Patents by Inventor Phillip Belgrader

Phillip Belgrader 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: 20240067953
    Abstract: The present disclosure provides methods, compositions and systems for analyzing individual cells or cell populations through a partitioned analysis of contents of individual cells or cell populations, such as cancer cells and cells of the immune system. Individual cells or cell populations may be co-partitioned with processing reagents for accessing cellular contents, and for uniquely identifying the content of a given cell or cell population, and subsequently analyzing the content of the cell and characterizing it as having derived from an individual cell or cell population, including analysis and characterization of nucleic acid(s) from the cell through sequencing.
    Type: Application
    Filed: April 17, 2023
    Publication date: February 29, 2024
    Inventors: Tarjei Sigurd MIKKELSEN, Phillip BELGRADER, Xinying ZHENG
  • Publication number: 20240035067
    Abstract: An integrated sample purification system includes a housing, a sample container rack, a filter holder, and a cylindrical magnet. The sample container rack and the filter device holder are disposed in the housing. The sample container rack is configured to hold one or more sample containers, the filter device holder is configured to hold one or more filter devices. The cylindrical magnet is adjacent to and external to the sample container rack, and is rotated about a central, longitudinal axis of the magnet by an electric motor disposed in the housing to lyse cells. Molecules of interest in the lysed cells are purified using filters that bind specifically to the molecules of interest. The system is readily amenable to automation and rapid purification and analysis of molecules of interest, such as nucleic acids and proteins.
    Type: Application
    Filed: July 10, 2023
    Publication date: February 1, 2024
    Inventors: Christopher G. COONEY, Rebecca HOLMBERG, Phillip BELGRADER, Peter Qiang QU
  • Publication number: 20240002837
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.
    Type: Application
    Filed: September 13, 2023
    Publication date: January 4, 2024
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Serge Saxonov, Paul Hardenbol, Rajiv Bharadwaj, Xinying Zheng, Phillip Belgrader
  • Patent number: 11845932
    Abstract: Nucleic acid-guided nuclease editing in mammalian cells may include passaging mammalian cells, in an automated closed cell editing instrument, into smaller aggregates when the aggregates exceed 50-300 microns in size. A library of viral particles may be delivered to the mammalian cells at a multiplicity of infection such that each mammalian cell receives one or no viral particle. The library may include viral vectors with an editing cassette including a pair of gRNA coding sequence and donor DNA. Conditions may be provided to allow a viral vector of the viral vectors to integrate into the mammalian cells. Enriching for mammalian cells may be done with an integrated viral vector. A nucleic acid-guided nuclease or nuclease fusion or a coding sequence for a nucleic acid-guided nuclease or nuclease fusion may be delivered to the enriched mammalian cells and conditions may be provided to allow editing in the mammalian cells.
    Type: Grant
    Filed: May 31, 2022
    Date of Patent: December 19, 2023
    Assignee: INSCRIPTA, INC.
    Inventors: Burak Dura, Phillip Belgrader, Christian Siltanen, William Watterson, Bruce Chabansky, David Stumbo, Eric Smith, Jorge Bernate
  • Publication number: 20230366006
    Abstract: The disclosure provides methods for separating and/or purifying one or more molecules released from one or more fluid compartments or partitions, such as one or more droplets. Molecules can be released from a fluid compartment(s) and bound to supports that can be isolated via any suitable method, including example methods described herein. The disclosure also provides devices that can aid in isolating supports bound to molecules.
    Type: Application
    Filed: March 3, 2023
    Publication date: November 16, 2023
    Inventors: Phillip Belgrader, Donald A. Masquelier
  • Patent number: 11767549
    Abstract: An integrated sample purification system includes a housing, a sample container rack, a filter holder, and a cylindrical magnet. The sample container rack and the filter device holder are disposed in the housing. The sample container rack is configured to hold one or more sample containers, the filter device holder is configured to hold one or more filter devices. The cylindrical magnet is adjacent to and external to the sample container rack, and is rotated about a central, longitudinal axis of the magnet by an electric motor disposed in the housing to lyse cells. Molecules of interest in the lysed cells are purified using filters that bind specifically to the molecules of interest. The system is readily amenable to automation and rapid purification and analysis of molecules of interest, such as nucleic acids and proteins.
    Type: Grant
    Filed: December 30, 2020
    Date of Patent: September 26, 2023
    Assignee: AKONNI BIOSYSTEMS, INC.
    Inventors: Christopher G. Cooney, Rebecca Holmberg, Phillip Belgrader, Peter Qiang Qu
  • Publication number: 20230287486
    Abstract: Method of haplotype analysis. In an exemplary method, an aqueous phase containing nucleic acid may be partitioned into a plurality of discrete volumes. At least one allele sequence may be amplified in the volumes from each of a first polymorphic locus and a second polymorphic locus that exhibit sequence variation in the nucleic acid. At least one measure of co-amplification of allele sequences from both loci in the same volumes may be determined. A haplotype of the first and second loci may be selected based on the at least one measure of co-amplification.
