Patents by Inventor Omer BARAD
Omer BARAD 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).
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Publication number: 20240043918Abstract: Described herein are methods of sequencing a polynucleotide and methods of analyzing sequencing data obtained from such sequencing methods. The sequencing methods can include accelerated primer extension through a region of the polynucleotide using labeled nucleotides provided according to a flow order, measuring a signal from labeled nucleotides incorporated into the primer, and determining distance information that indicates the length of the region using the measured signal.Type: ApplicationFiled: November 3, 2021Publication date: February 8, 2024Inventors: Omer BARAD, Yoav ETZIONI
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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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Publication number: 20240018599Abstract: Described herein are methods, devices, and systems for measuring a level, presence, recurrence, progression, or regression of a disease (such as cancer), for example a fraction of nucleic acid molecules (such as cell-free DNA) in a sample from an individual that relate to diseased tissue (such as cancer tissue). The methods include generating, using the sequencing data comprising sequencing reads associated with loci selected from a personalized disease-associated small nucleotide variant panel, a plurality of variant motif-specific models that each associate sequencing data corresponding to a respective variant motif, a background factor indicative of a false positive error rate for the respective variant motif, and an estimated fraction of the nucleic acid molecules associated with the disease. From the plurality of variant motif-specific models, a fraction of the nucleic acid molecules associated with the disease for the individual can be determined.Type: ApplicationFiled: November 17, 2021Publication date: January 18, 2024Inventors: Omer BARAD, Itai RUSINEK, Ilya SOIFER
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Publication number: 20230407385Abstract: Described herein are methods synchronizing sequencing primers within a sequencing cluster and methods of generating long-range sequencing reads. The methods can include hybridizing primers to polynucleotide copies within a sequencing cluster; extending the primers through a first region of the polynucleotide copies using labeled nucleotides according to a sequencing flow order; extending the primers through a second region of the polynucleotide copies using one or more re-phasing flow steps that each include at least two different types of nucleotide bases; and extending the primers through a third region of the polynucleotide copies using labeled nucleotides according to the sequencing cycle. The rephasing flow steps may be initiated after a predetermined number of sequencing flow steps, after a measured sequencing signal strength falls below a predetermined sequencing signal strength threshold, or a measured sequencing signal-to-noise ratio falls below a sequencing signal-to-noise ratio threshold.Type: ApplicationFiled: November 3, 2021Publication date: December 21, 2023Inventors: Omer BARAD, Mark PRATT, Eliane TREPAGNIER, Yoav ETZIONI, Florian OBERSTRASS, Gilad ALMOGY, Dumitru BRINZA
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Publication number: 20230343416Abstract: The present disclosure provides methods, systems, and media for accurate and efficient estimation of a genome of a genus. The methods and systems described herein may be used to accurately determine a base sequence of a polynucleotide. Additionally, the methods and systems may be used to identify base variants of a polynucleotide.Type: ApplicationFiled: September 10, 2021Publication date: October 26, 2023Inventors: Yoav ETZIONI, Omer BARAD, Avishai BARTOV, Ilya SOIFER, Ehud AMITAI, Asaf HALLE
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Publication number: 20230060685Abstract: 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: ApplicationFiled: August 26, 2022Publication date: March 2, 2023Inventors: Mark Pratt, Gilad Almogy, Dumitru Brinza, Eliane Trepagnier, Omer Barad, Yoav Etzioni, Florian Oberstrass
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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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Publication number: 20220170089Abstract: 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: ApplicationFiled: November 3, 2021Publication date: June 2, 2022Inventors: Mark PRATT, Gilad ALMOGY, Dumitru BRINZA, Eliane TREPAGNIER, Omer BARAD, Yoav ETZIONI, Florian OBERSTRASS
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Publication number: 20220042072Abstract: 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: ApplicationFiled: August 5, 2021Publication date: February 10, 2022Inventors: Gilad Almogy, Florian OBERSTRASS, Omer BARAD, Chandan SHEE
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Publication number: 20210054442Abstract: 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: ApplicationFiled: October 30, 2020Publication date: February 25, 2021Applicant: Ultima Genomics, Inc.Inventors: Mark PRATT, Gilad ALMOGY, Dumitru BRINZA, Eliane TREPAGNIER, Omer BARAD, Yoav ETZIONI, Florian OBERSTRASS
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Publication number: 20200392584Abstract: Described herein are methods, devices, and systems for measuring a level of a disease (such as cancer), for example a fraction of nucleic acid molecules (such as cell-free DNA) in a sample from an individual that relate to diseased tissue (such as cancer tissue). Also described are methods, devices, and systems for measuring a presence, recurrence, progression, or regression of the disease in the individual. Certain methods include comparing, using nucleic acid sequencing data associated with the individual, a signal indicative of a rate at which sequenced loci selected from a personalized disease-associated small nucleotide variant (SNV) locus panel are derived from a diseased tissue to a background factor indicative of a sequencing false positive error rate, or a noise factor indicative of a sampling variance, across the selected loci.Type: ApplicationFiled: May 15, 2020Publication date: December 17, 2020Inventors: Gilad ALMOGY, Mark PRATT, Omer BARAD, Simchon FAIGLER, Florian OBERSTRASS
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Publication number: 20200377937Abstract: 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: ApplicationFiled: May 1, 2020Publication date: December 3, 2020Inventors: Mark PRATT, Gilad ALMOGY, Dumitru BRINZA, Eliane TREPAGNIER, Omer BARAD, Yoav ETZIONI, Florian OBERSTRASS