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IP Roundup: Jun 14, 2011

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Callida Genomics of Sunnyvale, Calif., has received US Patent No. 7,960,104, "Self-assembled single molecule arrays and uses thereof." Methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene-expression analysis and gene copy number assessment, are claimed. Random arrays used in the invention are self-assembled in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes, into an addressable array of probe sequences, the patent claims.


Illumina of San Diego has received US Patent No. 7,960,119, "Combinatorial decoding of random nucleic acid arrays." The patent claims nucleic acids, where each nucleic acid includes an invariant sequence, a variable sequence, and a label, as well as a method for decoding an array. The method includes providing an array that consists of a substrate with a surface containing discrete sites and a population of microspheres. According to the patent, these probes include an identifier nucleic acid sequence consisting of a primer sequence and a decoder sequence. A set of combinatorial decoding probes consisting of decoding nucleotides and a label is added to the priming sequences, and the presence of the label is subsequently detected.


Illumina has also received US Patent No. 7,960,685, "Confocal imaging methods and apparatus. "An imaging apparatus useful for obtaining a high-resolution image of a sample at rapid scan rates is claimed. The scanning device can be configured to scan the sample in a scan-axis dimension, where the vertical dimension of a rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and where the vertical dimension for such an array is short enough to achieve confocality in a single axis.


SRU Biosystems of Woburn, Mass., US Patent No. 7,960,170, "Grating-based sensor combining label-free binding detection and fluorescence amplification and readout system for sensor." A grating-based sensor is described that is designed for both evanescent resonance fluorescence detection and label-free detection applications. According to the patent, ER detection can be carried out using the sensor when the sample is both dry and liquid. One- and two-dimensional gratings in the sensor, characterized by unit cells with central posts, central holes, and two-level, two-dimensional gratings, are also described, as is a readout system for such sensors.


George Mason University of Fairfax, Va., has received US Patent No. 7,960,184, "Methods and devices for active bioassays." According to the method, a probe molecule is immobilized on a surface. An analyte is then placed in fluidic connection with the probe molecule on the surface. A force is then applied to the analyte to move it toward the surface to facilitate contact and possibly binding of the analyte to the probe. Optionally, another force can be applied or the force can be reversed, to remove unbound or weakly bound analyte from the surface. The analyte that remains bound to the surface is then detected. This detection can include rolling or sliding beads over an analyte or probes on the substrate, and then detecting the bound beads.


Receptors of Chaska, Minn., has received US Patent No. 7,960,311, "Methods employing combinatorial artificial receptors." The patent claims methods employing artificial receptors, such as combinatorial artificial receptor arrays. Such receptors include heterogeneous and immobilized combinations of building block molecules. In certain embodiments, combinations of two, three, four, or five distinct building block molecules immobilized near one another on a support provide molecular structures that can then be used to detect the receptor's ligand and to find compounds that disrupt one or more binding interactions.


TessArae of Potomac Falls, Va., has received US Patent No. 7,961,323, "Microarray imaging system and associated methodology." A device is provided for creating an image of a microarray. It includes at least one light source configured to direct light toward the microarray and an excitation filter configured to filter the light into a first frequency band towards a dichromatic mirror, which reflects light onto the microarray, causing it to emit electromagnetic energy. The apparatus also includes an emission filter configured to filter the electromagnetic energy within a second frequency band, as well as an imaging unit having a charged coupled device with an imaging surface masked by a pinhole blind, so that when the pinhole blind receives electromagnetic energy from the emission filter, an image is created of the entire microarray.


Affymetrix of Santa Clara, Calif., has received US Patent No. 7,962,289, "System, method, and computer product for exon array analysis." A method for analyzing data generated by probe arrays is described. It includes receiving user selections of two or more data files and an identification of one or more subsets of intensity values acquired from a biological probe array. The method includes iteratively opening each data file, identifying the selected subset of intensity values associated with each open data file, determining parameters for processing, storing the parameters and the identified intensity values, and closing the open data file prior to the subsequent iteration. The method then includes processing the stored intensity values using the parameters to identify one or more biological events.


Affymetrix has also received US Patent No. 7,962,291, "Methods and computer software for detecting splice variants." The patent claims a computer-implemented method for identifying exons that are differentially spliced between a first and second sample. It includes obtaining an exon intensity measurement for a first exon in a first gene in a first sample and in a second sample; calculating a gene-level measurement for the genes, where the gene level measurements are median normalized intensity values from all exons present; calculating a splicing index measurement for the first exon, where the splicing index is equal to the log2 of the normalized intensity for said first exon divided by the normalized intensity for the first exon in the second sample; and identifying the first exon as being differentially spliced if the absolute value of the splicing index obtained is greater than a threshold value, where exon array background correction is performed by use of a background probe collection.

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