    Type: Application
    Filed: November 14, 2022
    Publication date: September 14, 2023
    Applicant: Bio-Rad Laboratories, Inc.
    Inventors: John F. REGAN, Serge SAXONOV, Michael Y. LUCERO, Benjamin J. HINDSON, Phillip BELGRADER, Simant DUBE, Austin SO, Jeffrey Clark MELLEN, Nicholas Jack HEREDIA, Kevin D. NESS, Billy W. COLSTON, Jr.
  • Patent number: 11739290
    Abstract: The present disclosure provides instruments, modules and methods for improved detection of edited cells following nucleic acid-guided nuclease genome editing. The disclosure provides improved automated instruments that perform methods—including high throughput methods—for screening cells that have been subjected to editing and identifying cells that have been properly edited.
    Type: Grant
    Filed: December 17, 2021
    Date of Patent: August 29, 2023
    Assignee: INSCRIPTA, INC
    Inventors: Andrew Garst, Richard Fox, Phillip Belgrader, Don Masquelier
  • Patent number: 11732302
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization.
    Type: Grant
    Filed: June 2, 2022
    Date of Patent: August 22, 2023
    Assignee: 10X Genomics, Inc.
    Inventors: Phillip Belgrader, Josephine Harada, Tarjei Sigurd Mikkelsen, Katherine Pfeiffer, Serge Saxonov, John R. Stuelpnagel
  • Publication number: 20230250420
    Abstract: Compositions of matter, methods, modules, and automated instruments may relate to synthesizing a library including an editing cassette including a different gRNA and donor DNA pair, amplifying the editing cassette in a partition separate from other editing cassettes in the library, adding nuclease to the partition, and adding lipofectamine to the editing cassette and nuclease to form a lipofectamine/nucleic acid/nuclease complex. A microcarrier coated in extracellular matrix or a cell adhesion molecule coating may be added to the lipofectamine/nucleic acid/nuclease complex. Cell growth material, the microcarrier, and mammalian cells may be transferred to a growth module in an automated closed cell editing instrument via a liquid handling system. The mammalian cells may be allowed to seed on the microcarrier. Conditions may be provided for the mammalian cells to take-up and be edited by a payload associated with the lipofectamine/nucleic acid/nuclease complex.
    Type: Application
    Filed: February 24, 2023
    Publication date: August 10, 2023
    Applicant: Inscripta, Inc.
    Inventors: Phillip Belgrader, Nathan Bade, Christian Siltanen, Aamir Mir, Xi-Jun Chen, Janine Mok, Burak Dura, Bruce Chabansky, David Stumbo, Eric Smith, Jorge Bernate
  • Publication number: 20230203577
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization.
    Type: Application
    Filed: August 24, 2022
    Publication date: June 29, 2023
    Inventors: Phillip Belgrader, Zachary Bent, Rajiv Bharadwaj, Vijay Kumar Sreenivasa Gopalan, Josephine Harada, Christopher Hindson, Mohammad Rahimi Lenji, Michael Ybarra Lucero, Geoffrey McDermott, Elliott Meer, Tarjei Sigurd Mikkelsen, Christopher Joachim O'Keeffe, Katherine Pfeiffer, Andrew D. Price, Paul Ryvkin, Serge Saxonov, John R. Stuelpnagel, Jessica Michele Terry, Tobias Daniel Wheeler, Indira Wu, Solongo Batjargal Ziraldo, Stephane Claude Boutet, Sarah Taylor, Niranjan Srinivas
  • Patent number: 11685889
    Abstract: The present disclosure provides automated modules and instruments for improved detection of nuclease genome editing of live cells. The disclosure provides improved modules—including high throughput modules—for screening cells that have been subjected to editing and identifying and selecting cells that have been properly edited.
    Type: Grant
    Filed: April 30, 2022
    Date of Patent: June 27, 2023
    Assignee: INSCRIPTA, INC.
    Inventors: Andrew Garst, Richard Fox, Eileen Spindler, Amy Hiddessen, Phillip Belgrader, Don Masquelier, Bruce Chabansky, Michael Graige
  • Publication number: 20230087127
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.
    Type: Application
    Filed: November 14, 2022
    Publication date: March 23, 2023
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Serge Saxonov, Paul Hardenbol, Rajiv Bharadwaj, Xinying Zheng, Phillip Belgrader
  • Patent number: 11603554
    Abstract: The disclosure provides methods for separating and/or purifying one or more molecules released from one or more fluid compartments or partitions, such as one or more droplets. Molecules can be released from a fluid compartment(s) and bound to supports that can be isolated via any suitable method, including example methods described herein. The disclosure also provides devices that can aid in isolating supports bound to molecules.
    Type: Grant
    Filed: June 26, 2020
    Date of Patent: March 14, 2023
    Assignee: 10x Genomics, Inc.
