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: 20190177778
    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: February 14, 2019
    Publication date: June 13, 2019
    Applicant: Prognosys Biosciences, Inc.
    Inventor: Mark S. CHEE
  • Patent number: 10308982
    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: June 20, 2016
    Date of Patent: June 4, 2019
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Patent number: 10288608
    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: Grant
    Filed: November 7, 2014
    Date of Patent: May 14, 2019
    Assignee: Prognosys Biosciences, Inc.
    Inventors: Igor A. Kozlov, John Andrew Altin, Petr Capek, Mark S. Chee
  • Patent number: 10266884
    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: December 7, 2016
    Date of Patent: April 23, 2019
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Patent number: 10266883
    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: November 11, 2016
    Date of Patent: April 23, 2019
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Publication number: 20180328936
    Abstract: The present invention provides methods for constructing peptide construct sets and methods of use of these peptide construct sets in assay systems for peptide analysis, and in particular for use in high throughput peptide analysis. The methods allow for analysis of large sets of peptide constructs in a cost-effective manner, employing molecular biological techniques that are both robust and easily parallelized. Thus, the methods allow for the construction of peptide construct sets encompassing, e.g., the human proteome.
    Type: Application
    Filed: April 30, 2018
    Publication date: November 15, 2018
    Applicant: Prognosys Biosciences, Inc.
    Inventors: Igor A. Kozlov, Mark S. Chee, Petr Capek, David A. Routenberg
  • Patent number: 10119165
    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: November 11, 2016
    Date of Patent: November 6, 2018
    Assignee: PROGNOSYS BIOSCIENCES, INC.
    Inventor: Mark S. Chee
  • Publication number: 20180201980
    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: December 4, 2017
    Publication date: July 19, 2018
    Applicant: Prognosys Biosciences, Inc.
    Inventors: Mark S. Chee, David A. Routenberg
  • Patent number: 10000800
    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: July 29, 2016
    Date of Patent: June 19, 2018
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Patent number: 9958454
    Abstract: The present invention provides methods for constructing peptide construct sets and methods of use of these peptide construct sets in assay systems for peptide analysis, and in particular for use in high throughput peptide analysis. The methods allow for analysis of large sets of peptide constructs in a cost-effective manner, employing molecular biological techniques that are both robust and easily parallelized. Thus, the methods allow for the construction of peptide construct sets encompassing, e.g., the human proteome.
    Type: Grant
    Filed: October 31, 2013
    Date of Patent: May 1, 2018
    Assignee: Prognosys Biosciences, Inc.
    Inventors: Igor A. Kozlov, Mark S. Chee, Petr Capek, David A. Routenberg
  • Publication number: 20180094316
    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 30, 2017
    Publication date: April 5, 2018
    Inventors: Arnold Oliphant, John R. Stuelpnagel, Mark S. Chee, Scott L. Butler, Jian-Bing Fan, Min-Jui Richard Shen
  • Patent number: 9879313
    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: Grant
    Filed: June 25, 2014
    Date of Patent: January 30, 2018
    Assignee: Prognosys Biosciences, Inc.
    Inventors: Mark S. Chee, David A. Routenberg
  • Patent number: 9868979
    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: Grant
    Filed: June 25, 2014
    Date of Patent: January 16, 2018
    Assignee: PROGNOSYS BIOSCIENCES, INC.
    Inventors: Mark S. Chee, David A. Routenberg
  • Publication number: 20180010123
    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: July 27, 2017
    Publication date: January 11, 2018
    Inventors: John R. Stuelpnagel, Mark S. Chee
  • Patent number: 9850536
    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: Grant
    Filed: November 13, 2014
    Date of Patent: December 26, 2017
    Assignee: Illumina, Inc.
    Inventors: Arnold Oliphant, John R. Stuelpnagel, Mark S. Chee, Scott L. Butler, Jian-Bing Fan, Min-Jui Richard Shen
  • Patent number: 9783847
    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: May 27, 2015
    Date of Patent: October 10, 2017
    Assignee: PROGNOSYS BIOSCIENCES, INC.
    Inventor: Mark S. Chee
  • Publication number: 20170144126
    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: November 17, 2016
    Publication date: May 25, 2017
    Inventors: John R. Stuelpnagel, Mark S. Chee, Steven R. Auger, Gan G, Wang, Laura S. Casas, Shawn Christopher Baker, Robert C. Kain
  • Publication number: 20170088881
    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: December 7, 2016
    Publication date: March 30, 2017
    Inventor: Mark S. CHEE
  • Publication number: 20170058345
    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: 20170058339
    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