Patents by Inventor Florian Oberstrass
Florian Oberstrass 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: 20220348994Abstract: The disclosure provides methods for sequencing nucleic acids using, including with nucleotide analogs and subsequently appended labels.Type: ApplicationFiled: April 4, 2022Publication date: November 3, 2022Inventors: Linda LEE, Steven MENCHEN, Theo NIKIFOROV, Gilad ALMOGY, Florian OBERSTRASS
-
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
-
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
-
Publication number: 20220154272Abstract: The present disclosure provides methods for nucleic acid sequence identification. The methods may comprise bringing a plurality of nucleic acid molecules in contact with a reaction mixture including a concentration of nucleotides that results in fractional labeling of the nucleic acid molecules. The methods may comprise starting a next reversibly-terminated, sequencing cycle prior to completion of unblocking of reversible terminators in a previous sequencing cycle.Type: ApplicationFiled: November 1, 2021Publication date: May 19, 2022Inventors: Florian OBERSTRASS, Gilad ALMOGY, Linda LEE, Eliane TREPAGNIER, Geunwon JUNG
-
Patent number: 11332778Abstract: The disclosure provides methods and systems for nucleic acid amplification including isothermal nucleic acid amplification.Type: GrantFiled: November 25, 2019Date of Patent: May 17, 2022Assignee: GENAPSYS, INC.Inventor: Florian Oberstrass
-
Patent number: 11326203Abstract: The disclosure provides methods for sequencing nucleic acids using, including with nucleotide analogs and subsequently appended labels.Type: GrantFiled: March 18, 2020Date of Patent: May 10, 2022Assignee: Ultima Genomics, Inc.Inventors: Linda Lee, Steven Menchen, Theo Nikiforov, Gilad Almogy, Florian Oberstrass
-
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
-
Patent number: 11220710Abstract: 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: January 26, 2021Date of Patent: January 11, 2022Assignee: ULTIMA GENOMICS, INC.Inventors: Florian Oberstrass, Gilad Almogy
-
Patent number: 11220709Abstract: 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: January 26, 2021Date of Patent: January 11, 2022Assignee: ULTIMA GENOMICS, INC.Inventors: Florian Oberstrass, Gilad Almogy
-
Publication number: 20210230669Abstract: The present disclosure provides methods and systems for processing nucleic acid samples. Methods for processing a nucleic acid sample may comprise providing a double-stranded nucleic acid molecule comprising a partially denaturable region; partially denaturing the partially denaturable region of the double-stranded nucleic acid molecule, thereby generating a region comprising two single strands; and hybridizing a priming sequence to a sequence of one of the single strands. The methods described herein may facilitate amplification without the need for a multitude of complex steps or numerous reagents.Type: ApplicationFiled: January 15, 2021Publication date: July 29, 2021Inventors: Abizar LAKDAWALLA, Florian OBERSTRASS, Chandan SHEE
-
Publication number: 20210147930Abstract: 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: ApplicationFiled: January 26, 2021Publication date: May 20, 2021Inventors: Florian OBERSTRASS, Gilad ALMOGY
-
Publication number: 20210147931Abstract: 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: ApplicationFiled: January 26, 2021Publication date: May 20, 2021Inventors: Florian OBERSTRASS, Gilad ALMOGY
-
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
-
Publication number: 20210017593Abstract: 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: ApplicationFiled: July 31, 2020Publication date: January 21, 2021Inventors: Gilad ALMOGY, Florian OBERSTRASS
-
Publication number: 20210010075Abstract: 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: ApplicationFiled: July 10, 2020Publication date: January 14, 2021Inventors: Florian OBERSTRASS, Gilad ALMOGY
-
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
-
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
-
Publication number: 20200372971Abstract: 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 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: ApplicationFiled: May 1, 2020Publication date: November 26, 2020Inventors: Yoav ETZIONI, Simchon FAIGLER, Gilad ALMOGY, Mark PRATT, Florian OBERSTRASS
-
Publication number: 20200318170Abstract: The disclosure provides methods for sequencing nucleic acids using, including with nucleotide analogs and subsequently appended labels.Type: ApplicationFiled: March 18, 2020Publication date: October 8, 2020Inventors: Linda LEE, Steven MENCHEN, Theo NIKIFOROV, Gilad ALMOGY, Florian OBERSTRASS
-
Publication number: 20200308640Abstract: Recognized herein is the need for methods and processes for increasing the efficiency and accuracy of paired end sequencing.Type: ApplicationFiled: April 7, 2020Publication date: October 1, 2020Inventors: Gilad Almogy, Mark Pratt, Florian Oberstrass