Patents Assigned to ULTIMA GENOMICS, INC.
  • Publication number: 20250059593
    Abstract: The disclosure provides methods for sequencing nucleic acids using, including with nucleotide analogs and subsequently appended labels.
    Type: Application
    Filed: July 18, 2024
    Publication date: February 20, 2025
    Applicant: ULTIMA GENOMICS, INC.
    Inventors: Linda LEE, Steven MENCHEN, Theo NIKIFOROV, Gilad ALMOGY, Florian OBERSTRASS
  • Patent number: 12119087
    Abstract: The present disclosure provides methods and systems for accurate and efficient context-aware base calling of sequences. In an aspect, disclosed herein is a method for sequencing a nucleic acid molecule, comprising: (a) sequencing the nucleic acid molecule to generate a plurality of sequence signals; and (b) determining base calls of the nucleic acid molecule based at least in part on (i) the plurality of sequence signals and (ii) quantified context dependency for at least a portion of the plurality of sequence signals.
    Type: Grant
    Filed: January 12, 2022
    Date of Patent: October 15, 2024
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Mark Pratt, Gilad Almogy, Avishai Bartov
  • Patent number: 11904322
    Abstract: The present disclosure provides methods and processes for increasing the efficiency and accuracy of nucleic acid sequencing using techniques such as polymerase chain reaction (PCR). Methods and systems provided herein may facilitate performing reactions such as emulsion PCR (ePCR) on samples comprising nucleic acids and beads. The methods provided herein may provide a higher throughput compared to existing technologies.
    Type: Grant
    Filed: February 16, 2022
    Date of Patent: February 20, 2024
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Jose Martin Sosa, Joseph Anthony, Nathan Beckett, Gilad Almogy, Chandan Shee, Phillip You Fai Lee, Yuto Watanabe
  • Patent number: 11891658
    Abstract: The present disclosure provides methods and processes for increasing the efficiency and accuracy of nucleic acid sequencing using techniques such as polymerase chain reaction (PCR). The methods described herein can be used to achieve clonal amplification even with a greater than Poisson distribution of beads and/or nucleic acid templates into an emulsion. A PCR method may comprise generating a partition (e.g., a droplet) comprising at least two beads and/or at least two nucleic acid molecules and generating clonal amplification products corresponding to the nucleic acid molecule, at least a subset of which may be attached to a bead.
    Type: Grant
    Filed: August 5, 2021
    Date of Patent: February 6, 2024
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Gilad Almogy, Florian Oberstrass, Omer Barad, Chandan Shee
  • Patent number: 11747323
    Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate configured to rotate. The open substrate can comprise an array of immobilized analytes. A solution comprising a plurality of probes may be directed, via centrifugal force, across the array during rotation of the substrate, to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via continuous rotational area scanning of the substrate.
    Type: Grant
    Filed: October 7, 2022
    Date of Patent: September 5, 2023
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Kristopher Barbee, Nathan Beckett, Denis Pristinski, Derek Schulte, Avishai Bartov, Jamie Sullivan, Dumitru Brinza, Abizar Lakdawalla, Steven Menchen, Gilad Almogy, Mark Pratt
  • Patent number: 11655501
    Abstract: Recognized herein is the need for methods and processes for increasing the efficiency and accuracy of paired end sequencing.
    Type: Grant
    Filed: April 7, 2020
    Date of Patent: May 23, 2023
    Assignee: ULTIMA GENOMICS INC.
    Inventors: Gilad Almogy, Mark Pratt, Florian Oberstrass
  • Patent number: 11649493
    Abstract: The present disclosure provides methods and systems for processing a nucleotide mixture. A nucleotide mixture can be purified. A nucleotide mixture can be processed for use in nucleic acid synthesis. A nucleotide mixture can be processed for use in nucleic acid sequencing.
    Type: Grant
    Filed: July 30, 2019
    Date of Patent: May 16, 2023
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Mark Pratt, Florian Oberstrass, Linda Lee, Steven Menchen
  • Patent number: 11584963
    Abstract: The present disclosure provides methods and systems for sequencing nucleic acid molecules using a single frequency during detection, or fewer frequencies than types of nucleotide bases identified during detection. Methods and systems of the present disclosure may involve transiently binding nucleotides. Methods and systems provided herein may enable sequences to be determined at a higher accuracy and efficiency.
    Type: Grant
    Filed: July 31, 2020
    Date of Patent: February 21, 2023
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Gilad Almogy, Florian Oberstrass
  • Patent number: 11505820
    Abstract: The present disclosure provides methods and systems for sequencing nucleic acid molecules in a manner that enables higher sequencing accuracy. Methods and systems provided herein may enable sequences that may have low-accuracy reads, such as homopolymer sequences or other repeating sequences, to be determined at a higher accuracy and efficiency.
    Type: Grant
    Filed: July 23, 2020
    Date of Patent: November 22, 2022
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Eliane Trepagnier, Mark Pratt, Theo Nikiforov, Gilad Almogy
  • Patent number: 11499962
    Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate configured to rotate. The open substrate can comprise an array of immobilized analytes. A solution comprising a plurality of probes may be directed, via centrifugal force, across the array during rotation of the substrate, to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via continuous rotational area scanning of the substrate.
