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IP Roundup: Mar 29, 2011


Cornell Research Foundation has received US Patent No. 7,914,981, "Detection of nucleic acid sequence differences using the ligase detection reaction with addressable arrays." The patent describes a method for identifying sequences differing by one or more single base changes, insertions, deletions, or translocations in target nucleotide sequences. The method includes a ligation phase, a capture phase, and a detection phase. The ligation phase uses a ligation detection reaction between one oligonucleotide probe, which has a target sequence-specific portion and an addressable array-specific portion, and a second oligonucleotide probe, having a target sequence-specific portion and a detectable label. After the ligation phase, the capture phase is carried out by hybridizing the ligated oligonucleotide probes to a solid support with an array of immobilized capture oligonucleotides at least some of which are complementary to the addressable array-specific portion. Following completion of the capture phase, a detection phase is carried out to detect the labels of ligated oligonucleotide probes hybridized to the solid support, according to the patent.

GE Healthcare has received US Patent No. 7,914,983, "Detection method for gene expression." The patent describes an approach for generating oligonucleotide probes and the use of the probes in gene-expression profiling by hybridization to test oligonucleotides on arrays or beads. The approach involves labeling of the complement oligonucleotide probes using a mixture of dye- or hapten-labeled ddNTPs in solution. The labeled oligonucleotide probes are then used to hybridize to the test oligonucleotides on the solid support. Success in hybridization is monitored by associated signal on the solid support. According to the inventors, the approach "greatly reduces hybridization time, due to the simplification of the probe content." It is also "especially useful when analyzing a small number of genes, such as a signature set of genes for a disease or condition," the inventors stated.

Illumina of San Diego has received US Patent No. 7,914,988, "Gene expression profiles to predict relapse of prostate cancer." A method for preparing a reference model for cancer relapse prediction that "provides higher resolution grading than Gleason score alone" is provided. The method encompasses: a) obtaining from different individuals prostate carcinoma tissue samples of known clinical outcome representing different Gleason scores; b) selecting a set of signature genes having an expression pattern that correlates positively or negatively in a statistically significant manner with the Gleason scores; c) independently deriving a prediction score that correlates gene expression of each individual signature gene with Gleason score for each signature gene in the samples; d) deriving a prostate cancer gene-expression score that correlates gene expression of the signature genes with the Gleason score based on the combination of independently derived prediction scores in samples; and correlating this expression score with the clinical outcome for each prostate carcinoma tissue sample.

Illumina has also received US Patent No. 7,914,739, "Continuous polymer synthesizer." The patent claims a method for synthesizing polymeric molecules such as oligonucleotides and polypeptides. A described system is capable of continuously synthesizing molecules by providing an array of reaction sites and an array of stations for carrying out synthetic manipulations, according to the patent. The reaction sites in the former array can be placed in a fixed order and at fixed intervals relative to each other. Similarly, the stations can be placed in a fixed order and at fixed intervals relative to each other. The two arrays can be moved relative to each other so that the stations carry out desired steps of a reaction scheme at each reaction site, and the relative locations of the stations and the schedule for the relative movement can correlate with the order and duration of reaction steps in the reaction scheme so that once a reaction site has completed a cycle of interacting with the full array of stations, the reaction scheme is complete.

Samsung Electronics of Seoul, Korea, has received US Patent No. 7,914,996, "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 by determining in a nucleic acid sample the nucleotide base at a specific polymorphic site. According to the patent, the operation of determining the nucleotide base of the polymorphic site includes hybridizing the nucleic acid sample onto a microarray and detecting a hybridization result.

Biosigma of Colina, Chile, has received US Patent No. 7,915,031, "DNA fragments array from biomining microorganisms and method for detection of them." The patent claims a method to identify microorganisms in a sample using an array. The inventors claim the method is useful in biomining, where microorganisms are used to leach out desired minerals and a "global understanding of the present microbiological diversity is required." The approach can also be used to "assess the presence of some microorganism with biomining relevance, either on the mineral, or in a bioleaching heap, in the biomining laboratory or in any other circumstance involving biomining microorganisms," according to the patent.

New York University has received US Patent No. 7,917,297, "Methods, software arrangements, storage media, and systems for genotyping or haplotyping polymorphic genetic loci or strain identification." Microarrays, each containing a set of oligonucleotide probes capable of detecting known genotypes and haplotypes at given polymorphic genetic loci or identifying pathogen strain variants, are claimed. According to the patent, the arrays may be employed to quickly identify viral or bacterial pathogens for which genome-sequence information is available.

The Scan

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.

Family Genetic Risk Score Linked to Diagnostic Trajectory in Psychiatric Disorders

Researchers in JAMA Psychiatry find ties between high or low family genetic risk scores and diagnostic stability or change in four major psychiatric disorders over time.

Study Questions Existence of Fetal Microbiome

A study appearing in Nature this week suggests that the reported fetal microbiome might be the result of sample contamination.

Fruit Fly Study Explores Gut Microbiome Effects on Circadian Rhythm

With gut microbiome and gene expression experiments, researchers in PNAS see signs that the microbiome contributes to circadian rhythm synchronicity and stability in fruit flies.