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See Which Patents are in Play in Affymetrix vs. Illumina

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In Affymetrix's July 26, 2004 lawsuit against Illumina, the firm alleged in US District Court that Illumina has been infringing on six of its patents listed below. Illumina fired back in September of last year, stating that they are not infringing or that the Affy patents should be invalidated, according to Illumina's attorney, Marc Sernel.

Listed below are the patents in question.

Title: Computer-aided visualization and analysis system for sequence evaluation

Number: 5,795,716

Received: August 18, 1998

Lead Inventor: Mark Chee

Assignee: None

The patent describes a method of identifying an unknown base in a sample nucleic acid sequence comprising measuring probe intensities for a plurality of nucleic acid probes that differ by a base at an interrogation position corresponding to the unknown base, where each probe intensity indicates hybridization affinity between a nucleic acid probe and the sample nucleic acid sequence. The patent also describes a method for analyzing the probe intensities and at least one probe intensity from a nucleic acid probe with an interrogation position corresponding to a position near the unknown base in the sample nucleic acid sequence, and generating a base call identifying the unknown base according to results of the analysis. A computer analysis method is also described.


Title: Computer-aided visualization and analysis system for sequence evaluation

Number: 6,607,887

Received: August 19, 2003

Lead Inventor: Mark Chee

Assignee: Affymetrix

The patent describes a computer program product that identifies an unknown base in a sample nucleic acid sequence, comprising a computer code that receives a plurality of signals corresponding to probe intensities for a plurality of nucleic acid probes; a computer code that performs a comparison of a plurality of probe intensities to each other; and a computer code that generates a base call identifying said unknown base according to results of the comparison and sequences of said nucleic acid probes. A processor and a computer readable medium that stores the computer codes are described as well.


Title: Methods for making a device for concurrently processing multiple biological chip assays

Number: 5,545,531

Received: August 13, 1996

Lead Inventor: Robert Rava

Assignee: Affymax

The patent describes methods for processing multiple biological chip assays. A biological chip plate comprising a plurality of test wells is described where each test has a molecular probe array. According to the patent, the method involves introducing samples into the test wells; subjecting the biological chip plate to manipulation by a fluid handling device that automatically performs steps to carry out reactions between target molecules in the samples and probes; and subjecting the biological chip plate to a biological chip plate reader that interrogates the probe arrays to detect any reactions between target molecules and probes.


Title: Products for detecting nucleic acids

Number: 6,355,432

Received: March 12, 2002

Lead Inventor: Stephan Fodor

Assignee: Affymetrix

The patent provides methods and apparatus for sequencing, fingerprinting and mapping biological macromolecules, typically biological polymers. The methods make use of a plurality of sequence specific recognition reagents which can also be used for classification of biological samples, and to characterize their sources, the patent states.


Title: Bioarray chip reaction apparatus and its manufacture

Number: 6,399,365

Received: June 4, 2002

Lead Inventor: Donald Besemer

Assignee: Affymetrix

Methods and devices for packaging a substrate having an array of probes fabricated on its surface are described in the patent. According to the patent, a substrate having an array of probes is attached to a cavity inside a body using an adhesive. The body includes inlets that allow fluids into and through the cavity, according to the patent. A seal is provided for each inlet to retain the fluid within the cavity. An opening is formed below the cavity to receive a temperature controller for controlling the temperature in the cavity. By forming a sealed thermostatically controlled chamber in which fluids can easily be introduced, a medium for sequencing by hybridization is provided, the patent states.


Title: Nucleic acid reading and analysis system

Number: 6,646,243

Received: November 11, 2003

Lead Inventor: Michael Pirrung

Assignee: Affymetrix

A method and apparatus for preparation of a substrate containing a plurality of sequences are described. Photoremovable groups are attached to a surface of a substrate and selected regions of the substrate are exposed to light so as to activate the selected areas. A monomer, also containing a photoremovable group, is provided to the substrate to bind at the selected areas, the patent's abstract states. The process is repeated using a variety of monomers such as amino acids until sequences of a desired length are obtained. Detection methods and apparatus are also disclosed in the patent.

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