Patents Represented by Attorney, Agent or Law Firm Philip L. McGarrigle
  • Patent number: 7323307
    Abstract: Novel means and methods for analyzing hybridization data derived from hybridization assays between a target nucleic acid and differently sequenced polynucleotide probes involve selecting probe sets that define reference sequences for sequence signatures and deriving useful data about the nature of the target nucleic acid molecule based on its hybridization to the probes. The methods are useful for determining whether the target contains a nucleic acid or polypeptide sequence signature, whether the target encodes a member of a gene family, or whether the target is derived from one of any number of genes.
    Type: Grant
    Filed: August 4, 2004
    Date of Patent: January 29, 2008
    Assignee: Affymetrix, Inc.
    Inventors: David J. Lockhart, Gordon G. Wong, Pennina Langer-Safer
  • Patent number: 7317415
    Abstract: In one embodiment, a system is described for reducing a dark period between successive data acquisition periods associated with the detection of one or more target molecules hybridized to at least one of a plurality of probes disposed upon a biological probe array. The system comprises a switch that alternately directs an analog signal between a first circuit and a second circuit, where a period of time is required to alternate between the first and second circuits; an integrator associated with the first circuit that integrates the analog signal to generate a first integrated value; a second integrator associated with the second circuit that integrates the analog signal to generate a second integrated value; and an analog/digital converter that produces a digital value for each of the first integrated value and the second integrated values.
    Type: Grant
    Filed: August 6, 2004
    Date of Patent: January 8, 2008
    Assignee: Affymetrix, Inc.
    Inventor: Michael D. Kaiser
  • Patent number: 7314595
    Abstract: A system is described for automatic retrieval of microplates from a carousel. The system includes an effector arm that retrieves a selected microplate from the carousel, a microplate retainer that receives the selected microplate from the effector arm, and a controller that directs the effector arm to the carousel for retrieval of the selected microplate and directs the effector arm to the microplate retainer so that it may receive the selected microplate. The carousel may revolve around a vertical axis. A system also is described for washing depositing elements used to spot biological materials on a substrate. Graphical user interfaces also are described for enabling a user to determine which microplates will be used to provide biological probe materials, and in what patterns those probe materials should be deposited on the substrate. The interfaces enable the user to place multiple fractions of biological materials on a same location on a substrate.
    Type: Grant
    Filed: May 2, 2002
    Date of Patent: January 1, 2008
    Assignee: Affymetrix, Inc.
    Inventors: Peter D. Honkanen, Timothy J. Woolaver, Eric E. McKenzie, David P. Bradbury, Mark R. Jones
  • Patent number: 7312919
    Abstract: A wide field of view scanning microscope includes a light source, a light detector, optics, a scanning assembly, a translation system, and a data collection control and processing unit. The scanning assembly is constructed to provide from the light source a light beam in a scanning motion to an examined surface. The optics includes an objective lens associated with the scanning assembly arranged to provide an optical path to the light detector. The translation system is constructed to produce a movement of the examined surface. The data collection control and processing unit is arranged to collect data during the scanning motion and process the collected data.
    Type: Grant
    Filed: December 27, 2001
    Date of Patent: December 25, 2007
    Assignee: Affymetrix, Inc.
    Inventor: James W. Overbeck
  • Patent number: 7095032
    Abstract: Microscopes, including viewing and other microscopic systems, employ a hinged, tiltable plate to adjust focus on a flat object such as a microscope slide or biochip by motion, achieved by tilting, which is substantially normal to the focus point on the plane of the object. By employing two such tiltable arrangements, relatively long scan lines of e.g., flying objective, single pixel on-axis scanning can be accommodated. The tilting support plate is specifically constructed to provide tailored locations for different objects in series along the Y axis of the plate. The plate can accommodate beaters and cooled plates and/or the flat object being examined. In a fluorescence scanning microscope, locations are specifically adapted to receive microscope slides and biochip cartridges such as Affymetrix's “Gene Chip®”. A scanning microscope under computer control, employing such a focusing action, enables unattended scanning of biochips with a simple and economical instrument.
    Type: Grant
    Filed: June 3, 2005
    Date of Patent: August 22, 2006
    Inventors: Jean I. Montagu, James W. Overbeck
  • Patent number: 6996475
    Abstract: Methods and computer software products are provided for analyzing gene expression data. In one embodiment, multiple probes are used to detect a single transcript. The hybridization intensities of each probe is adjusted by dividing the intensities by the affinities of the probes. The minimal adjusted hybridization intensity may be used as the measurement of the gene expression.
    Type: Grant
    Filed: December 9, 2002
    Date of Patent: February 7, 2006
    Assignee: Affymatrix, Inc
    Inventor: David Balaban
  • Patent number: 6830936
    Abstract: The present invention provides a miniaturized integrated nucleic acid diagnostic device and system. The or more sample acquisition and preparation operations, in combination with one or more sample analysis operations. For example, the device can integrate several or all of the operations involved in sample acquisition and storage, sample preparation and sample analysis, within a single integrated unit. The device is useful in a variety of applications, and most notably, nucleic acid based diagnostic applications and de novo sequencing applications.
