Patents by Inventor Mark S. Chee

Mark S. Chee has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Patent number: 8236493
    Abstract: Methods for discriminating between fully complementary hybrids and those that differ by one or more base pairs and libraries of unimolecular, double-stranded oligonucleotides on a solid support. In one embodiment, the present invention provides methods of using nuclease treatment to improve the quality of hybridization signals on high density oligonucleotide arrays. In another embodiment, the present invention provides methods of using ligation reactions to improve the quality of hybridization signals on high density oligonucleotide arrays. In yet another embodiment, the present invention provides libraries of unimolecular or intermolecular, double-stranded oligonucleotides on a solid support. These libraries are useful in pharmaceutical discovery for the screening of numerous biological samples for specific interactions between the double-stranded oligonucleotides, and peptides, proteins, drugs and RNA.
    Type: Grant
    Filed: August 7, 2008
    Date of Patent: August 7, 2012
    Assignee: Affymetrix, Inc.
    Inventors: David J. Lockhart, Mark S. Chee, Martin Digglemann, Dirk Vetter
  • Publication number: 20120164693
    Abstract: Methods for discriminating between fully complementary hybrids and those that differ by one or more base pairs and libraries of unimolecular, double-stranded oligonucleotides on a solid support. In one embodiment, the present invention provides methods of using nuclease treatment to improve the quality of hybridization signals on high density oligonucleotide arrays. In another embodiment, the present invention provides methods of using ligation reactions to improve the quality of hybridization signals on high density oligonucleotide arrays. In yet another embodiment, the present invention provides libraries of unimolecular or intermolecular, double-stranded oligonucleotides on a solid support. These libraries are useful in pharmaceutical discovery for the screening of numerous biological samples for specific interactions between the double-stranded oligonucleotides, and peptides, proteins, drugs and RNA.
    Type: Application
    Filed: December 4, 2007
    Publication date: June 28, 2012
    Applicant: Affymetrix, INC.
    Inventors: David J. Lockhart, Mark S. Chee, Dirk Vetter, Martin Digglemann
  • Patent number: 8206917
    Abstract: Methods disclosed herein relate to identification of nucleotides in a nucleotide sequence.
    Type: Grant
    Filed: June 13, 2011
    Date of Patent: June 26, 2012
    Assignee: Illumina, Inc.
    Inventors: Mark S. Chee, David R. Walt
  • Publication number: 20120129248
    Abstract: The present invention provides assay tools for the detection of biological or chemical activity in a sample. The assay tools of the invention provide direct detection using a positive signal generated on a surface of the assay tool. These assay tools provide improved methods for detection and/or identification of multiple agents (e.g., enzymes) in a sample, analysis of substrate specificity of such agents, and binding affinities and specificities of such agents. Upon activity a component is released from a first immobilised construct and then captured by a capture surface. At least two different immobilised constructs are used.
    Type: Application
    Filed: August 2, 2010
    Publication date: May 24, 2012
    Applicant: PROGNOSYS BIOSCIENCES, INC.
    Inventors: Mark S. Chee, Igor A. Kozlov
  • Publication number: 20120129716
    Abstract: The invention relates generally to methods and apparatus for conducting analyses, particularly microfluidic devices for the detection of target analytes.
    Type: Application
    Filed: November 17, 2011
    Publication date: May 24, 2012
    Applicant: ILLUMINA, INC.
    Inventors: Mark S. Chee, Todd A. Dickinson, Kevin Gunderson, Don O'Neil, John R. Stuelpnagel
  • Publication number: 20120071327
    Abstract: The invention relates to a method for acquisition of genetic information, in particular for personalized medicine.
    Type: Application
    Filed: December 11, 2009
    Publication date: March 22, 2012
    Applicant: FEBIT HOLDING GMBH
    Inventors: Peer F. Staehler, Cord F. Staehler, Markus Beier, Mark S. Chee, Nadine Schracke
  • Publication number: 20120065081
    Abstract: The present invention provides oligonucleotide constructs, sets of such oligonucleotide constructs, and methods of using such oligonucleotide constructs to provide validated sequences or sets of validated sequences corresponding to desired ROIs. Such validated ROIs and constructs containing these have a wide variety of uses, including in synthetic biology, quantitative nucleic acid analysis, polymorphism and/or mutation screening, and the like.
    Type: Application
    Filed: April 29, 2010
    Publication date: March 15, 2012
    Inventor: Mark S. Chee
  • Publication number: 20120028815
    Abstract: The invention relates to DNA sequencing by synthesis techniques, including those utilizing the detection of pyrophosphate (PPi) generated during the DNA synthesis reaction (pyrosequencing). The methods and compositions utilize biosensor arrays comprising microspheres distributed on a surface.
    Type: Application
    Filed: June 21, 2011
    Publication date: February 2, 2012
    Applicant: Illumina, Inc.
    Inventor: Mark S. CHEE
  • Patent number: 8080380
    Abstract: The invention relates generally to methods and apparatus for conducting analyses, particularly microfluidic devices for the detection of target analytes.
    Type: Grant
    Filed: July 23, 2004
    Date of Patent: December 20, 2011
    Assignee: Illumina, Inc.
    Inventors: Mark S. Chee, Todd A. Dickinson, Kevin Gunderson, Don O'Neil, John R. Stuelpnagel
  • Publication number: 20110245101
    Abstract: The invention provides a new assay format for high throughput molecular binding studies at a single molecule level. The invention enables creation of binding event identifiers in a highly parallel way. Individual binding events occur between two agents of a binding pair, e.g., a protein-based binding pair or a binding pair comprising a protein and a chemical moiety. The binding event identifier created through the binding of the two binding agents is unique to that pair, and identification of the binding event identifier is indicative of the binding of these specific may be assessed through a readout that is digital in nature. The invention enables very large sets of thousands or more of different binding agents or potential binding agents to be assayed simultaneously, resolving millions or more of potential interactions, and distinguishing specific interactions from those that are less specific.
