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Affymetrix, Agilent Technologies, BioDiscovery, Illumina, Jean Montagu, James Overbeck, National Semiconductor Corp.

Affymetrix has received US Patent No. 7,097,976, “Methods of analysis of allelic imbalance.” Methods are claimed for identification of imprinted genes as well as identification and analysis of genes whose expression shows allelic imbalance. The expression products transcribed from genes that are present in the genome as two or more alleles may be distinguished by hybridization to an array designed to interrogate individual alleles, the patent’s abstract states. Genes whose transcription products are present in amounts that vary from expected are candidates for allelic imbalance, imprinting and imprinting errors.

Affymetrix has also received US Patent No. 7,098,286, “Functionalized silicon compounds and methods for their synthesis and use.” The patent claims functionalized silicon compounds and methods for their synthesis and use. The compounds include at least one activated silicon group and at least one derivable functional group. Examples of such functional groups include hydroxyl, amino, carboxyl and thiol. The functionalized silicon compounds can be covalently attached to surfaces to form functionalized surfaces which may be used in a wide range of different applications. For example, the silicon compounds can be attached to the surface of a substrate to provide a functionalized surface on the substrate, to which molecules, including polypeptides and nucleic acids, may be attached. Therefore, the method can enable the formation of high-density arrays of nucleic acids immobilized on a substrate, which may be used in conducting high volume nucleic acid hybridization assays, according to the patent’s abstract.

Affymetrix has also received US Patent No. 7,099,777, “Techniques for identifying confirming, mapping, and categorizing nucleic acids.” The patent claims systems and methods for identifying, confirming, mapping, and categorizing sample polymers, such as nucleic acid sequences. According to the patent’s abstract, an estimation of the fraction of first and second polymers in a sample of polymers can be calculated by inputting a hybridization value indicating the hybridization affinity of the sample of polymers to polymers’ probes that are complementary to the first polymer. A second hybridization value indicative of hybridization affinity of the sample of polymers to polymers’ probes is then inputted that is also complementary to the second polymer. The estimation of the fraction of the first and second polymers in the sample of polymers can then be calculated by dividing the first hybridization value by a sum of the first and second hybridization values, the abstract states. Estimations of the fractions of alleles in a sample can then be clustered to form a fraction pattern usable for identifying, confirming, mapping, and genotyping sample nucleic acids.

Agilent Technologies has received US Patent No. 7,094,537, “Microarrays with structured and unstructured probes.” The patent claims an apparatus and method for determining a signal produced by a microarray. The apparatus uses an unstructured probe and structured probe. The unstructured probe binds to a target and provides a first signal that can be compared to a second signal produced by the structured probe. A more accurate level of intensity of the first signal can be determined by comparing to the second signal produced by the structured probe, the patent’s abstract states. A method for determining a more accurate level of signal intensity produced from the unstructured probes bound to the target is also described.

BioDiscovery of El Segundo, Calif., has received US Patent No. 7,099,502, “System and method for automatically processing microarrays.” The patent claims a digital image processing-based system and method for quantitatively processing a plurality of nucleic acid species expressed in a microarray. The system includes a scanner that has a digital scanning sensor. The scanner scans the microarray and transmits from an output a digital image of the microarray. A processor receives the digital image of the microarray from the scanner and then processes the digital image, identifying each of the microarray's sub-grids. The processor then detects in each of the sub-grids a center-representing pixel of a signal of a chemical material and an approximate radius of the signal. Then, the processor segments the signal and calculates a characterizing measure for the segmented signal.

Illumina has received US Patent No. 7,092,160, “Method of manufacturing of diffraction grating-based optical identification element.” The patent claims a method for manufacturing a diffusion grating-based optical identification element. The optical identification element includes a known fiber substrate, having a diffraction grating where the grating is indicative of a code when exposed to incident light. According to the patent’s abstract, a large number of elements or microbeads all having the same identification codes can be manufactured by cutting the substrate transversely where the grating is located, thereby creating a plurality of elements. The elements may be manufactured in many different ways, including winding the fiber onto a basket, forming the gratings in the basket openings or bays, removing the fiber and cutting the fiber to form the elements. Each bay may have a set of elements with a unique set of codes, according to the abstract.

Jean Montagu of Brookline, Mass., and James Overbeck of Hingham, Mass., have received US Patent No. 7,095,032, “Focusing of microscopes and reading of microarrays.” A scanning microscope under computer control that uses a tiltable plate-based focusing action for scanning biochips is claimed. Also described are a support plate to define the hinge axis, techniques for determining position and focus, and an oscillating flying micro-objective scanner combined with the tilting plane focus system. Construction and control techniques are also claimed and methods of examination of biological materials, including ordered arrays of nucleotides and nucleic acid fragments carried upon a microscope slide or other substrate are claimed.

National Semiconductor Corp. of Santa Clara, Calif., has received US Patent No. 7,095,096, “Microarray lead frame.” The patent claims processes for packaging integrated circuits in microarray packages. According to the patent’s abstract, a first side of a metal sheet is etched to define a lead frame panel having a plurality of device areas. Each device area includes an array of contact posts suitable for forming contact pads and a plurality of lead traces. Each lead trace is coupled to an associated contact pad. The resulting etched leadframe panel is suited for use in microarray packages.

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