Patents Assigned to ULTIMA GENOMICS, INC.
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Patent number: 11946097Abstract: The present disclosure provides labeling reagents for labeling substrates such as nucleotides, proteins, antibodies, lipids, and cells. The labeling reagents provided herein may comprise fluorescent labels and semi-rigid linkers. Methods for nucleic acid sequencing using materials comprising such labeling reagents are also provided here.Type: GrantFiled: March 17, 2022Date of Patent: April 2, 2024Assignee: Ultima Genomics, Inc.Inventors: Linda G. Lee, Gilad Almogy, Steven Menchen
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Patent number: 11904322Abstract: 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: GrantFiled: February 16, 2022Date of Patent: February 20, 2024Assignee: ULTIMA GENOMICS, INC.Inventors: Jose Martin Sosa, Joseph Anthony, Nathan Beckett, Gilad Almogy, Chandan Shee, Phillip You Fai Lee, Yuto Watanabe
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Patent number: 11891658Abstract: 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: GrantFiled: August 5, 2021Date of Patent: February 6, 2024Assignee: ULTIMA GENOMICS, INC.Inventors: Gilad Almogy, Florian Oberstrass, Omer Barad, Chandan Shee
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Patent number: 11807851Abstract: The present disclosure provides modified substrates such as modified polynucleotides, proteins, antibodies, lipids, and cells and uses thereof. Method of generating the modified substrates, which may comprise cleavage of a cleavable group linking the substrate to a labeling moiety, are also provided herein.Type: GrantFiled: February 16, 2021Date of Patent: November 7, 2023Assignee: Ultima Genomics, Inc.Inventors: Linda G. Lee, Steven Menchen
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Patent number: 11763915Abstract: Methods for detecting a short genetic variant in a test sample are described herein. In some exemplary methods, the short genetic variant is called using one or more match scores, which are determined using one or more sequencing data sets obtained from a test nucleic acid molecule, wherein the test sequencing data sets are determined by sequencing the test nucleic acid molecule using non-terminating nucleotides provided in separate nucleotide flows according to a flow-cycle order. Also described herein are methods of sequencing a test nucleic acid molecule using two or more different flow-cycle orders and/or extended flow cycle orders having five or more nucleotide flows per flow cycle.Type: GrantFiled: May 1, 2020Date of Patent: September 19, 2023Assignee: Ultima Genomics, Inc.Inventors: Yoav Etzioni, Simchon Faigler, Gilad Almogy, Mark Pratt, Florian Oberstrass
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Patent number: 11747323Abstract: 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: GrantFiled: October 7, 2022Date of Patent: September 5, 2023Assignee: 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
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Patent number: 11732298Abstract: Provided are methods for biological sample processing and analysis. A method can comprise providing a substrate configured to rotate. The substrate can comprise an array having immobilized thereto a biological analyte. A solution comprising a plurality of probes may be directed, via centrifugal force, across the substrate during rotation of the substrate, to couple at least one of the plurality of probes with the biological analyte. A detector can be configured to detect a signal from the at least one probe coupled to the biological analyte, thereby analyzing the biological analyte.Type: GrantFiled: May 20, 2019Date of Patent: August 22, 2023Assignee: Ultima Genomics, Inc.Inventors: Gilad Almogy, Kristopher Barbee, Nathan Beckett
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Patent number: 11655501Abstract: Recognized herein is the need for methods and processes for increasing the efficiency and accuracy of paired end sequencing.Type: GrantFiled: April 7, 2020Date of Patent: May 23, 2023Assignee: ULTIMA GENOMICS INC.Inventors: Gilad Almogy, Mark Pratt, Florian Oberstrass
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Patent number: 11649493Abstract: 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: GrantFiled: July 30, 2019Date of Patent: May 16, 2023Assignee: ULTIMA GENOMICS, INC.Inventors: Mark Pratt, Florian Oberstrass, Linda Lee, Steven Menchen
