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BioInform s Patent Roundup: Recent Patents of Interest in Bioinformatics: Jan 13, 2003

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US Patent 6,505,125. Methods and computer software products for multiple probe gene expression analysis. Inventor: Ming-Hsiu Ho. Assignee: Affymetrix.

Protects methods and computer software products for analyzing gene expression data. In one embodiment of the invention, the expression of a gene is determined by multiple probes in several experiments. The method uses principal components analysis to obtain the relative expression of the genes in these experiments.

 

US Patent 6,502,039. Mathematical analysis for the estimation of changes in the level of gene expression. Inventors: Joachim Theilhaber, Steven Bushnell, Rainer Fuchs. Assignee: Aventis Pharmaceuticals.

Protects a mathematically based methodology for quantifying the levels of differential gene expression from microassay protocols. The approach relies on a Bayesian framework that improves upon methods that seek a point estimate of the fold change of the level of gene expression, according to the inventors. Instead, the method uses a mathematical formula to determine the a posteriori distribution of all the fold changes of differential gene expression that may be inferred from the given measurements.

 

US Patent 6,498,863. Method, system, and product for analyzing a digitized image of an array to create an image of a grid overlay. Inventors: Yuri Gaidoukevitch, Kevin Ryan, Dean Sequera. Assignee: Media Cybernetics.

Covers a method, system, and product for analyzing a digitized image of an array to create an image of a grid overlay. The method locates the center of each object on the array, determines a standard shape and size for the objects, and creates a final image of the grid overlay.

 

US Patent 6,490,532. Method to construct protein structures. Inventor: Christopher Hogue, Howard Feldman. Assignee: Mount Sinai Hospital.

Covers a computer-implemented method for creating all-atom, real-space protein conformers. The method uses a novel pipelined residue addition approach, according to the inventors, in which the leading edge of the protein is constructed three residues at a time for optimal protein geometry.

 

US Patent 6,484,183. Method and system for providing a polymorphism database. Inventors: David Balaban, Joyti Baid, Anthony Berno. Assignee: Affymetrix.

Covers a database model that interrelates information about subjects from whom samples are extracted and primers used in extracting the DNA from the subjects, as well as information about the samples themselves, experiments done on the samples, the arrays used to perform experiments, analysis procedures performed on the samples, and analysis results. The model is scalable and readily translatable into database languages such as SQL, according to the patent.

 

US Patent 6,470,346. Remote computation framework. Inventor: Mark Morwood. Assignee: Millennium Pharmaceuticals.

Covers a computer system of remote servers to provide additional memory and processing time for bioinformatics applications. The patent describes a remote computation system to enable a requesting client to invoke any arbitrary command line on a remote server. The remote computation process dispatches computation requests received from clients to appropriate computation servers, manages the computation requests, and allows vending or gathering of results that are sent back to the requesting client.

 

US Patent 6,470,277. Techniques for facilitating identification of candidate genes. Inventors: Daniel Chin, Donna Hendrix, Oliver Zhao. Assignee: AGY Therapeutics.

Covers techniques for extracting and integrating information from various information sources and analyses and storing the integrated information in a form that is “conducive to identification of candidate genes.” Stored information may include results of a DNA sequence homology search, annotative information, gene expression profile data, or clustering results.

 

US Patent 6,468,476. Methods for using-co-regulated gene sets to enhance detection and classification of gene expression patterns. Inventors: Stephen Friend, Roland Stoughton, Yudong He. Assignee: Rosetta Inpharmatics.

Describes several methods for enhanced detection of biological response patterns. In one embodiment, genes are grouped into basis gene sets according to the co-regulation of their expression. The expression values of gene sets, rather than the expression of individual genes, are then used as the basis for comparison and detection of biological response.

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The Scan

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.