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IP Roundup: Dec 7, 2010


Roche NimbleGen has received US Patent No. 7,846,660, "Microarrays having multiple oligonucleotides in single array features." The patent claims a method for synthesizing microarrays that have different oligonucleotides present within one feature area of the array. The method relies on techniques common to microarray synthesis, but limits the duration in which the selected feature areas on the array are initially dosed with light so as to only de-protect a calculated ratio of the compounds forming the array's binding layer. The compounds initially de-protected are then capped with a non-photosensitive protecting group, such as di-methoxy-trityl, to inhibit their involvement in the synthesis of a first group of DNA strands built onto the array. Once the first group of DNA strands has been synthesized, the original de-protected group may then be further processed to build one or more groups of DNA strands in the same feature area as the first group of DNA strands, according to the patent.

NuGen Technologies of San Carlos, Calif., has received US Patent No. 7,846,666, "Methods of RNA amplification in the presence of DNA." The patent claims methods for the amplification of RNA in the presence of DNA. The methods involve producing a marked first primer extension product from a target RNA in the presence of a DNA-dependent DNA polymerase inhibitor, which prevents replication of DNA by the reverse transcriptase enzyme. The marked nucleic acid products are subsequently selectively amplified in the presence of non-marked nucleic acids. According to the patent, the methods are useful for production and analysis of polynucleotide sequences complementary to an RNA sequence, as well as the preparation of nucleic acid libraries and substrates for the analysis of gene expression of cells in biological samples.

NuGen has also received US Patent No. 7,846,733, "Methods and compositions for transcription-based nucleic acid amplification." The patent claims methods for the isothermal exponential amplification of a target polynucleotide. The methods employ two transcription modules: the first module provides linear amplification resulting in RNA transcripts, and a second module provides for further, generally cyclical amplification resulting in more RNA transcripts. In one aspect of the patent, the amplification of the first module is composite-primer based. In a second aspect, the amplification of the first module is based on target switching to generate a primer extension product that includes a promoter sequence. In all aspects, the RNA transcripts of the first transcription module are subjected to further amplification by creating an intermediate product made up of a double-stranded promoter region from which transcription can occur.

Randox Laboratories of Crumlin, UK, has received US Patent No. 7,846,713, "Calibrating microarrays." The patent described an assay for measuring the amount of an analyte in a sample. It includes: a) contacting the sample with a device that contains reaction sites that include ligands with an affinity for the particular analyte, as well as other reaction sites that include different known concentrations of an immobilized second analyte; b) removing any unbound first analytes; c) contacting the device with a second ligand that is detectably labeled and which has affinity for the first analyte, and a third ligand that is detectably labeled and which has affinity for the second analyte; d) removing any unbound second and third ligands; and e) measuring the amount of second and third ligands, where the measurement of the third ligand is used to establish a calibration curve, which is in turn used to determine the amount of first analyte present in sample.

Rensselaer Polytechnic Institute of Troy, NY, and the University of California of Oakland have received US Patent No. 7,846,747, "Biocatalytic solgel microarrays." The patent describes a system for high-throughput screening to detect a reaction. The system includes an apparatus containing independent, permeable micromatrices encapsulating test compositions. The apparatus is contacted with tissue or cells that are subsequently cultured. The tissue or cells are then assayed for a biological response indicative of a reaction between the test composition and the applied composition.

Children's Hospital Medical Center of Cincinnati has received US Patent No. 7,847,088, "Classification and diagnosis of the molecular basis of cholestasis." The patent describes a cholestasis-related gene resequencing microarray suitable for determining the nucleotide sequence of a region of a cholestasis-related gene. Knowledge of the nucleotide sequence of one or more regions of a patient's cholestasis related gene allows diagnosis of the patient's syndrome, according to the patent.

Affymetrix has received US Patent No. 7,846,659, "Arrays of nucleic acid probes for analyzing biotransformation genes." The patent provides arrays of immobilized probes for detecting mutations in biotransformation genes, such as cytochrome P450. For example, one such array includes four probe sets, where the probes in the first set make up a segment of at least three nucleotides exactly complementary to a subsequence of a reference sequence from a biotransformation gene, and the segment includes at least one interrogation position complementary to a corresponding nucleotide in the reference sequence. Second, third and fourth probe sets contain corresponding probes for each probe in the first probe set, according to the patent.

The Englehardt Institute of Molecular Biology of Moscow, Russian Federation, has received US Patent No. 7,846,656, "Composition for polymerizing immobilization of biological molecules and method for producing said composition." The patent claims a method for the immobilization in polymer carriers of oligonucleotides, proteins, nucleic acids, or any other molecules, which structure comprises active groups, including amino- or sulfhydryl groups. The resulting immobilized molecules may be used in various applications including microchips for DNA sequencing and mapping, mutation detection, and medical applications.

The Scan

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EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

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Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.