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PATENT WATCH: Jun 8, 2001

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Incyte Confident About Affymetrix Suit After May Rulings

Incyte is confident that it will prevail in patent infringement litigation with Affymetrix after two recent rulings in its favor, said Incyte general counsel Lee Bendekgey.

In a May 2 ruling, Judge Jeremy Fogel of the U.S. District Court for the Northern District of California ruled that Incyte’s cDNA arrays do not infringe upon Affymetrix’s patent 5,445,934, which covers an “array of oligonucleotides on a solid substrate” because cDNA is not an oligonucleotide, granting Incyte’s motion for partial summary judgment.

This was the patent Affymetrix asserted against Incyte in the original infringement suit it filed in January 1998.

Fogel also held in this ruling that Incyte is not infringing on claims in Affymetrix’s patent 5,744,305, which refers to “arrays of materials attached to a substrate.”

The court previously ruled that “oligonucleotide” was defined as “polymers of nucleotides ranging in length from 2 to about 100 nucleotides.” Based on this definition, it held that cDNAs, which range in length from 500 to 5,000 nucleotides, could not be covered by the ‘934 patent or similar claims in the ‘305 patent.

“Affymetrix’ general assertion that cDNA molecules are oligonucleotides is precluded by this court’s determination that ‘oligonucleotides’ are polymers of less than 100 nucleotides in length,” wrote Judge Fogel.

One of Affymetrix’s remaining infringement claims against Incyte hangs on patent number 5,800,992, which outlines “a method of detecting nucleic acids.” In a May 8 ruling, Judge Fogel held that the language of the first claim in this patent referring to “a sequence substantially complementary to a nucleic acid of said array” was indefinite and narrowed down other terms in this patent.

Based on this second ruling, “we have a pretty clear non infringement argument,” said Bendekgey. “We’re reasonably confident than when [the patents are] properly construed, Affymetrix won’t have any valid patents that apply to our arrays.”

Judge Fogel is scheduled to hear additional motions on June 25, according to a docket clerk. The trial, said Bendekgey, is tentatively slated for next January.

Incyte also filed separate patent infringement claims against Affymetrix in August 2000 covering gene expression data technologies. This suit, which has not yet gone to trial, involves Incyte’s non-PCR based RNA amplification technology. Incyte recently settled a similar suit with Gene Logic for infringement of these patents, Nos. 5,716,785 and 5,891,636.

Nanogen Awarded Two Patents For Microarrays

Nanogen has been awarded two new US patents that cover its electronic microarray technology.

The first patent, No. 6,238,624, covers methods for electronically transporting charged entities in order to replicate arrays, as well as methods for executing and controlling multiplex and multiple step reactions on electronic matrix devices.

“Such multi-step active electronic transport techniques exemplify the ability to carry out more complex DNA hybridization assays on one chip,” Michael Heller, Nanogen’s chief technical officer and inventor on the ‘624 patent, said in a statement. “The ‘624 patent also has unique claims related to methods for using active microarray devices to create replicate DNA microarrays from a master device.”

This patent, which is entitled “Methods for Electronic Transport in Molecular Biological Analysis and Diagnostics,” is the twenty-third US patent issued to the company.

The second US patent, issued June 4, is the first granted to both Nanogen and Becton, Dickinson, which launched a joint technology venture in 1997. The patent, No. 6,238,868 is entitled “Multiplex Amplification And Separation Of Nucleic Acid Sequences Using Ligation-Dependent Strand Displacement Amplification and Bioelectronic Chip Technology.”

This patent covers a kit and methods for strand displacement amplification on a bioelectronic chip in order to amplify, detect, and analyze nucleic acid sequences. The kit is designed to increase the speed of nucleic acid sequence analysis, according to the companies. Nanogen and Becton, Dickinson are planning to jointly develop devices for diagnosing and monitoring infectious diseases.

Genomic Solutions Awarded Automated Hybridization Patent

Genomic Solutions has been awarded a US patent for automated hybridization of DNA microarrays. This patent, number 6,238,910, describes a device for hybridizing a microarray in a way that automates the introduction of reagents and control of temperature. The method described also provides automated agitation of fluid within the cavity to improve the success of hybridization.

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