Patents Examined by B. J. Forman
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Patent number: 6942968Abstract: The invention relates methods of improving signal detection from an array and methods for background subtraction in an array. The invention provides for novel array compositions including arrays with wells with different shapes, or surfaces coated with reflective or selectively absorptive coatings. In addition, the array include a signal transducer element.Type: GrantFiled: August 30, 2000Date of Patent: September 13, 2005Assignee: Illumina, Inc.Inventors: Todd A. Dickinson, Shawn Meade, Steven M. Barnard, Anthony W. Czarnik, James Bierle, Bahram G. Kermani, Mark S. Chee
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Patent number: 6933114Abstract: Methods are provided for generating nucleic acid ligands of Prostate Specific Membrane Antigen (PSMA). The methods of the invention use the SELEX method for the isolation of nucleic acid ligands. The invention also includes nucleic acid ligands to PSMA, and methods and compositions for the treatment and diagnosis of disease using the nucleic acid ligands.Type: GrantFiled: October 16, 2001Date of Patent: August 23, 2005Assignee: Gilead Sciences, Inc.Inventors: Shawn E. Lupold, Yun Lin, Brian J. Hicke, Donald S. Coffey
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Patent number: 6919181Abstract: Methods of producing ligand arrays, e.g., polypeptide and nucleic acid arrays, as well as the arrays produced thereby, methods for use of the arrays and kits that include the same, are provided. In the subject methods, a substrate having a surface displaying carboxylic ester functional groups that produce surface bound hydroxyl functional groups upon hydrolysis is first provided. Next, the functional groups are hydrolyzed to hydroxyl functional groups. The resultant substrate, optionally after an additional functionalization step, is then contacted with ligands, e.g., via deposition of each different ligand onto a different region of the surface, resulting in covalent attachment of the contacted ligands to the surface.Type: GrantFiled: March 25, 2002Date of Patent: July 19, 2005Assignee: Agilent Technologies, Inc.Inventor: John S. Hargreaves
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Patent number: 6916621Abstract: The invention provides computer systems, computer program products and methods for in silico array-based methods for determining the relative amount of biological molecules (e.g., nucleic acid sequences) in two or more samples. The invention also provides novel arrays comprising immobilized calibration molecules (e.g., nucleic acids) for normalizing the results of array-based binding assays (e.g., hybridization reactions).Type: GrantFiled: March 27, 2002Date of Patent: July 12, 2005Assignee: Spectral Genomics, Inc.Inventor: Shishir Shah
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Patent number: 6916608Abstract: The present invention relates to a method and composition for stabilizing clinical specimens (i.e., cells in biological samples) for transport and subsequent testing for diagnosis. The composition is specifically capable of maintaining nucleic acid in the cells intact for hybridization with oligonucleotide capture and detector probes.Type: GrantFiled: September 10, 1999Date of Patent: July 12, 2005Assignee: Becton, Dickinson and CompanyInventors: Dolores M. Berger, Daretta A. Yursis, William A. Nussbaumer, Anne B. Brown
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Patent number: 6897026Abstract: A method for imaging molecules contained in an array of discrete reaction sites on the surface of a solid support comprises: (i) imaging the array and detecting a first molecule located on the solid support at a known position with respect to the array; (ii) by reference to the first molecule, aligning inspection windows in registration with the discrete reaction sites; and (iii) determining the amount of detectable signal in each window. The method is used to locate the reaction sites accurately on the array, and to correct for any misalignments.Type: GrantFiled: January 17, 2002Date of Patent: May 24, 2005Assignee: Randox Laboratories Ltd.Inventors: John Victor Lamont, Robert Ivan McConnell, Stephen Peter Fitzgerald
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Patent number: 6881538Abstract: Materials for use in miniaturized arrays, the arrays, and methods of manufacturing. Materials for making arrays described include a substrate with a silicon-containing layer, optionally with linking agents and reactants.Type: GrantFiled: March 5, 2000Date of Patent: April 19, 2005Assignee: 3M Innovative Properties CompanyInventors: Louis C. Haddad, Moses M. David, Kurt J. Halverson, Sanjay L. Patil, Jerald K. Rasmussen, James I. Hembre
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Patent number: 6855496Abstract: This invention is directed to a method for identifying nucleic acid ligands by the SELEX method wherein the participation of fixed sequences is eliminated or minimized.Type: GrantFiled: July 17, 2001Date of Patent: February 15, 2005Assignee: Gilead Sciences, Inc.Inventors: Nikos Pagratis, Larry Gold, Timur Shtatland, Brenda Javornik