    Type: Application
    Filed: April 5, 2011
    Publication date: October 6, 2011
    Applicant: Prognosys Biosciences, Inc.
    Inventors: Mark S. Chee, Igor A. Kozlov, Anita D. Wentworth, Stephanie J. Kosakovsky Pond
  • Publication number: 20110245111
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: April 5, 2011
    Publication date: October 6, 2011
    Applicant: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Patent number: 8003354
    Abstract: The invention is directed to a variety of multiplexing methods used to amplify and/or genotype a variety of samples simultaneously.
    Type: Grant
    Filed: February 15, 2008
    Date of Patent: August 23, 2011
    Assignee: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Arnold Oliphant, Scott L. Butler, John R. Stuelpnagel, Mark S. Chee, Kenneth M. Kuhn, Jian-Bing Fan
  • Publication number: 20110143965
    Abstract: An apparatus for high-throughput combinatorial synthesis of organic molecules including a reaction vessel for containing a combinatorial chemistry synthetic reaction, a liquid dispenser for dispensing the liquid, a liquid aspirator and an adjustment mechanism. The reaction vessel includes an ingress aperture allowing a liquid to enter into an interior of the vessel and an egress aperture for aspirating the liquid from the vessel. The liquid dispenser dispenses liquid through the ingress aperture. The liquid aspirator aspirates liquid through the egress aperture and includes a rotor for carrying the vessel and orbiting the vessel about an axis of rotation. The rotor is oriented generally in a horizontal plane and includes an adjustment mechanism for adjusting the angle of the vessel relative to the horizontal plane in response to the centrifugal force generated by orbiting the vessel about the axis or rotation. A method of combinatorial synthesis of organic molecules is also disclosed.
    Type: Application
    Filed: February 8, 2011
    Publication date: June 16, 2011
    Inventors: Michal Lebl, Mark S. Chee, Steven M. Barnard, David L. Heiner, Vit Pokorny, Mark J. Nibbe, Aaron Christopher Jones
  • Patent number: 7960119
    Abstract: Methods disclosed herein relate to identification of nucleotides in a nucleotide sequence.
    Type: Grant
    Filed: July 20, 2009
    Date of Patent: June 14, 2011
    Assignee: Illumina, Inc.
    Inventors: Mark S. Chee, David R. Walt
  • Patent number: 7955794
    Abstract: The invention is directed to a variety of multiplexing methods used to amplify and/or genotype a variety of samples simultaneously.
    Type: Grant
    Filed: June 20, 2002
    Date of Patent: June 7, 2011
    Assignee: Illumina, Inc.
    Inventors: Mun-Jui Richard Shen, Arnold Oliphant, Scott L. Butler, John E. Stuelpnagel, Mark S. Chee, Kenneth M. Kuhn, Jian-Bing Fan
  • Publication number: 20110092382
    Abstract: Oligonucleotide analogue arrays attached to solid substrates and methods related to the use thereof are provided. The oligonucleotide analogues hybridize to nucleic acids with either higher or lower specificity than corresponding unmodified oligonucleotides. Target nucleic acids which comprise nucleotide analogues are bound to oligonucleotide and oligonucleotide analogue arrays.
    Type: Application
    Filed: September 9, 2010
    Publication date: April 21, 2011
    Applicant: AFFYMETRIX, INC.
    Inventors: GLENN HUGH MCGALL, CHARLES GARRETT MIYADA, MAUREEN T. CRONIN, JENNIFER DEE TAN, MARK S. CHEE
  • Patent number: 7901897
    Abstract: 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: Grant
    Filed: March 16, 2009
    Date of Patent: March 8, 2011
    Assignee: Illumina, Inc.
    Inventors: John R Stuelpnagel, Mark S Chee, Steven R Auger, Gan G Wang, Laura S Casas, Shawn Christopher Baker, Robert C Kain
  • Publication number: 20100311064
    Abstract: The invention is directed to a variety of multiplexing methods used to amplify and/or genotype a variety of samples simultaneously.
    Type: Application
    Filed: May 28, 2010
    Publication date: December 9, 2010
    Applicant: Illumina, Inc.
    Inventors: Arnold Oliphant, John R. Stuelpnagel, Mark S. Chee, Scott L. Butler, Jian-Bing Fan, Min-Jui Richard Shen
  • Patent number: 7803537
    Abstract: The present invention relates to parallel genotyping (or other sample analysis) of multiple patients by direct sample immobilization onto microspheres of an array. The patient beads can then be used in a variety of target analyte analyses.
    Type: Grant
    Filed: January 16, 2004
    Date of Patent: September 28, 2010
    Assignee: Illumina, Inc.
    Inventors: Jian-Bing Fan, Mark S Chee
  • Patent number: 7794943
    Abstract: Oligonucleotide analogue arrays attached to solid substrates and methods related to the use thereof are provided. The oligonucleotide analogues hybridize to nucleic acids with either higher or lower specificity than corresponding unmodified oligonucleotides. Target nucleic acids which comprise nucleotide analogues are bound to oligonucleotide and oligonucleotide analogue arrays.
    Type: Grant
    Filed: May 20, 2008
    Date of Patent: September 14, 2010
    Assignee: Affymetrix, Inc.
    Inventors: Glenn H. McGall, Charles G. Miyada, Maureen T. Cronin, Jennifer Dee Tan, Mark S. Chee