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Fred Hutchinson Cancer Research Center, Institute of Systems Biology, SurModics, Nanogen, Affymetrix, Agilent Technologies

Fred Hutchinson Cancer Research Center and the Institute of Systems Biology, both of Seattle, have received US Patent No. 7,300,755, “Methods for haplotyping genomic DNA.” The patent claims a method for separating large fragments of genomic DNA by haplotype by: a) providing a flat solid surface containing covalently bound oligonucleotide probes with a nucleotide sequence complementary to each haplotype of an HLA allele; b) contacting the oligonucleotide probes with a sample of genomic DNA under conditions conducive to specific hybridization of the genomic DNA to the oligonucleotide probes to form a genomic DNA/oligonucleotide complex; c) removing excess genomic DNA; d) denaturing the genomic DNA/oligonucleotide complex; and e) separately collecting the genomic DNA corresponding to each haplotype and separating the large fragments of genomic DNA by haplotype.

SurModics of Eden Prairie, Minn., has received US Patent No. 7,300,756, “Epoxide polymer surfaces.” The patent claims a method and a reagent composition for the covalent attachment of target molecules, such as nucleic acids, onto the surface of a substrate. The reagent composition includes epoxide groups capable of covalently binding to the target molecule. Optionally, the composition can contain photoreactive groups for use in attaching the reagent composition to the surface.

Nanogen has received US Patent No. 7,300,757, “Electronic systems and component devices for macroscopic and microscopic molecular biological reaction, analyses, and diagnostics.” The patent claims methods for the design, fabrication, and uses of an electronic system that can actively carry out and control multi-step and multiplex reactions in macroscopic or microscopic formats, including nucleic acid hybridizations, nucleic acid amplification, sample preparation, antibody/antigen reactions, clinical diagnostics, combinatorial chemistry and selection, drug screening, oligonucleotide and nucleic acid synthesis, peptide synthesis, biopolymer synthesis, and catalytic reactions.

Affymetrix has received US Patent No. 7,300,788, “Method for genotyping polymorphisms in humans.” The patent claims nucleic acid sequences that are complementary to a wide variety of human polymorphisms and can be used in a variety of analyses including genotyping a large number of SNPs in parallel. The patent also provides a collection of human SNPs that is useful for genetic analysis within and across populations.

Agilent Technologies has received US Patent No. 7,300,798, “Chemical arrays.” The patent claims a method and apparatus for using arrays of polymers, where each array contains a pattern of features over a corresponding region on a surface of a flexible elongated web. The web may be transported in a lengthwise direction past a reading location at which a characteristic of the features is read, while restraining the web on both surfaces on either side of the reading location to assist in maintaining the reading location flat. According to the patent, each array region also may be exposed to a corresponding continuous volume of a sample fluid.

Agilent has also received US Patent No. 7,302,348, “Method and system for quantifying and removing spatial-intensity trends in microarray data.” The patent claims a method and system for quantifying and correcting spatial-intensity trends for each channel of a microarray data. The method calls for the selection of a set of features from each channel of a microarray data set. Based on the selected set of features, a surface is used to determine the intensities for all features in each channel of the set. Spatial-intensity trends within the microarray data set are then quantified, based on the surface to the intensities for each channel of the set. After the surface has been determined, the spatial-intensity trend can be removed from the array data set, the patent states.

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