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PATENT WATCH: Oct 19, 2001


Lose a patent, gain a patent: Just after a US District Court Judge declared one of its other patents invalid (see p. 1), Affymetrix was awarded a new patent for its microarray technology, US Patent Number 6,303,301. The patent, “Expression monitoring for gene function identification,” describes ways to use massive parallel monitoring of gene expression to map the regulatory relationship between groups of genes.

In the invention, the expression levels of groupsof 10 or more, or as many as 5,000 genes are monitored in large samples of cells.

The invention uses antisense genes and oligonucleotides to block expression of specific genes. The consequent changes in gene expression downstream of these genes can be used to define the regulatory functions of genes, as well as mutations in the regulatory genes. The gene expression data can be used to generate cluster maps of gene networks.

The patent also includes specific methods for detecting mutations in the p53 gene. Affymetrix currently markets a p53 chip for experiments to detect mutations in this tumor-suppressor pathway.

Affymetrix sees this invention as providing models of gene malfunction in a number of diseases, and foresees its use in the pharmaceutical and diagnostic industries.


Nanogen has received US Patent Number 6,303,082, “Permeation layer attachment chemistry and method.” The patent covers the method that the San Diego-based maker of electronically addressable biochips uses to attach a porous top layer to the surface of its chips. This permeation layer includes the charged moieties that provide the probes, which are covalently bound to the metal-silicide surface of the chip’s electrodes.


Rosetta Inpharmatics, now a wholly owned subsidiary of Merck, has received US Patent Number 6,303,291, “Methods for comparing a number of primary targets for two or more drug compositions.” The patent involves using microarrays, among other methods, to identify “expression sets” of cellular components that are affected by a certain concentration of the drug. The invention also involves measuring the responses of the cellular constituents to exposure to the drug, and identifying a minimum “inflection concentration” at which the drug affects the constituents. These methods can also be coordinated through computer systems, according to the patent.

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