    Inventors: Phillip Belgrader, Donald A. Masquelier
  • Patent number: 11597921
    Abstract: In an illustrative embodiment, automated multi-module cell editing instruments are provided to automate multiple edits into nucleic acid sequences inside one or more cells.
    Type: Grant
    Filed: March 11, 2022
    Date of Patent: March 7, 2023
    Assignee: Inscripta, Inc.
    Inventors: Jorge Bernate, Kevin Ness, Phillip Belgrader, Don Masquelier, Ryan Gill
  • Patent number: 11591592
    Abstract: This invention relates to compositions of matter, methods, modules and automated, end-to-end closed instruments for automated mammalian cell growth, reagent bundle creation and mammalian cell transfection followed by nucleic acid-guided nuclease editing in live mammalian cells. The disclosed compositions and method entail making “reagent bundles” comprising many (hundreds of thousands to millions) clonal copies of an editing cassette and delivering or co-localizing the reagent bundles with live mammalian cells such that the editing cassettes edit the cells and the edited cells continue to grow.
    Type: Grant
    Filed: April 23, 2021
    Date of Patent: February 28, 2023
    Assignee: Inscripta, Inc.
    Inventors: Phillip Belgrader, Nathan Bade, Christian Siltanen, Aamir Mir, Xi-Jun Chen, Janine Mok, Burak Dura, Bruce Chabansky, David Stumbo, Eric Smith, Jorge Bernate
  • Publication number: 20220389503
    Abstract: The present disclosure provides methods, compositions and systems for analyzing individual cells or cell populations through a partitioned analysis of contents of individual cells or cell populations, such as cancer cells and cells of the immune system. Individual cells or cell populations may be co-partitioned with processing reagents for accessing cellular contents, and for uniquely identifying the content of a given cell or cell population, and subsequently analyzing the content of the cell and characterizing it as having derived from an individual cell or cell population, including analysis and characterization of nucleic acid(s) from the cell through sequencing.
    Type: Application
    Filed: March 11, 2022
    Publication date: December 8, 2022
    Inventors: Tarjei Sigurd MIKKELSEN, Phillip BELGRADER, Xinying ZHENG
  • Publication number: 20220362764
    Abstract: The present disclosure provides methods and compositions for detecting polynucleotides in a sample and for quantifying polynucleotide load in a sample. The polynucleotides can be associated with a disease, disorder, or condition. In some applications, methylated DNA is quantified, e.g., in order to determine the load of polynucleotides in a sample. The present disclosure also provides methods and compositions for determining the load of fetal polynucleotides in a biological sample, e.g., the load of fetal polynucleotides (e.g., DNA, RNA) in maternal plasma. The present disclosure provides methods and compositions for detecting cellular processes such as cellular viability, growth rates, and infection rates. This disclosure also provides compositions and methods for detecting differences in copy number of a target polynucleotide. In some embodiments, the methods and compositions provided herein are useful for diagnosis of fetal genetic abnormalities, when the starting sample is maternal tissue (e.g.
    Type: Application
    Filed: May 20, 2022
    Publication date: November 17, 2022
    Applicant: Bio-Rad Laboratories, Inc.
    Inventors: Benjamin J. HINDSON, Serge SAXONOV, Phillip BELGRADER, Kevin D. NESS, Michael Y. LUCERO, Billy W. COLSTON, JR., Shawn Paul HODGES, Nicholas J. HEREDIA, Jeffrey Clark MELLEN, Camille Bodley TROUP, Paul WYATT
  • Patent number: 11499181
    Abstract: Method of haplotype analysis. In an exemplary method, an aqueous phase containing nucleic acid may be partitioned into a plurality of discrete volumes. At least one allele sequence may be amplified in the volumes from each of a first polymorphic locus and a second polymorphic locus that exhibit sequence variation in the nucleic acid. At least one measure of co-amplification of allele sequences from both loci in the same volumes may be determined. A haplotype of the first and second loci may be selected based on the at least one measure of co-amplification.
    Type: Grant
    Filed: December 28, 2018
    Date of Patent: November 15, 2022
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: John F. Regan, Serge Saxonov, Michael Y. Lucero, Benjamin J. Hindson, Phillip Belgrader, Simant Dube, Austin P. So, Jeffrey C. Mellen, Nicholas J. Heredia, Kevin D. Ness, Billy W. Colston, Jr.
  • Publication number: 20220355292
    Abstract: This invention provides compositions and methods for detecting differences in copy number of a target polynucleotide. In some cases, the methods and compositions provided herein are useful for diagnosis of fetal genetic abnormalities, when the starting sample is maternal tissue (e.g., blood, plasma). The methods and materials described apply techniques for allowing detection of small, but statistically significant, differences in polynucleotide copy number.
    Type: Application
    Filed: May 20, 2022
    Publication date: November 10, 2022
    Applicant: Bio-Rad Laboratories, Inc.
    Inventors: Benjamin J. HINDSON, Serge SAXONOV, Phillip BELGRADER, Kevin D. NESS, Michael Y. LUCERO, Billy W. COLSTON, JR.