    Type: Grant
    Filed: April 29, 2020
    Date of Patent: November 15, 2022
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Kristopher Barbee, Nathan Beckett, Denis Pristinski, Derek Schulte, Avishai Bartov, Jamie Sullivan, Dumitru Brinza, Abizar Lakdawalla, Steven Menchen, Gilad Almogy, Mark Pratt
  • Patent number: 11326207
    Abstract: The present disclosure provides methods and systems for nucleic acid sequencing. Such systems and methods may achieve context-independent incorporation, have reduced context-dependence or have context-dependence that is amenable to calibration and modeling. Such systems and methods may also reduce misincorporation.
    Type: Grant
    Filed: November 14, 2019
    Date of Patent: May 10, 2022
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Gilad Almogy, Linda Lee
  • Patent number: 11276480
    Abstract: The present disclosure provides methods and systems for accurate and efficient context-aware base calling of sequences. In an aspect, disclosed herein is a method for sequencing a nucleic acid molecule, comprising: (a) sequencing the nucleic acid molecule to generate a plurality of sequence signals; and (b) determining base calls of the nucleic acid molecule based at least in part on (i) the plurality of sequence signals and (ii) quantified context dependency for at least a portion of the plurality of sequence signals.
    Type: Grant
    Filed: August 19, 2021
    Date of Patent: March 15, 2022
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Mark Pratt, Gilad Almogy, Avishai Bartov
  • Patent number: 11220709
    Abstract: Described herein are methods for determining a sequence of a region of interest from an mRNA molecule. Sequenced polynucleotides can include a barcode region, a homopolymer region (e.g., a poly-A region), and a target region associated with the mRNA molecule. According to some methods, the barcode region omits the same base present in the homopolymer region. According to some methods, extension of the primer used for sequencing is stalled within the homopolymer region. According to some methods, sequencing flow cycles and the different barcode regions of the polynucleotides configured are such that the primer is extended to the end of the barcode region across the plurality of polynucleotides before being extended into the homopolymer region. According to some methods, two primers or a cleavable primer is used to separately sequence the barcode region and the target region.
    Type: Grant
    Filed: January 26, 2021
    Date of Patent: January 11, 2022
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Florian Oberstrass, Gilad Almogy
  • Patent number: 11220710
    Abstract: Described herein are methods for determining a sequence of a region of interest from an mRNA molecule. Sequenced polynucleotides can include a barcode region, a homopolymer region (e.g., a poly-A region), and a target region associated with the mRNA molecule. According to some methods, the barcode region omits the same base present in the homopolymer region. According to some methods, extension of the primer used for sequencing is stalled within the homopolymer region. According to some methods, sequencing flow cycles and the different barcode regions of the polynucleotides configured are such that the primer is extended to the end of the barcode region across the plurality of polynucleotides before being extended into the homopolymer region. According to some methods, two primers or a cleavable primer is used to separately sequence the barcode region and the target region.
    Type: Grant
    Filed: January 26, 2021
    Date of Patent: January 11, 2022
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Florian Oberstrass, Gilad Almogy
  • Patent number: 11155868
    Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.
    Type: Grant
    Filed: January 22, 2021
    Date of Patent: October 26, 2021
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Gilad Almogy, Nathan Beckett, Jacob A. Wolf, Nathan Caswell, Joseph Anthony, Jose Martin Sosa, Phillip Lee, Stephanie Kubecka
  • Patent number: 11118223
    Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.
    Type: Grant
    Filed: November 19, 2020
    Date of Patent: September 14, 2021
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Gilad Almogy, Nathan Beckett, Stephanie Kubecka
  • Patent number: 11107554
    Abstract: The present disclosure provides methods and systems for accurate and efficient context-aware base calling of sequences. In an aspect, disclosed herein is a method for sequencing a nucleic acid molecule, comprising: (a) sequencing the nucleic acid molecule to generate a plurality of sequence signals; and (b) determining base calls of the nucleic acid molecule based at least in part on (i) the plurality of sequence signals and (ii) quantified context dependency for at least a portion of the plurality of sequence signals.
    Type: Grant
    Filed: November 5, 2020
    Date of Patent: August 31, 2021
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Mark Pratt, Gilad Almogy, Avishai Bartov
  • Patent number: 10852518
    Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.
    Type: Grant
    Filed: November 7, 2019
    Date of Patent: December 1, 2020
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Gilad Almogy, Nathan Beckett, Nathan Caswell, Jacob A. Wolf, Gene Polovy, Denis Pristinski
  • Patent number: 10830703
    Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.
    Type: Grant
    Filed: November 7, 2019
    Date of Patent: November 10, 2020
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Gilad Almogy, Nathan Beckett, Nathan Caswell, Gene Polovy
  • Patent number: D998172
    Type: Grant
    Filed: March 12, 2021
    Date of Patent: September 5, 2023
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Jacob Wolf, Nathan Beckett