Patents by Inventor Garry P. Nolan

Garry P. Nolan 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).

  • On-slide staining by primer extension
    Patent number: 10017808
    Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.
    Type: Grant
    Filed: December 5, 2017
    Date of Patent: July 10, 2018
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Nikolay Samusik, Garry P. Nolan, Yury Goltsev
  • On-slide straining by primer extension
    Patent number: 10006082
    Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.
    Type: Grant
    Filed: December 5, 2017
    Date of Patent: June 26, 2018
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Nikolay Samusik, Garry P. Nolan, Yury Goltsev
  • On-slide staining by primer extension
    Patent number: 10000796
    Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.
    Type: Grant
    Filed: December 5, 2017
    Date of Patent: June 19, 2018
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Nikolay Samusik, Garry P. Nolan, Yury Goltsev
  • Compressed Sensing for Simultaneous Measurement of Multiple Different Biological Molecule Types in a Sample
    Publication number: 20180150596
    Abstract: A method and apparatus for simultaneously determining multiple different biological molecule types in a sample include labeling each different biological molecule type in a biological sample with a unique combination of a plurality of labels. Each different biological molecule type is selected from a population of M different biological molecules types. The plurality of labels is selected from a population of L different labels; and, M is greater than L. Measurements are obtained of relative abundances of the L different labels in the sample. Relative abundance of up to M different biological molecule types in the sample are determined based on the measurements and a method of compressed sensing.
    Type: Application
    Filed: March 22, 2017
    Publication date: May 31, 2018
    Inventors: Karen Sachs, Mohammed N. AlQuraishi, Solomon Itani, Garry P. Nolan, Sean C. Bendall, Tyler J. Burns
  • On-Slide Staining by Primer Extension
    Publication number: 20180119208
    Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.
    Type: Application
    Filed: December 5, 2017
    Publication date: May 3, 2018
    Inventors: Nikolay Samusik, Garry P. Nolan, Yury Goltsev
  • On-Slide Staining by Primer Extension
    Publication number: 20180105869
    Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.
    Type: Application
    Filed: December 5, 2017
    Publication date: April 19, 2018
    Inventors: Nikolay Samusik, Garry P. Nolan, Yury Goltsev
  • On-Slide Staining by Primer Extension
    Publication number: 20180087095
    Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.
    Type: Application
    Filed: December 5, 2017
    Publication date: March 29, 2018
    Inventors: Nikolay Samusik, Garry P. Nolan, Yury Goltsev
  • On-slide staining by primer extension
    Patent number: 9909167
    Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.
    Type: Grant
    Filed: December 4, 2014
    Date of Patent: March 6, 2018
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Nikolay Samusik, Garry P. Nolan, Yury Goltsev
  • HIGHLY-MULTIPLEXED FLUORESCENT IMAGING
    Publication number: 20180030504
    Abstract: Provided herein is a method and system for analyzing a sample. In some embodiments the method makes use of a plurality of capture agents that are each linked to a different oligonucleotide and a corresponding plurality of labeled nucleic acid probes, wherein each of the labeled nucleic acid probes specifically hybridizes with only one of the oligonucleotides. The sample is labeled with the capture agents en masse, and sub-sets of the capture agents are detected using iterative cycles using corresponding subsets of the labeled nucleic acid probes.
    Type: Application
    Filed: July 26, 2017
    Publication date: February 1, 2018
    Inventors: Garry P. Nolan, Nikolay Samusik, Julia Kennedy-Darling, Yury Goltsev
  • DETECTION OF TARGET NUCLEIC ACIDS IN A CELLULAR SAMPLE
    Publication number: 20170362642
    Abstract: Methods of assaying cells of a cellular sample for the presence of a target nucleic acid are provided. Aspects of the methods include evaluating a cellular sample that has been contacted with a nuclease inhibitor for the presence of a target nucleic acid. Also provided are devices and kits that find use in practicing the methods described herein.
    Type: Application
    Filed: August 30, 2017
    Publication date: December 21, 2017
    Inventors: Garry P. Nolan, Yury Goltsev, Quan Nguyen, Yunqing Ma, Chunfai Lai
  • SINGLE CELL ANALYSIS USING SECONDARY ION MASS SPECTROMETRY
    Publication number: 20170343529
    Abstract: A method of analyzing a population of cells is disclosed. In certain embodiments, the method includes i) obtaining an array of cells on a substrate, wherein the cells are labeled with one or more mass tags and are separated from one another, ii) measuring, using secondary ion mass spectrometry (SIMS), the abundance of the one or more mass tags at a plurality of locations occupied by the cells, thereby generating, for each individual cell measured, a set of data, and iii) outputting the set of data for each of the cells analyzed. Also provided herein are systems that find use in performing the subject method. In some embodiments, the system is an automated system for analyzing a population of cells using SIMS.
    Type: Application
    Filed: August 16, 2017
    Publication date: November 30, 2017
    Inventors: Garry P. Nolan, Sean C. Bendall, Robert M. Angelo
  • METHODS OF IDENTIFYING MULTIPLE EPITOPES IN CELLS
    Publication number: 20170321251
    Abstract: The invention provides methods, compositions, kits and devices for the detection of target molecules. In some embodiments, the invention allows for multiplexed target molecule detection.