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Patent number: 6818400Abstract: The present invention aims at producing a biochip by an inkjet system without wasting a DNA solution. A biochip-producing solution is prepared to contain a combination of a DNA solution 6 to be spotted on a plate 5 and a low-cost buffer solution 7 to be remained in the device after the production. The buffer solution 7 used has a different specific gravity from that of the DNA solution 6 and thus is not mixed therewith.Type: GrantFiled: May 3, 2001Date of Patent: November 16, 2004Assignee: Hitachi Software Engineering Co., Ltd.Inventors: Toshiaki Ito, Kenji Yamamoto, Junji Yoshii, Atsumi Tsujimoto, Hisanori Nasu
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Patent number: 6808886Abstract: The invention provides computer systems, computer program products and methods for in silico array-based methods for determining the relative amount of biological molecules (e.g., nucleic acid sequences) in two or more samples. The invention also provides novel arrays comprising immobilized calibration molecules (e.g., nucleic acids) for normalizing the results of array-based binding assays (e.g., hybridization reactions).Type: GrantFiled: March 27, 2002Date of Patent: October 26, 2004Assignee: Spectral Genomics, Inc.Inventor: Shishir Shah
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Patent number: 6783934Abstract: A method for determining a threshold cycle number or time value in a nucleic acid amplification reaction comprising the steps of amplifying a nucleic acid sequence in a reaction mixture; at a plurality of different times during the amplification reaction, measuring at least one signal whose intensity is related to the quantity of the nucleic acid sequence in the reaction mixture; and storing signal values defining a growth curve for the nucleic acid sequence. A derivative of the growth curve is determined and the threshold cycle number or time value is calculated as a cycle number or time value corresponding to a characteristic (e.g., maximum, minimum, or zero-crossing) of the derivative.Type: GrantFiled: May 1, 2000Date of Patent: August 31, 2004Assignee: Cepheid, Inc.Inventors: William A. McMillan, Lee A. Christel, David A. Borkholder, Steven J. Young
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Patent number: 6770441Abstract: The invention relates to sensor compositions comprising a composite array of individual arrays, to allow for simultaneous processing of a number of samples. The invention further provides methods of making and using the composite arrays. The invention further provides a hybridization chamber for use with a composite array.Type: GrantFiled: August 16, 2001Date of Patent: August 3, 2004Assignee: Illumina, Inc.Inventors: Todd Dickinson, Kenneth D. Coblentz, Edward Carlson
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Patent number: 6753144Abstract: When genetic analyses are performed using the DNA microarray of the present invention, the inspection accuracy is improved. A sample solution is supplied onto a base plate 10 to prepare the DNA microarray 20 which includes a large number of spots 80 containing capture solutions arranged on the base plate 10. The capture solutions are adapted to specifically react with a specimen and provide information about a structure within the specimen. In the microarray 20, the planar configuration of the spots 80 are substantially circular, and a plurality of spots having different spot sizes are formed on the base plate.Type: GrantFiled: June 21, 2001Date of Patent: June 22, 2004Assignee: NGK Insulators, Ltd.Inventors: Toshikazu Hirota, Takao Ohnishi
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Patent number: 6750023Abstract: A porous inorganic substrate and method of fabricating such substrate for attaching an array of biological or chemical molecules to be used in a high-density microarray device. The substantially planar substrate comprises a porous inorganic layer adhered to a flat, rigid, non-porous, inorganic understructure having a coefficient of thermal expansion compatible with that of the porous inorganic layer. The porous inorganic layer is characterized as having dispersed throughout it a plurality of interconnecting voids as defined by a network of contiguous inorganic material, each of a predetermined mean size. The continuous inorganic material and contents of the voids exhibit a high contrast in their indices of refraction relative to each other. The substrate further comprises a uniform coating of a binding agent over at least a part of the surface area of the voids and the top surface of the porous inorganic layer.Type: GrantFiled: March 18, 2002Date of Patent: June 15, 2004Assignee: Corning IncorporatedInventors: Cameron W. Tanner, Patrick D. Tepesch, Raja R. Wusirika
