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Recent Patents in Bioinformatics, Sept. — Oct. 2007

US Patent 7,286,941. Method for haplotype analysis. Inventor: Alun Thomas. Assignee: Myriad Genetics.
Protects a method for determining haplotypes that is “capable of providing phase information from a set of unphased genotype observations in an efficient robust manner,” according to the patent abstract. The patent states that the method estimates the frequency of haplotypes and infers haplotypes from genotypes for a set of individuals. The amethod first provides a set of genotypes from at least two individuals comprising three or more polymorphic markers; then combines two or more markers, one or more markers and one or more loci, or two or more loci from the set of genotypes to give a new locus; then removes any haplotypes from the new locus that have a sufficiently low maximum likelihood estimate after at least one iteration of expectation maximum on the new locus. These steps are repeated until all the genotypes have been combined into a final locus, and then the expectation maximum is run to give the estimated frequency of haplotypes and inferred haplotypes from the set of genotypes.

US Patent 7,286,940. Method of predicting functions of proteins using ligand database. Inventors: Akiko Itai; Masazumi Imamura. Assignee: Akiko Itai.
Protects a method of predicting the biological function of one or more proteins using a three-dimensional structure database, according to the patent abstract. The method first selects from the database at least one bio-active compound capable of binding to the query protein and then predicts whether the biological function of the query protein is identical or similar to the biological functions of proteins with predetermined biological functions to which the ligand candidates bind.

US Patent 7,283,912. DNA probe design device and information processing method for DNA probe design. Inventors: Hiroto Yoshii; Toshifumi Fukui. Assignee: Canon.
Covers an information processing method for designing a DNA probe. According to the patent claims, the method first counts, with regard to a first base sequence data group containing a target base sequence, “the number of times of manifestation of each of a plurality of partial base sequences obtained from data of said target base sequence.” In a second counting step, the method determines the same for a second base sequence data group that is distinguished from the first base sequence data group. Next, an identification step identifies probe candidates based on frequency information in the first and second counting steps.

US Patent 7,280,922. System, method, and computer software for genotyping analysis and identification of allelic imbalance. Inventors: Rui Mei; Teresa Webster. Assignee: Affymetrix.
Protects methods, systems, and computer software products for determining genotype of a sample using a plurality of probes. In one preferred embodiment, “a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call,” according to the patent abstract.

US Patent 7,280,921. Method for visualizing large-scale protein interaction data. Inventors: Kyungsook Han; Byong-Hyon Ju. Assignee: Inha University Foundation.
Protects a method for visualizing large-scale protein interaction data. The method first produces an initial layout by placing all nodes of protein interaction data on the surface of a sphere by increasing horizontal and vertical angles of polar coordinates. The method then creates a graph by an iterative process in which each node of the initial layout is moved to an “equilibrium position considering global spring forces between non-adjacent nodes as well as local spring forces between adjacent nodes,” according to the patent abstract.

US Patent 7,277,798.Methods for extracting similar expression patterns and related biopolymers. Inventors: Tsunehiko Watanabe; Yasuyuki Nozaki; Ryo Nakashige; Takuro Tamura. Assignee: Hitachi Software Engineering
Protects computer-implemented methods for extracting similar expression patterns and related biopolymers. A segment of experiment cases that includes an expression of interest is first selected as a search range among an expression pattern of a reference gene or the like. “By comparing the selected segment of the expression pattern with expression patterns of a group of candidate genes or the like, genes having an expression pattern with at least a partial similarity are searched from the group of candidate genes,” according to the patent abstract.

US Patent 7,272,506. Computer algorithm for automatic allele determination from fluorometer genotyping device. Inventors: Stephen Glanowski; Jeremy Heil; Emily Winn-Deen; Ivy McMullen. Assignee: Applera.
Covers an automated method of identifying allele values from data files derived from processed fluorophore emissions that are detected when analyzing polymorphic DNA. These methods are used in the “rapid and efficient distinguishing of targeted polymorphic DNA sites without control samples,” according to the patent abstract.

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The Scan

Genetic Testing Approach Explores Origins of Blastocyst Aneuploidy

Investigators in AJHG distinguish between aneuploidy events related to meiotic missegregation in haploid cells and those involving post-zygotic mitotic errors and mosaicism.

Study Looks at Parent Uncertainties After Children's Severe Combined Immunodeficiency Diagnoses

A qualitative study in EJHG looks at personal, practical, scientific, and existential uncertainties in parents as their children go through SCID diagnoses, treatment, and post-treatment stages.

Antimicrobial Resistance Study Highlights Key Protein Domains

By screening diverse versions of an outer membrane porin protein in Vibrio cholerae, researchers in PLOS Genetics flagged protein domain regions influencing antimicrobial resistance.

Latent HIV Found in White Blood Cells of Individuals on Long-Term Treatments

Researchers in Nature Microbiology find HIV genetic material in monocyte white blood cells and in macrophages that differentiated from them in individuals on HIV-suppressive treatment.