    Type: Application
    Filed: May 17, 2017
    Publication date: November 9, 2017
    Inventor: Garry P. Nolan
  • Detection of target nucleic acids in a cellular sample
    Patent number: 9783841
    Abstract: Methods of assaying cells of a cellular sample for the presence of a target nucleic acid are provided. Aspects of the methods include evaluating a cellular sample that has been contacted with a nuclease inhibitor for the presence of a target nucleic acid. Also provided are devices and kits that find use in practicing the methods described herein.
    Type: Grant
    Filed: October 3, 2013
    Date of Patent: October 10, 2017
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Garry P. Nolan, Yury Goltsev, Quan Nguyen, Yunqing Ma, Chunfai Lai
  • ANALYSIS OF CELL NETWORKS
    Publication number: 20170285008
    Abstract: The present invention provides an approach for the determination of activation state of a plurality of discrete cell populations and/or the state of one or more cellular networks in an individual.
    Type: Application
    Filed: November 21, 2016
    Publication date: October 5, 2017
    Inventors: Garry P. NOLAN, Alessandra CESANO
  • Single cell analysis using secondary ion mass spectrometry
    Patent number: 9766224
    Abstract: A method of analyzing a population of cells is disclosed. In certain embodiments, the method includes i) obtaining an array of cells on a substrate, wherein the cells are labeled with one or more mass tags and are separated from one another, ii) measuring, using secondary ion mass spectrometry (SIMS), the abundance of the one or more mass tags at a plurality of locations occupied by the cells, thereby generating, for each individual cell measured, a set of data, and iii) outputting the set of data for each of the cells analyzed. Also provided herein are systems that find use in performing the subject method. In some embodiments, the system is an automated system for analyzing a population of cells using SIMS.
    Type: Grant
    Filed: March 11, 2016
    Date of Patent: September 19, 2017
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Garry P. Nolan, Sean C. Bendall, Robert M. Angelo
  • Metal-based covalent viability reagent for single cell analysis
    Patent number: 9739765
    Abstract: The present invention provides a robust viability stain for methods utilizing elemental analysis. A population of cells is contacted with an effective dose of a non-chelated biomacromolecule-reactive metal derivative, which selectively crosses the plasma membrane of non-viable cells, and which covalently modifies a biological macromolecule within the cell, for a period of time sufficient to permit entry into non-viable cells. The population of cells is then washed free of unbound viability reagent; and the presence of the metal within the cells is detected, wherein non-viable cells are selectively labeled with the viability reagent.
    Type: Grant
    Filed: May 2, 2014
    Date of Patent: August 22, 2017
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Bernd Bodenmiller, Erin F. Simonds, Harris G. Fienberg, Garry P. Nolan
  • APPARATUS AND METHOD FOR SUB-MICROMETER ELEMENTAL IMAGE ANALYSIS BY MASS SPECTROMETRY
    Publication number: 20170178882
    Abstract: A mass spectrometer system for elemental analysis of a planar sample is provided. In some embodiments, the mass spectrometer system comprises: a primary ion source capable of irradiating a segment on planar sample with a beam of primary ions that is less than 1 mm in diameter, c) an orthogonal ion mass-to-charge ratio analyzer positioned downstream of sample interface, the analyzer being configured to separate secondary elemental atomic ions according to their mass-to-charge ratio by time of flight; d) an ion detector for detecting the secondary elemental atomic ions and producing mass spectra measurements; and e) a synchronizer, wherein the system is configured so that so that the beam of primary ions scans across the planar sample in two dimensions and the synchronizer associates the mass spectra measurements with positions on the planar sample.
    Type: Application
    Filed: March 30, 2015
    Publication date: June 22, 2017
    Inventors: Sean C. Bendall, Robert M. Angelo, Garry P. Nolan
  • ON-SLIDE STAINING BY PRIMER EXTENSION
    Publication number: 20170107563
    Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) labelling the planar sample with a capture agent that is linked to a nucleic acid, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the nucleic acid, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.
    Type: Application
    Filed: June 19, 2015
    Publication date: April 20, 2017
    Inventors: Nikolay Samusik, Garry P. Nolan, Yury Goltsev, David Robert McIlwain
  • METHODS OF PROGNOSIS AND DIAGNOSIS OF OVARIAN CANCER
    Publication number: 20170082628
    Abstract: Cellular markers indicating a poor prognosis for ovarian cancer patients are disclosed. In particular, the invention relates to methods utilizing the frequency of a subset of cells in ovarian tumor tissue expressing vimentin, cMyc, or HE4, or any combination thereof, to predict an ovarian cancer patient will relapse.
    Type: Application
    Filed: September 23, 2016
    Publication date: March 23, 2017
    Inventors: Jonathan Berek, Wendy Fantl, Veronica Gonzalez, Garry P. Nolan, Nikolay Samusik
  • Induced intercellular communication
    Patent number: 9459246
    Abstract: The present invention provides an approach for the determination of the activation state of discrete cell populations and/or the state of one or more cellular networks in an individual, when modulated with a modulator that acts on one cell population to communicate with other cell populations in the network. The status of discrete cell populations and/or the state of one or more cellular networks can be correlated with the diagnosis, prognosis, choice or modification of treatment, and/or monitoring of a condition, and with screening of agents.
    Type: Grant
    Filed: November 6, 2013
    Date of Patent: October 4, 2016
    Assignee: NODALITY, INC.
    Inventors: Rachael Hawtin, Drew Hotson, Alessandra Cesano, Garry P. Nolan