Tuesday, August 18, 2009


Affymetrix (NASDAQ: AFFX) is a manufacturer of DNA microarrays, based in Santa Clara, California, United States. The company was co-founded by Dr. Stephen Fodor in 1992. The company was begun as a unit in Affymax N.V. in 1991 by Fodor's group, which had in the late 1980s developed methods for fabricating DNA microarrays, called "GeneChips" according to the Affymetrix trademark, using semiconductor manufacturing techniques. The company's first product, an HIV genotyping GeneChip, was introduced in 1994 and the company went public in 1996. As a result of their pioneering work and the ensuing popularity of microarray products, Affymetrix derives significant benefit from its patent portfolio in this area.

Acquisitions have included Genetic MicroSystems for slide-based microarrays and scanners, Neomorphic for bioinformatics, ParAllele Bioscience for custom SNP genotyping, USB/Anatrace for biochemical reagents, and Panomics and True Materials to expand its offering of low to mid-plex applications. In 2000 Perlegen Sciences was spun out to focus on wafer-scale genomics for massive data creation and collection required for characterizing population variance of genomic markers and expression for the drug discovery process.

Description of product

Affymetrix makes quartz chips for analysis of DNA Microarrays. These chips are sold under the trademarked name GeneChip. Affymetrix's GeneChips assist researchers in quickly scanning for the presence of particular genes in a biological sample. Within this area, Affymetrix is focused on oligonucleotide microarrays. These microarrays are used to determine which genes exist in a sample by detecting specific pieces of mRNA. A single chip can be used to do thousands of experiments in parallel. Chips can be used only once.

Affymetrix sells both mass produced GeneChips intended to match scientifically important parts of human and other animal genomes. Affymetrix manufactures its GeneChips using photolithography. The company also manufactures machinery for high speed analysis of biological samples.

Affymetrix GeneChip Operating Software is a software system for managing Affymetrix microarray data.

Competitors in the DNA Microarray business include Illumina, GE Healthcare, Applied Biosystems, Beckman Coulter, Eppendorf Biochip Systems, and Agilent. There are also various inexpensive plastic-based technologies under development in small companies and laboratories around the world. It has been widely speculated that mass-produced plastic chips can be produced at lower prices than Affymetrix's quartz chips.

Affymetrix has established a licensing program to make its intellectual property accessible to stimulate the broad commercialization of genome analysis technologies. They have several collaboration relationships with other companies that utilize their patented GeneChip technology.

Future Innovations & Direction

It is unknown whether or not Affymetrix is currently focusing any effort on full genome sequencing, which is thought to be the next major breakthrough in genetic technology and could significantly disrupt the array markets. It's competitor, Illumina, as well as a number of private companies, such as Pacific Biosciences and Complete Genomics have been heavily invested in the race to commercialize full genome sequencing for a number of years. Complete Genomics has stated that they will be able to provide a full genome sequencing service for $5,000 by the summer of 2009. In June 2009, Illumina, Affymetrix's primary competitor, announced that they were launching their own Personal Full Genome Sequencing Service at a depth of 30X for $48,000 per genome. This is still too expensive for true commercialization but the price will most likely decrease substantially over the next few years as they realize economies of scale and given the competition with other companies such as Complete Genomics.

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