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IP Roundup: Affymetrix, Illumina, Tufts, Rosetta Genomics, University of Michigan, Roche

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Affymetrix of Santa Clara, Calif., has received US Patent No. 8,460,854, "Multiple step printing methods for microbarcodes." The patent claims a method for forming a microparticle, where a provided pattern defines a code element. The pattern is then printed on the substrate to form a first code element within a microparticle region, and printed again to create successive code elements, such that the first code element and the successive code elements are within the same microparticle region.


Illumina of San Diego has received US Patent No. 8,460,865, "Multiplex decoding of array sensors with microspheres." The described method includes providing an array of randomly distributed bioactive agents, where each of the sites further consists of at least a first and a second identifier binding ligand; detecting the binding of a first decoder binding ligand to the first IBL; detecting the binding of a second DBL to the second IBL; and determining the location of the first and second IBLs, decoding the position of the agents on the array.


Tufts University of Medford, Mass., has received US Patent No. 8,460,878, "Methods and arrays for detecting cells and cellular components in small defined volumes." A method is claimed for detecting a target analyte of a cell in a sample. It includes providing a sample and a solid support, where the sample contains cells in a first concentration, each cell includes a target analyte, and the solid support hosts at least 1,000 assay sites; contacting the support with the sample; and determining the number of assay sites on the support that contain the target analytes.


Tufts has also received US Patent No. 8,460,879, "Methods and arrays for target analyte detection and determination of target analyte concentration in solution." The patent claims a method of detecting a target analyte in a sample by providing a sample and a solid support, where the sample contains a biomolecule target analyte, the support hosts at least 1,000 assay sites, and each assay site has a defined volume of between 10 attoliters and 50 picoliters; b) contacting the support with the sample so that the assay sites of the solid support contain biomolecule target analytes that are bound to capture components within the assay sites; and determining the number of assay sites contacted with the sample that contain a biomolecule target analyte.


Rosetta Genomics of Rehovot, Israel, has received US Patent No. 8,461,315, "MicroRNAs and uses thereof." The patent claims polynucleotides associated with prostate and lung cancer. The polynucleotides are miRNAs and miRNA precursors, as well as methods that can be used for diagnosis, prognosis, and treatment of those medical conditions. The patent also described a biochip containing probes that are complementary to the provided miRNAs as expressed in prostate and lung cancer.


The University of Michigan of Ann Arbor, Mich., has received US Patent No. 8,461,317, "Linkers and co-coupling agents for optimization of oligonucleotide synthesis and purification on solid supports." The patent claims a method of modulating the synthesis capacity and cleavage properties of synthetic oligomers from a solid support. It relies on linker molecules attached to a solid surface and co-coupling agents that have similar reactivities to the coupling compounds with the surface functional groups. The method finds use in the synthesis of oligonucleotides, oligonucleotides microarrays, peptides, and peptide microarrays.


Roche Molecular Systems of Pleasanton, Calif., has received US Patent No. 8,463,590, "Algorithms for classification of disease subtypes and for prognosis with gene expression profiling." The claimed method includes receiving microarray data representing probe pairs for a single microarray; determining, for each probe pair, differences between intensities of perfect match probes and intensities of mismatched probes; determining a difference signal based on these differences; and scaling the difference signal to produce an expression signal. The method also includes normalizing the expression signal based on a theoretical distribution at the unit level to produce a normalized expression signal for the single microarray that is independent of other microarrays.

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