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).

  • Patent number: 12258619
    Abstract: The present disclosure relates to multiplex assay methods used to detect target nucleic acids of interest from several to many sources in a sample without amplification of the target nucleic acids of interest. The methods involve partitioning of first ribonucleoprotein complexes to detect short sequences from several to many loci scattered throughout a single source genome, and the addition of signal boosting second ribonucleoprotein complexes and reporter moieties.
    Type: Grant
    Filed: July 8, 2024
    Date of Patent: March 25, 2025
    Assignee: VedaBio, Inc.
    Inventor: Phillip Belgrader
  • Publication number: 20250091048
    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: September 18, 2024
    Publication date: March 20, 2025
    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
  • Publication number: 20250027150
    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: July 26, 2024
    Publication date: January 23, 2025
    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
  • Publication number: 20250002977
    Abstract: The present disclosure relates to multiplex assay methods used to detect target nucleic acids of interest from several to many sources in a sample without amplification of the target nucleic acids of interest. The methods involve partitioning of first ribonucleoprotein complexes to detect short sequences from several to many loci scattered throughout a single source genome, and the addition of signal boosting second ribonucleoprotein complexes and reporter moieties.
    Type: Application
    Filed: July 8, 2024
    Publication date: January 2, 2025
    Inventor: Phillip Belgrader
  • Patent number: 12162008
    Abstract: Methods of partition-based analysis. In an exemplary method, a device having a port fluidically connected to a chamber may be selected. A sample-containing fluid may be placed into the port. The sample-containing fluid may be moved from the port to the chamber. Partitions of the sample-containing fluid may be formed. A monolayer of the partitions in the chamber may be created. At least a portion of the monolayer may be imaged.
    Type: Grant
    Filed: September 27, 2021
    Date of Patent: December 10, 2024
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Billy Wayne Colston, Jr., Benjamin Joseph Hindson, Kevin Dean Ness, Donald Arthur Masquelier, Fred Paul Milanovich, Douglas N. Modlin, Vincent Riot, Samuel Burd, Anthony Joseph Makarewicz, Jr., Phillip Belgrader
  • Patent number: 12110549
    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: August 24, 2022
    Date of Patent: October 8, 2024
    Assignee: 10X GENOMICS, INC.
    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: 12097495
    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: Grant
    Filed: May 20, 2022
    Date of Patent: September 24, 2024
    Assignee: 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: 12084716
    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: September 13, 2021
    Date of Patent: September 10, 2024
    Assignee: 10X GENOMICS, INC.
    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
  • Publication number: 20240287623
    Abstract: The present disclosure relates to multiplex assay methods and systems used to detect several to many to a massively multiplexed number of target nucleic acids of interest in a sample without amplification of the target nucleic acids of interest. The method employs microfluidic droplet systems where each droplet is a “mini-reactor.” In some embodiments, a “bulk format” configuration is used, in other embodiments, a “sequential format” configuration is used.
    Type: Application
    Filed: February 23, 2024
    Publication date: August 29, 2024
    Inventors: Don Masquelier, Phillip Belgrader, Anurup Ganguli
  • Patent number: 12060602
    Abstract: The present disclosure relates to multiplex assay methods used to detect target nucleic acids of interest from several to many sources in a sample without amplification of the target nucleic acids of interest. The methods involve partitioning of first ribonucleoprotein complexes to detect short sequences from several to many loci scattered throughout a single source genome, and the addition of signal boosting second ribonucleoprotein complexes and reporter moieties.
    Type: Grant
    Filed: January 7, 2024
    Date of Patent: August 13, 2024
    Assignee: VedaBio, Inc.
    Inventor: Phillip Belgrader
  • Publication number: 20240263170
    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: Application
    Filed: January 12, 2024
    Publication date: August 8, 2024
    Applicant: Inscripta, Inc.
    Inventors: Jorge Bernate, Kevin Ness, Phillip Belgrader, Don Masquelier, Ryan Gill
  • Publication number: 20240240238
    Abstract: The present disclosure relates to multiplex assay methods used to detect target nucleic acids of interest from several to many sources in a sample without amplification of the target nucleic acids of interest. The methods involve partitioning of first ribonucleoprotein complexes to detect short sequences from several to many loci scattered throughout a single source genome, and the addition of signal boosting second ribonucleoprotein complexes and reporter moieties.
    Type: Application
    Filed: January 7, 2024
    Publication date: July 18, 2024
    Inventor: Phillip Belgrader
  • Publication number: 20240141331
    Abstract: This invention relates to compositions of matter, methods, modules and instruments for automated mammalian cell growth and mammalian cell transduction followed by nucleic acid-guided nuclease editing in live mammalian cells.
    Type: Application
    Filed: November 8, 2023
    Publication date: May 2, 2024
    Applicant: Inscripta, Inc.
    Inventors: Burak Dura, Phillip Belgrader, Christian Siltanen, William Watterson, Bruce Chabansky, David Stumbo, Eric Smith, Jorge Bernate
  • Patent number: 11965154
    Abstract: The present disclosure provides modules, instruments and methods to enrich for cells edited via nucleic acid-guided nuclease editing of live cells.
    Type: Grant
    Filed: August 20, 2019
    Date of Patent: April 23, 2024
    Assignee: Inscripta, Inc.
    Inventors: Eileen Spindler, Isaac Wagner, Clint Davis, Julia Swavola, Phillip Belgrader
  • 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
  • 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