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).

  • Publication number: 20100216656
    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: August 7, 2008
    Publication date: August 26, 2010
    Applicant: Affymetrix, INC.
    Inventors: David J. Lockhart, Mark S. Chee, Dirk Vetter, Martin Digglemann
  • Publication number: 20100151464
    Abstract: The present invention is directed to methods and compositions for generating a pool of oligonucleotides. The invention finds use in preparing a population or subpopulations of oligonucleotides in solution. The pool of oligonucleotides finds use in a variety of nucleic acid detection and/or amplification assays.
    Type: Application
    Filed: September 11, 2009
    Publication date: June 17, 2010
    Applicant: lllumina, lnc.
    Inventors: John R. Stuelpnagel, Mark S. Chee
  • Publication number: 20100015626
    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: July 21, 2009
    Publication date: January 21, 2010
    Applicant: Illumina, Inc.
    Inventors: Arnold Oliphant, John R. Stuelpnagel, Mark S. Chee, Scott L. Butler, Jian-Bing Fan, Min-Jui Richard Shen
  • Publication number: 20090298716
    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: Application
    Filed: April 6, 2009
    Publication date: December 3, 2009
    Applicant: 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: 20090286690
    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: May 20, 2008
    Publication date: November 19, 2009
    Applicant: Affymetrix, INC.
    Inventors: Glenn Hugh McGall, Charles Garrett Miyada, Maureen T. Cronin, Jennifer Dee Tan, Mark S. Chee
  • Patent number: 7604996
    Abstract: The present invention is directed to methods and compositions for generating a pool of oligonucleotides. The invention finds use in preparing a population or subpopulations of oligonucleotides in solution. The pool of oligonucleotides finds use in a variety of nucleic acid detection and/or amplification assays.
    Type: Grant
    Filed: August 18, 2000
    Date of Patent: October 20, 2009
    Assignee: Illumina, Inc.
    Inventors: John R. Stuelpnagel, Mark S. Chee
  • Publication number: 20090227472
    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: Application
    Filed: March 16, 2009
    Publication date: September 10, 2009
    Inventors: John R. Stuelpnagel, Mark S. Chee, Steven R. Auger, Gan G. Wang, Laura S. Casas, Shawn Christopher Baker, Robert C. Kain
  • Publication number: 20090221450
    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: Application
    Filed: March 16, 2009
    Publication date: September 3, 2009
    Inventors: John R Stuelpnagel, Mark S. Chee, Steven R. Auger, Gan G. Wang, Laura S. Casas, Shawn Christopher Baker, Robert C. Kain
  • Patent number: 7582420
    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: July 12, 2002
    Date of Patent: September 1, 2009
    Assignee: Illumina, Inc.
    Inventors: Arnold Oliphant, John R. Stuelpnagel, Mark S. Chee, Scott L. Butler, Jian-Bing Fan, Min-Jui Richard Shen
  • Publication number: 20090215649
    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: Application
    Filed: March 16, 2009
    Publication date: August 27, 2009
    Inventors: John R. Stuelpnagel, Mark S. Chee, Steven R. Auger, Gan G. Wang, Laura S. Casas, Shawn Christopher Baker, Robert C. Kain
  • Publication number: 20090186349
    Abstract: The present invention is directed to methods and compositions for the use of microsphere arrays to detect and quantify a number of nucleic acid reactions. The invention finds use in genotyping, i.e. the determination of the sequence of nucleic acids, particularly alterations such as nucleotide substitutions (mismatches) and single nucleotide polymorphisms (SNPs). Similarly, the invention finds use in the detection and quantification of a nucleic acid target using a variety of amplification techniques, including both signal amplification and target amplification. The methods and compositions of the invention can be used in nucleic acid sequencing reactions as well. All applications can include the use of adapter sequences to allow for universal arrays.
    Type: Application
    Filed: September 17, 2008
    Publication date: July 23, 2009
    Applicant: Illumina, Inc.
    Inventors: Kevin Gunderson, John R. Stuelpnagel, Mark S. Chee
  • Patent number: 7563576
    Abstract: The invention provides methods and compositions for combinatorially decoding arrays.
    Type: Grant
    Filed: January 22, 2007
    Date of Patent: July 21, 2009
    Assignee: Illumina, Inc.
    Inventors: Mark S. Chee, David R. Walt
  • Publication number: 20090023605
    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: June 17, 2008
    Publication date: January 22, 2009
    Inventors: Michal Lebl, Mark S. Chee, Steven M. Barnard, David L. Heiner, Vit Pokorny, Mark J. Nibbe, Aaron Christopher Jones
  • Patent number: 7455971
    Abstract: The invention relates to compositions and methods for multiplex decoding of microsphere array sensors.
    Type: Grant
    Filed: November 22, 2005
    Date of Patent: November 25, 2008
    Assignee: Illumina, Inc.
    Inventors: Mark S. Chee, John R. Stuelpnagel, Anthony W. Czarnik
  • Publication number: 20080242555
    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: February 15, 2008
    Publication date: October 2, 2008
    Applicant: 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: 20080182248
    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: Application
    Filed: October 16, 2007
    Publication date: July 31, 2008
    Applicant: Illumina, Inc.
    Inventors: Jian-Bing FAN, Mark S. Chee
  • Patent number: 7375198
    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: April 18, 2003
    Date of Patent: May 20, 2008
    Assignee: Affymetrix, Inc.
    Inventors: Glenn Hugh McGall, Charles Garrett Miyada, Maureen T. Cronin, Jennifer Dee Tan, Mark S. Chee
  • Patent number: 7285384
    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: February 16, 2001
    Date of Patent: October 23, 2007
    Assignee: Illuminia, Inc.
    Inventors: Jian-Bing Fan, Mark S. Chee
  • Patent number: 7252948
    Abstract: This invention provides oligonucleotide based arrays and methods for speciating and phenotyping organisms, for example, using oligonucleotide sequences based on the Mycobacterium tuberculosis rpoB gene. The groups or species to which an organism belongs may be determined by comparing hybridization patterns of target nucleic acid from the organism to hybridization patterns in a database.
    Type: Grant
    Filed: February 4, 2005
    Date of Patent: August 7, 2007
    Assignee: Affymetrix, Inc.
    Inventors: Thomas R. Gingeras, David Mack, Mark S. Chee, Anthony J. Berno, Lubert Stryer, Ghassan Ghandour, Ching Wang
  • Patent number: 7226734
    Abstract: The invention relates to compositions and methods for multiplex decoding of microsphere array sensors.
    Type: Grant
    Filed: June 28, 2002
    Date of Patent: June 5, 2007
    Assignee: Illumina, Inc.
    Inventors: Mark S. Chee, John R. Stuelpnagel, Anthony W. Czarnik