridization with fluorescent-labeled target nucleic acids. Once the sample is hybridized, scanners determine the locations of matches between each probe and the target, and since the sequence of the probes is known, the identity of the target nucleic acid can be determined.

The limitation of this technique is not the number of probes on the array, but the resolution of the scanner. The HP GeneArray System, with 3 mm resolution, boosts the usable capacity of the chip to up to at least 400,000 probes and scans for matches in as little as five minutes per chip. "This scanner will be especially useful for sequence analysis, genotyping, mutation analysis, and gene expression studies," says William Gette, product manager at H-P. "You could potentially resequence a region of 100,000 bases all at once."

Affymetrix has focused its initial efforts in DNA chip development on major diseases. The first commercially available chip, the HIV chip, contains 16,000 probes complementary to the reverse transcriptase and protease genes of the virus. The extraordinary number of variants found in naturally occurring isolates of the virus makes this choice especially compelling. The ability to sequence virus from individuals directly and quickly will facilitate the development of therapeutics and the analysis of drug efficacy.

While the GeneChip HIV-1 array and p53 tumor suppressor gene arrays are the only assays currently on the market, Affymetrix produces custom chips and plans to introduce chips for p450 metabolic gene analysis later this year.

Affymetrix sells the HP GeneArray Scanner as part of its GeneChip System, along with GeneChip Reagents, Probe Arrays, Fluidics Station, and Software. With a price tag of over $100,000, this system is likely to find a place in shared, core facilities and large clinical and diagnostic programs. While not a replacement for conventional DNA sequencing systems, this technology has broad applications in biomedical research, genomics, and diagnostics.

For more information, contact Affymetrix at 408-731-5000 or visit their web site: http://www.affymetrix.com/.

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