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Patent number: 11648554Abstract: Provided herein are methods for processing and/or detecting a sample. A method can comprise providing a barrier between a first region and a second region, wherein the first region comprises the sample, wherein the barrier maintains the first region at a first atmosphere that is different than a second atmosphere of the second region, wherein a portion of the barrier comprises a fluid in coherent motion; and using a detector at least partially contained in the first region to detect one or more signals from the sample while the first region is maintained at the first atmosphere that is different than the second atmosphere of the second region. The portion of the barrier comprising fluid may have a pressure lower than the first atmosphere, the second atmosphere, or both.Type: GrantFiled: October 28, 2019Date of Patent: May 16, 2023Assignee: Ultima Genomics, Inc.Inventors: Nathan Beckett, Nathan Caswell
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Patent number: 11591651Abstract: Provided are methods for biological sample processing and analysis. A method can comprise providing a substrate configured to rotate. The substrate can comprise an array having immobilized thereto a biological analyte. A solution comprising a plurality of probes may be directed, via centrifugal force, across the substrate during rotation of the substrate, to couple at least one of the plurality of probes with the biological analyte. A detector can be configured to detect a signal from the at least one probe coupled to the biological analyte, thereby analyzing the biological analyte.Type: GrantFiled: November 5, 2020Date of Patent: February 28, 2023Assignee: Ultima Genomics, Inc.Inventors: Gilad Almogy, Kristopher Barbee, Nathan Beckett
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Patent number: 11584963Abstract: 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: GrantFiled: July 31, 2020Date of Patent: February 21, 2023Assignee: ULTIMA GENOMICS, INC.Inventors: Gilad Almogy, Florian Oberstrass
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Patent number: 11578363Abstract: 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: GrantFiled: July 10, 2020Date of Patent: February 14, 2023Assignee: Ultima Genomics, Inc.Inventors: Florian Oberstrass, Gilad Almogy
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Patent number: 11512350Abstract: Provided are methods for biological sample processing and analysis. A method can comprise providing a substrate configured to rotate. The substrate can comprise an array having immobilized thereto a biological analyte. A solution comprising a plurality of probes may be directed, via centrifugal force, across the substrate during rotation of the substrate, to couple at least one of the plurality of probes with the biological analyte. A detector can be configured to detect a signal from the at least one probe coupled to the biological analyte, thereby analyzing the biological analyte.Type: GrantFiled: November 5, 2020Date of Patent: November 29, 2022Assignee: Ultima Genomics, Inc.Inventors: Gilad Almogy, Kristopher Barbee, Nathan Beckett
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Patent number: 11505820Abstract: 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: GrantFiled: July 23, 2020Date of Patent: November 22, 2022Assignee: ULTIMA GENOMICS, INC.Inventors: Eliane Trepagnier, Mark Pratt, Theo Nikiforov, Gilad Almogy
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Patent number: 11499962Abstract: 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: GrantFiled: April 29, 2020Date of Patent: November 15, 2022Assignee: 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
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Patent number: 11459609Abstract: Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.Type: GrantFiled: November 3, 2021Date of Patent: October 4, 2022Assignee: Ultima Genomics, Inc.Inventors: Mark Pratt, Gilad Almogy, Dumitru Brinza, Eliane Trepagnier, Omer Barad, Yoav Etzioni, Florian Oberstrass
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Patent number: 11462300Abstract: The present disclosure provides methods, systems, and media for accurate and efficient estimation of a genome of a genus.Type: GrantFiled: August 9, 2021Date of Patent: October 4, 2022Assignee: Ultima Genomics, Inc.Inventors: Avishai Bartov, Yoav Etzioni, Mark Geshel, Mark Pratt, Gilad Almogy
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Patent number: D998172Type: GrantFiled: March 12, 2021Date of Patent: September 5, 2023Assignee: ULTIMA GENOMICS, INC.Inventors: Jacob Wolf, Nathan Beckett
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Patent number: D1023338Type: GrantFiled: February 18, 2021Date of Patent: April 16, 2024Assignee: Ultima Genomics, Inc.Inventors: Nathan Beckett, Jacob Wolf, Keith Allen, Ryan Rosenfeld, Anh Nguyen, Hoang Nguyen