    Type: Grant
    Filed: December 31, 2000
    Date of Patent: December 14, 2004
    Assignee: Affymetrix Inc.
    Inventors: Rolfe C. Anderson, Robert J. Lipshutz, Richard P. Rava, Stephen P. A. Fodor
  • Patent number: 6829376
    Abstract: An image alignment tool is described for adjusting the alignment of a grid with an image. An initial grid aligner determines an initial, approximately aligned, position of the grid. An intensity scorer determines, for each of a plurality of test grid elements of the plurality of grid elements, a set of intensity scores. Each member of the set is based, at least in part, on intensities of pixels of one or more image features within the test grid element in one of the initial or additional positions. A combined-rank-score generator combines, for each of the initial and additional grid positions, members of sets of rank scores corresponding to the grid position in order to generate a combined rank score for the grid position. A grid alignment adjuster adjusts the alignment of the grid based on a comparison among the combined rank scores.
    Type: Grant
    Filed: June 11, 2001
    Date of Patent: December 7, 2004
    Assignee: Affymetrix, Inc.
    Inventor: Daniel M. Bartell
  • Patent number: 6828104
    Abstract: This invention provides nucleic acid affinity matrices that bear a large number of different nucleic acid affinity ligands allowing the simultaneous selection and removal of a large number of preselected nucleic acids from the sample. Methods of producing such affinity matrices are also provided. In general the methods involve the steps of a) providing a nucleic acid amplification template array comprising a surface to which are attached at least 50 oligonucleotides having different nucleic acid sequences, and wherein each different oligonucleotide is localized in a predetermined region of said surface, the density of said oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and all of said different oligonucleotides have an identical terminal 3′ nucleic acid sequence and an identical terminal 5′ nucleic acid sequence.
    Type: Grant
    Filed: August 14, 2002
    Date of Patent: December 7, 2004
    Assignee: Affymetrix, Inc.
    Inventors: Robert J. Lipshutz, MacDonald S. Morris, Mark S. Chee, Thomas R. Gingeras
  • Patent number: 6803196
    Abstract: Methods and compounds are provided for detecting target molecules in a sample using specific binding assays. In particular, methods are provided for detecting a nucleic acid target in a sample. In one embodiment, the presently claimed invention provides a method of labeling a hybridized target wherein the target comprises a binding ligand. In another embodiment, the presently claimed invention provides methods of signal amplification.
    Type: Grant
    Filed: October 13, 2000
    Date of Patent: October 12, 2004
    Assignee: Affymetrix, Inc.
    Inventors: William A. Lyon, Huu Minh Tran
  • Patent number: 6804679
    Abstract: A data manager is described for providing a publish database for access by data mining tools and other data processing software applications. The data manager includes a results-for-publication identifier that identifies synthesized probe array results and spotted probe array results for publishing. This identification may be based, at least in part, on user selections. The data in the publish database is organized in accordance with an integrated database schema. The data manager may also include an experimental results registration processor that registers the synthesized probe array results and the spotted probe array results for publishing. This registration may be based, at least in part, on user selections. For example, a user may select certain probe array results from a graphical user interface displaying a tree of files containing probe array results from multiple experiments with synthesized and/or spotted probe arrays.
    Type: Grant
    Filed: March 8, 2002
    Date of Patent: October 12, 2004
    Assignee: Affymetrix, Inc.
    Inventors: Luis Jevons, Derek Bernhart, Conrad G. Sheppy
  • Patent number: 6800439
    Abstract: Improved nucleic acid arrays are provided which have been prepared in a non-oxidizing atmosphere.
    Type: Grant
    Filed: February 7, 2001
    Date of Patent: October 5, 2004
    Assignee: Affymetrix, Inc.
    Inventors: Glenn McGall, Lisa Kajisa, Mark Trulson
  • Patent number: 6794138
    Abstract: The present invention relates to the amplification of nucleic acids, preferably from mRNA. A primer and promoter are added to a target sequence to be amplified and then the target is amplified in an in vitro transcription reaction and the product of this reaction is used as template for subsequent rounds of amplification.
    Type: Grant
    Filed: September 24, 2001
    Date of Patent: September 21, 2004
    Assignee: Affymetrix, Inc.
    Inventors: Yanxiang Cao, Linda Hsie
  • Patent number: 6789040
    Abstract: Systems, methods, and computer program products are described for specifying a scanning area of a substrate. In accordance with one method, steps include receiving location data corresponding to a plurality of probe-feature locations on the substrate, storing the location data, accessing the location data, and scanning the substrate based on the accessed location data. A scanning system is described that includes a computer, a scanner, and a computer program product. The product, when executed on the computer, accesses location data corresponding to a plurality of probe-feature locations on a substrate, and controls the scanner's scanning of the substrate based on the accessed location data.
