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IP Roundup, Oct 26, 2010

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The University of Maryland has received US Patent No. 7,820,227, "Biolithographical deposition and materials and devices formed therefrom." The patent claims a method for the biolithographical deposition of molecules. A reactive layer, such as a polysaccharide mass, with a surface region coated with a biologically compatible resist is provided. A portion of the biologically compatible resist is selectively removed to expose an exposed portion of the reactive layer. Molecules, such as biomolecules and cellular species, are then conjugated to the exposed portion of the reactive layer.


Third Wave Technologies, now Hologic, of Madison, Wis., has received US Patent No. 7,820,387, "Reactions on a solid surface." The patent claims methods for forming a nucleic acid cleavage structure on a solid support and cleaving the nucleic acid cleavage structure in a site-specific manner. According to the patent, the solid support may include a bead, a multi-well plate, a column, or a microarray. In some embodiments, a 5' nuclease activity from any of a variety of enzymes is used to cleave the target-dependent cleavage structure, indicating the presence of specific nucleic acid sequences or their specific variations.


Osmetech Molecular Diagnostics, now GenMark Diagnostics, of Pasadena, Calif., has received US Patent No. 7,820,391, "Baseless nucleotide analogues and uses thereof." The patent claims a method of detecting a target nucleic acid. The method includes providing a substrate composed of an electrode; a self-assembled monolayer; and a capture probe. According to the patent, the capture probe binds to the target nucleic acid by forming a complex that includes the capture probe, nucleic acid, and a label probe comprising described compounds. Electron transfer from a redox active moiety of the label probe to the conductive surface of said electrode is then monitored to detect the target nucleic acid.


The Wisconsin Alumni Research Foundation of Madison, Wis., has received US Patent No. 7,820,412, "Method of error reduction in nucleic acid populations." A method is described for the direct synthesis of double-stranded DNA molecules of a variety of sizes and with any desired sequence. According to the patent, a DNA molecule is broken up into smaller overlapping DNA segments. A maskless microarray synthesizer is then used to make a DNA microarray on a substrate in which each element or feature of the array is populated by DNA of one of the overlapping DNA segments. The complement of each segment is also made in the microarray. The DNA segments are released from the substrate and held under conditions favoring hybridization of DNA, under which conditions the segments will hybridize to form duplexes. The duplexes are then separated using a DNA-binding agent, which binds to improperly formed DNA helixes to remove errors from the set of DNA molecules. The segments can then be hybridized to each other to assemble the larger target DNA sequence.


Fluidigm of South San Francisco, Calif., has received US Patent No. 7,820,427, "Microfluidic device and methods of using same." A variety of elastomeric-based microfluidic devices and methods for using and manufacturing such devices are claimed in this patent. Some of the devices have arrays of reaction sites to facilitate high-throughput analyses. Some devices also include reaction sites located at the end of blind channels at which reagents have been previously deposited during manufacture. The reagents become suspended once sample is introduced into the reaction site. The devices can be used with a variety of heating devices and can be used in a variety of analyses requiring temperature control, including thermocycling applications such as nucleic acid amplification reactions, genotyping, and gene-expression analyses, according to the patent.


Affymetrix has received US Patent No. 7,822,555, "Methods for identifying DNA copy number changes." The patent claims methods of identifying allele-specific changes in genomic DNA copy number and methods for identifying homozygous deletions and genetic amplifications. The methods rely on an array of probes designed to detect presence or absence of different sequences. According to the patent, the probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to normal tissue, or to diagnose cancer and other diseases associated with chromosomal anomalies.


The Jackson Laboratory of Bar Harbor, Maine, has received US Patent No. 7,822,556, "Expression data analysis systems and methods." The patent describes global pattern recognition, a system for analyzing the results of RT-PCR experiments run on microarrays or microtiter plates. According to the patent, the system employs a set of self-normalizing housekeeping primers or oligonucleotides on the arrays and relies on an algorithmic approach to normalizing expression data from all primers on the plate based on the reaction products of several of the self-normalizing gene primers or oligonucleotides. More specifically, normalization is accomplished using simplex reactions involving these self-normalizing primers or oligonucleotides; the normalization parameters are then useable across all control and experimental reactions of the array or plate. A ranked list of genes whose amount of change is statistically significant can be determined using the system.


Agilent Technologies has received US Patent No. 7,822,559, "Methods and systems for detrending signal intensity data from chemical arrays." The patent clams a method of removing trends in signal intensity values from features on a chemical array. The method includes: inputting signal intensity values to a system configured for removing trends in signal intensity values from features on a chemical array; calculating, using a processor, a log transform of each signal intensity value to provide log-signal intensity values; calculating a surface approximation of the log signal intensity values; normalizing surface fit values on the calculated surface approximation in locations corresponding to locations of the features on the array; calculating a reverse-log transform of the normalized surface fit values; de-trending the inputted signal intensity values as a function of the normalized surface values; and outputting de-trended signal intensity values.

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