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Patent number: 6746840Abstract: A micro array, which comprises a stimulable phosphor sheet, and multiple kinds of biomolecules arrayed and fixed on the stimulable phosphor sheet, is prepared. A biomolecule labeled with an energy generating substance is brought into contact with the micro array and is subjected to hybridization with a fixed biomolecule, which is among the multiple kinds of the biomolecules fixed on the stimulable phosphor sheet. The stimulable phosphor sheet is caused to store energy from the energy generating substance acting as the label of the labeled biomolecule having been hybridized with the fixed biomolecule. The stimulable phosphor sheet is then exposed to stimulating rays, a which cause it to emit light in proportion to the amount of energy stored thereon. The emitted light is photoelectrically detected, and the fixed biomolecule having been hybridized with the labeled biomolecule is thus detected.Type: GrantFiled: July 24, 2000Date of Patent: June 8, 2004Assignee: Fuji Photo Film Co., Ltd.Inventor: Keiko Neriishi
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Patent number: 6743581Abstract: An integrated biosensor system for the simultaneously detection of a plurality of different types of targets includes at least one sampling platform, the sampling platform including a plurality of receptors for binding to the targets. The plurality of receptors include at least one protein receptor and at least one nucleic acid receptor. At least one excitation source of electromagnetic radiation at a first frequency is provided for irradiating the receptors, wherein electromagnetic radiation at a second frequency different from the first frequency is emitted in response to irradiating when at least one of the different types of targets are bound to the receptor probes. An integrated circuit detector system having a plurality of detection channels is also provided for detecting electromagnetic radiation at said second frequency, the detection channels each including at least one detector.Type: GrantFiled: April 29, 2002Date of Patent: June 1, 2004Assignee: UT-Battelle, LCInventor: Tuan Vo-Dinh
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Patent number: 6720143Abstract: A genetic analysis device particularly for determining the presence or absence of Single Nucleotide Polymorphisms (SNPs) within specific sequences of DNA. The device includes a housing, at least one glass slide member, and an elastomeric member with channels thereon. Oligo arrays are spotted on the glass slide member(s) and subjected to DNA samples, reagents or the like. A plurality of openings or ports allow entry of samples, reagents or wash materials, while a plurality of exit ports or openings allow removal of such materials. The assay devices can be used for multiple samples or a single sample. A plurality of synthesis devices can be positioned in a support base in order to allow sampling in an automated manner. The synthesis devices can be provided in a 96 well microtiter format.Type: GrantFiled: April 27, 2001Date of Patent: April 13, 2004Assignee: Orchid BioSciences, Inc.Inventors: Robert D. Juncosa, Rene Bongard, Johannes Dapprich, Richard Scribner
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Patent number: 6716577Abstract: Electrochemical test strips and methods for their use in the detection of an analyte in a physiological sample are provided. The subject test strips have a reaction zone defined by opposing metal electrodes separated by a thin spacer layer. The metal surface of at least one of the electrodes is modified by a homogenous surface modification layer made up of linear self-assembling molecules having a first sulfhydryl end group and a second sulfonate end group separated by a short chain alkyl linking group, where 2-mercaptoethane sulfonic acid or a salt thereof is preferred in certain embodiments. The subject electrochemical test strips find application in the detection of a wide variety of analytes, and are particularly suited for use the detection of gluose.Type: GrantFiled: February 2, 2000Date of Patent: April 6, 2004Assignee: LifeScan, Inc.Inventors: Yeung Siu Yu, Mahesh Shah
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Patent number: 6716580Abstract: The present invention includes a method and device for performing automated SELEX. The steps of the SELEX process are performed at one or more work stations on a work surface by a robotic manipulator controlled by a computer. The invention also includes methods and reagents to obviate the need for size-fractionation of amplified candidate nucleic acids before beginning the next round of the SELEX process.Type: GrantFiled: March 22, 2001Date of Patent: April 6, 2004Assignee: SomaLogic, Inc.Inventors: Larry Gold, Dominic A. Zichi, Robert D. Jenison, Daniel J. Schneider
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Patent number: 6713616Abstract: Methods are described for the identification and preparation of high-affinity nucleic acid ligands to TGF&bgr;2. Included in the invention are specific RNA ligands to TGF&bgr;2 identified by the SELEX method. Also included are RNA ligands that inhibit the interaction of TGF&bgr;2 with its receptor.Type: GrantFiled: February 23, 2001Date of Patent: March 30, 2004Assignee: Gilead Sciences, Inc.Inventors: Nikos Pagratis, Michael Lochrie, Larry Gold