    Type: Grant
    Filed: July 17, 2001
    Date of Patent: September 7, 2004
    Assignee: Affymetrix, Inc.
    Inventor: Shantanu V. Kaushikkar
  • Patent number: 6773888
    Abstract: In one aspect of the invention, photoactivatable silane compounds and methods for their synthesis and use are provided. In one embodiment, the photoactivatable silane compounds synthesized are represented by a formula: PG-LS-SN, wherein PG is a photoactivatable group, LS is a linkage and spacer group, and SN is a silane group. The silanes allow the photoactivatable silane compounds to be covalently bound to the surface of a substrate such as silica. The photoactivatable group forms a hydrophobic layer that can be photochemically cross-linked with a layer of hydrophilic functional polymers. In another embodiment, a method is disclosed to synthesize a substrate of hydrophobic layers and hydrophilic functional polymer layers thereafter onto glass surfaces. An array of biopolymers such as nucleic acids and peptides may then be covalently attached to the substrate using photolithography and biopolymer synthesis.
    Type: Grant
    Filed: July 9, 2002
    Date of Patent: August 10, 2004
    Assignee: Affymetrix, Inc.
    Inventors: Handong Li, Glenn McGall
  • Patent number: 6747143
    Abstract: A method and apparatus for preparation of a substrate containing a plurality of sequences. Photoremovable groups are attached to a surface of a substrate. Selected regions of the substrate are exposed to light so as to activate the selected areas. A monomer, also containing a photoremovable group, is provided to the substrate to bind at the selected areas. The process is repeated using a variety of monomers such as amino acids until sequences of a desired length are obtained. Detection methods and apparatus are also disclosed.
    Type: Grant
    Filed: May 20, 2002
    Date of Patent: June 8, 2004
    Assignee: Affymetrix, Inc.
    Inventors: Lubert Stryer, Stephen P. A. Fodor, J. Leighton Read, Michael C. Pirrung
  • Patent number: 6733977
    Abstract: A body 300 having a cavity 310 for mounting a substrate 120 fabricated with probe sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, is provided. The cavity includes inlets 350 and 360 for introducing selected fluids into the cavity to contact the probes. Accordingly, a commercially feasible device for use in high throughput assay systems is provided.
    Type: Grant
    Filed: August 28, 2002
    Date of Patent: May 11, 2004
    Assignee: Affymetrix, Inc.
    Inventors: Donald M. Besemer, Virginia W. Goss, James L. Winkler
  • Patent number: 6722395
    Abstract: For depositing fluid dots in an array, e.g., for microscopic analysis, a deposit device, e.g. a pin, cooperating with a fluid source defines a precisely sized drop of fluid of small diameter on a drop carrying surface. Transport mechanism positions the device precisely over the receiving surface and drive mechanism moves the deposit device toward and away from the surface. By repeated action, minute drops of fluid can be deposited precisely in a dense array, preferably under computer control. The drop-carrying surface shown has a diameter less than 375, preferably less than 300, preferably between about 15 and 250 micron, and is bound by a sharp rim that defines the perimeter of the fluid drop. The deposit device is compliant in the direction of deposition motion, e.g. by overcoming resistance of a resilient member. When depositing, the deposit device is laterally constrained to a reference position, e.g.
    Type: Grant
    Filed: May 21, 2001
    Date of Patent: April 20, 2004
    Inventors: James W. Overbeck, Peter T. Flowers, Jean I. Montagu, Myles L. Mace, Peter Honkanen
  • Patent number: 6643015
    Abstract: An apparatus is described that includes an emission signal detector and an emission signal filter. An excitation beam scans an array of biological materials, and the emission signal detector detects an emission signal indicative of an emission beam responsive to the excitation beam. The emission signal filter is a linear-phase filter that provides a filtered emission signal having substantially symmetrical rise and fall edges. A linear-phase excitation signal filter may also be provided that provides a filtered excitation signal having substantially symmetrical rise and fall edges. The emission signal filter and the excitation signal filter may be matched. In some applications, they may be high-order Bessel filters. Linear-phase filtering enables sampling of emission signals to be accomplished consistently irrespective of the scanning direction, and thus is particularly advantageous in bi-directional scanning applications.
    Type: Grant
    Filed: December 3, 2001
    Date of Patent: November 4, 2003
    Assignee: Affymetrix, Inc.
    Inventor: Nathan K. Weiner
  • Patent number: 6638770
    Abstract: An apparatus for depositing an array of spots on a receiving surface includes a fluid source, a deposit device that includes a drop-carrying surface, and a cleaning device. The deposit device and a fluid source are cooperatively arranged to deposit a spot(usually created by a drop) on a receiving surface. The cleaning device is constructed and arranged to clean the drop-carrying surface by employing a flow of cleaning fluid or another cleaning matter such as small particles the flow being arranged to prevent contaminating back flow.
    Type: Grant
    Filed: July 20, 2002
    Date of Patent: October 28, 2003
    Assignee: Affymetrix, Inc.
    Inventor: Jean I. Montagu