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: 20170058340
    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: November 11, 2016
    Publication date: March 2, 2017
    Inventor: Mark S. CHEE
  • Publication number: 20170051340
    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: August 31, 2016
    Publication date: February 23, 2017
    Inventors: Kevin Gunderson, John R. Stuelpnagel, Mark S. Chee, Jian-Bing Fan
  • Publication number: 20160362733
    Abstract: The invention relates to compositions and methods for multiplex decoding of microsphere array sensors.
    Type: Application
    Filed: June 21, 2016
    Publication date: December 15, 2016
    Inventors: Mark S. Chee, John R. Stuelpnagel, Anthony W. Czarnik
  • Publication number: 20160333403
    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: July 29, 2016
    Publication date: November 17, 2016
    Inventor: Mark S. CHEE
  • Publication number: 20160298180
    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: June 20, 2016
    Publication date: October 13, 2016
    Applicant: Prognosys Biosciences, Inc.
    Inventor: Mark S. CHEE
  • Publication number: 20160291007
    Abstract: The present disclosure provides polynucleotide conjugates, methods, and assay systems for use in detecting the presence, absence, and/or amount of an analyte in a sample. Various polynucleotide conjugates, conjugate pairs, sets, libraries, and assay systems comprising the same are disclosed. In particular, methods and assay systems for antibody detection and analysis are provided. For example, assays capable of high levels of multiplexing are used for antibody detection and analysis in a biological sample, e.g., Lyme disease patient samples. The presently disclosed polynucleotide conjugates, methods, and assay systems can be used to provide sensitive and reliable diagnosis, even at early stages of a disease or condition. Use for monitoring disease progression and prognosis is also disclosed.
    Type: Application
    Filed: November 7, 2014
    Publication date: October 6, 2016
    Applicant: Prognosys Biosciences, Inc.
    Inventors: Igor A. KOZLOV, John Andrew ALTIN, Petr CAPEK, Mark S. CHEE
  • Patent number: 9441267
    Abstract: The present invention is directed to methods and compositions for the use of micro sphere 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: Grant
    Filed: July 2, 2014
    Date of Patent: September 13, 2016
    Assignee: ILLUMINA, INC.
    Inventors: Kevin Gunderson, John R. Stuelpnagel, Mark S. Chee, Jian-Bing Fan
  • Patent number: 9399795
    Abstract: The invention relates to compositions and methods for multiplex decoding of microsphere array sensors.
    Type: Grant
    Filed: July 2, 2014
    Date of Patent: July 26, 2016
    Assignee: ILLUMINA, INC.
    Inventors: Mark S. Chee, John R. Stuelpnagel, Anthony W. Czarnik
  • Patent number: 9371598
    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: Grant
    Filed: April 5, 2011
    Date of Patent: June 21, 2016
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Publication number: 20160145677
    Abstract: The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents, in particular, microfluidic device based instrumentation; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: June 25, 2014
    Publication date: May 26, 2016
    Applicant: Prognosys Biosciences, Inc.
    Inventors: Mark S. CHEE, David A. ROUTENBERG
  • Publication number: 20160138091
    Abstract: The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the biological targets comprise proteins, and the methods and assay systems do not depend on imaging techniques for the spatial information of the targets. The present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents; and a decoding scheme providing a readout that is digital in nature.
    Type: Application
    Filed: June 25, 2014
    Publication date: May 19, 2016
    Applicant: Prognosys Biosciences, Inc.
    Inventors: Mark S. CHEE, David A. ROUTENBERG
  • Patent number: 9289766
    Abstract: The invention relates generally to methods and apparatus for conducting analyzes, particularly microfluidic devices for the detection of target analytes.
    Type: Grant
    Filed: October 7, 2014
    Date of Patent: March 22, 2016
    Assignee: Illumina, Inc.
    Inventors: Mark S. Chee, Todd A. Dickinson, Kevin Gunderson, Don O'Neil
  • Patent number: 9279148
    Abstract: The present invention is directed to methods and compositions for the use of micro sphere 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: Grant
    Filed: June 10, 2013
    Date of Patent: March 8, 2016
    Assignee: Illumina, Inc.
    Inventors: Kevin Gunderson, John R. Stuelpnagel, Mark S. Chee, Jian-Bing Fan
  • Publication number: 20160025726
    Abstract: Provided herein are compositions and methods for detecting the binding of a peptide to an MHC molecule, and the binding of a peptide: MHC complex to a TCR. In preferred embodiments, the compositions and methods are in a highly-multiplexed way. The compositions and methods disclosed herein can be used to provide direct information on which peptides are bound to an MHC molecule. Also provided is a method for simultaneously detecting a large number of peptides for binding to an MHC molecule and/or a T cell. A method for detecting competitive binding of a large number of peptides to an MHC molecule and/or a T cell is also disclosed. Also provided herein is a method for simultaneously detecting a large number of specific TCRs. The compositions and methods of the present invention are useful for vaccine design, research and monitoring of autoimmune and infectious disease, immunogenicity testing of therapeutics, and tissue typing.
    Type: Application
    Filed: March 14, 2014
    Publication date: January 28, 2016
    Applicant: Prognosys Biosciences, Inc.
    Inventors: John Andrew ALTIN, Mark S. CHEE
  • Publication number: 20160024576
    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: May 27, 2015
    Publication date: January 28, 2016
    Inventor: Mark S. CHEE
  • Patent number: 9163283
    Abstract: Methods disclosed herein relate to identification of nucleotides in a nucleotide sequence.
    Type: Grant
    Filed: September 24, 2013
    Date of Patent: October 20, 2015
    Assignee: Illumina, Inc.
    Inventors: Mark S. Chee, David R. Walt
  • Publication number: 20150292006
    Abstract: The invention relates to compositions and methods for multiplex decoding of microsphere array sensors.
    Type: Application
    Filed: July 2, 2014
    Publication date: October 15, 2015
    Inventors: Mark S. Chee, John R. Stuelpnagel, Anthony W. Czarnik
  • Publication number: 20150203913
    Abstract: A method for detecting nucleic acids by (a) providing a sample having target nucleic acids, each nucleic acid having contiguous first, second, and third domains; (b) contacting the sample with probe sets to form hybridization complexes, wherein each probe set includes (i) a first probe having a sequence that is complementary to the first domain; and (ii) a second probe having a sequence substantially complementary to the third domain; (c) extending the first probes along the second domains of the complexes while the complexes are immobilized on a solid support; (d) ligating the extended first probes to the second probes to form templates; (e) amplifying the templates with primers that are complementary to the first and second priming sequences to produce amplicons; and (f) detecting the amplicons on the surface of a nucleic acid array.
    Type: Application
    Filed: November 13, 2014
    Publication date: July 23, 2015
    Applicant: ILLUMINA, INC.
    Inventors: Arnold Oliphant, John R. Stuelpnagel, Mark S. Chee, Scott L. Butler, Jian-Bing Fan, Min-Jui Richard Shen
  • Patent number: 9085798
    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: Grant
    Filed: April 29, 2010
    Date of Patent: July 21, 2015
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Publication number: 20150024965
    Abstract: The invention relates generally to methods and apparatus for conducting analyses, particularly microfluidic devices for the detection of target analytes.
    Type: Application
    Filed: October 7, 2014
    Publication date: January 22, 2015
    Inventors: Mark S. Chee, Todd A. Dickinson, Kevin Gunderson, Don O'Neil