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BioInform s Patent Roundup: Recent Patents of Interest in Bioinformatics: Jul 14, 2003


US Patent 6,591,196. Method and system for extracting data from surface array deposited features. Inventors: Zohar Yakhini, Cynthia Enderwick, Glenda Delenstarr, Paul Wolber, Nicholas Sampas. Assignee: Agilent Technologies.

Protects a method for automatically extracting data signals from a scanned molecular array image. Horizontal and vertical projections of pixel values are computationally produced from the scanned image and then analyzed to determine the positions of peaks. The positions of the first and last peaks in the row and column vectors are used to estimate the positions of the corner features, which are used to create an initial feature coordinate grid. A refined feature coordinate grid is then calculated based on the positions of strong features, and is used to identify the positions of weak features and the positions of the local background regions surrounding all features.


US Patent 6,586,183. Association of ß2-adrenergic receptor haplotypes with drug response. Inventors: Connie Drysdale; Richard Judson; Stephen Liggett; Krishnan Nandabalan; Catherine Stack; Claiborne Stephens. Assignee: Genaissance Pharmaceuticals.

Protects methods for predicting genetic predisposition to disease associated with the ß2-adrenergic receptor gene, methods for predicting response to ß-agonists, and genotypes and haplotypes for thirteen polymorphic sites in the ß2-adrenergic receptor gene. The invention also provides a computer system for storing and displaying polymorphism data determined for the ß2-adrenergic receptor gene that comprises a computer processing unit, a display, and a database containing the polymorphisms, the genotypes, and the haplotypes identified for the ß2-adrenergic receptor gene in a reference population and a patient population.


US Patent 6,584,410. Polymorphism detection utilizing clustering analysis. Inventor: Anthony Berno. Assignee: Affymetrix.

Covers systems and methods for clustering hybridization affinity information of sample polymers to detect polymorphisms, even in the presence of random and systematic errors. In one embodiment, multiple sets of hybridization affinity information are clustered into multiple clusters such that all sets of hybridization affinity information in each cluster are more similar to each other than to the sets of hybridization affinity information in another cluster. The multiple clusters can then be analyzed to detect if there are differences in the sample polymers.


US Patent 6,581,011. Online database that includes indices representative of a tissue population. Inventors: Peter Johnson, Mary Brady. Assignee: TissueInformatics.

Protects methods for storing structural, mechanical, and/or cell function indices for tissue populations in a database. The patent includes a subscription-based business model among its claims: “providing to the subscriber, in exchange for a fee, access to said average indices and dispersion indices in said database.”


US Patent 6,577,956. Automated DNA array image segmentation and analysis. Inventor: Soheil Shams. Assignee: BioDiscovery.

Covers a method for automatically segmenting DNA array images into individual DNA spot images using a computer system. The system automatically deforms a grid to locate and quantify DNA spot images, measures the local signal and background intensity values for the spot images, and displays the values.

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The Scan

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.

Breast Cancer Risk Gene Candidates Found by Multi-Ancestry Low-Frequency Variant Analysis

Researchers narrowed in on new and known risk gene candidates with variant profiles for almost 83,500 individuals with breast cancer and 59,199 unaffected controls in Genome Medicine.

Health-Related Quality of Life Gets Boost After Microbiome-Based Treatment for Recurrent C. Diff

A secondary analysis of Phase 3 clinical trial data in JAMA Network Open suggests an investigational oral microbiome-based drug may lead to enhanced quality of life measures.

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.