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IP Roundup: Jan 5, 2010


Samsung Electronics has received US Patent No. 7,638,274, "Polynucleotide associated with a colon cancer comprising single nucleotide polymorphism, microarray and diagnostic kit comprising the same and method for diagnosing a colon cancer using the polynucleotide." The patent claims a method of determining an increased risk of developing colorectal cancer in a human by identifying in a sample a nucleotide base at a specified polymorphic site. According to the patent, the base is determined by hybridizing the nucleic acid sample onto a microarray on which is immobilized a polynucleotide including at least 10 contiguous nucleotides of the specific sequence, and detecting the hybridization result.

The University of Illinois at Urbana has received US Patent No. 7,638,275, "Gene expression profiles that identify genetically elite cattle." Methods are provided for the genetic selection of elite animals with a desired phenotype such as high milk production for breeding to improve production levels. The method to select an animal with a specific phenotype includes creating a gene expression index for a specific phenotype and using the index to identify candidate animals for breeding by comparing the index to gene-expression profiles of the animals.

Stanford University has received US Patent No. 7,638,278, "Markers of DNA copy number alteration for improved prognostication in prostate cancer." The patent describes a method for phenotyping a cancer sample by screening for the presence of a copy number alteration in a sample of human genomic DNA isolated from a suspected primary prostate tumor cell. The method includes hybridizing on an array a probe containing a nucleic acid to a target genomic sequence in the 21q22 region and detecting the formation of the hybridization complex. A reduction of hybridization complexes relative to a normal control is indicative of loss of the 21g22 region and is associated with a clinically aggressive subtype II tumor, according to the inventors.

Boston Probes of Bedford, Mass., has received US Patent No. 7,638,279, "Methods, kits and compositions pertaining to combination oligomers and libraries for their preparation." The patent describes the block synthesis of combination oligomers in the absence of a template, as well as related methods, kits, libraries, and other compositions. The oligomer composition includes a polynucleobase strand, and a combination oligomer that includes a first oligomer block and a second oligomer block that are each independently a peptide nucleic acid, PNA chimera, or PNA combination oligomer. The first and second oligomer blocks are linked covalently to each other by a linker that is at least three atoms in length, and the first and second oligomer blocks are sequence-specifically hybridized to a target sequence of contiguous nucleobases in the polynucleobase strand to form a double-stranded target sequence-combination oligomer complex such that there is no gap or gap base, according to the patent.

The Estonian Biocentre of Tartu, Estonia, has received US Patent No. 7,638,310, "Method to determine single nucleotide polymorphisms and mutations in nucleic acid sequence." The patent claims a genotyping method and a prepared oligo microarray that can be used to determine SNPs and mutations. The method uses two specific APEX-2 primers per each SNP or mutation to be determined. The same primers are used in the amplification phase and in the single-base extension phase on an array. All SNP-containing sequences can be genotyped and amplified in one reaction tube and visualized on a microarray, according to the inventors.

Biocept of San Diego has received US Patent No. 7,638,464, "Three dimensional format biochips." The patent claims a biochip formed with optically clear hydrogel cells attached to the top surface of a solid substrate in the form of an array. Each of the cells is formed of a hydrogel of polyethylene glycol, polypropylene glycol or a copolymer with reactive isocyanate groups. Binding entities are immobilized in the cells, which can be used to hybridize to or sequester a target biomolecule, according to the inventors.

The Wistar Institute of Anatomy & Biology of Philadelphia has received US Patent No. 7,640,114, "Method of diagnosis of cancer based on gene expression profiles in cells." The patent claims a method of diagnosing a cancer by examining a sample containing the subject's immune cells and detecting a variance in the expression of a statistically significant number of genes from those same genes in a characteristic disease or healthy gene-expression profile. A significant variance in expression of these genes when compared to a gene expression profile, preferably an average gene expression profile of a normal control, or significant similarities to an average gene profile of subjects with cancer, correlates with a specific type of cancer and location of tumor, according to the patent.

Siemens has received US Patent No. 7,642,053, "Method and device for PCR-amplification and detection of nucleotide sequences." The patent claims a DNA chip that includes a flat carrier and an array of spots containing probe molecules. Each spot is associated with a microelectrode arrangement for spectroscopic detection of binding events occurring between the probe molecules and target molecules. In order to increase the sensitivity or the binding specific measuring effects of the biochip, the electrode arrangement is embedded in a hydrophilic reaction layer, which contains the probe molecules and which is permeable to target molecules.

The Scripps Research Institute of La Jolla, Calif., US Patent No. 7,642,085, "Protein arrays." The patent relates to protein arrays, which are arrays of polypeptides on solid supports, and methods for making them. The methods claimed allow the coupling of a polypeptide to a solid support in a way that preserves the function of the polypeptides. The covalent or non-covalent attachment generally does not affect the structure, function, or biological activity of the polypeptide, according to the patent. The polypeptides that are used in the arrays incorporate at least one unnatural amino acid, and where the side chain of the amino acid has a reactive group that can be used to couple the polypeptide to any suitable solid support.

Agilent Technologies has received US Patent No. 7,642,097, "Manufacture and use of non-standard size microarray slides." The patent claims a method for processing a non-standard size slide with an array of chemical compounds attached to a surface of the slide. According to the patent, a sample is exposed to the surface of the non-standard size slide where the components in the sample bind to the chemical compounds on the surface of the slide. The sample and the slide are incubated under conditions for carrying out the binding reactions, and the surface of the non-standard size slide is examined for the results of the binding reactions. Prior to the exposing step or the incubating step or the examining step, the non-standard size slide is placed into a slide holder. The non-standard size slide may also include an identifier such as a bar code.

Rosetta Genomics of Rehovot, Israel, has received US Patent No. 7,642,348, "Prostate cancer-related nucleic acids." The patent claims polynucleotides associated with prostate cancer. The polynucleotides are microRNAs, miRNA precursors, and associated nucleic acids. The patent also claims methods that can be used for diagnosis, prognosis, and treatment of prostate cancer. Also described are the methods for linear amplification and labeling of a targeted nucleic acid. The amplified targeted molecules may be used in hybridization techniques like Luminex and microarray analysis, according to the patent.

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.