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    ADAPTIVE BASE CALLING SYSTEMS AND METHODS
    1.
    发明公开
    ADAPTIVE BASE CALLING SYSTEMS AND METHODS 审中-公开

    公开(公告)号：US20240249797A1

    公开(公告)日：2024-07-25

    申请号：US18424587

    申请日：2024-01-26

    Applicant: Ultima Genomics, Inc.

    Inventor： Yoav ETZIONI ,  Edward PERELMAN ,  Asaf HALLE

    IPC: G16B30/00 ,  C12Q1/6874 ,  G16B40/20

    CPC classification number: G16B30/00 ,  C12Q1/6874 ,  G16B40/20

    Abstract: Methods for updating a system comprising a sequencer are described herein. In some exemplary methods, the system is updated through generating sequencing data for a plurality of nucleic acid molecule colonies, selecting sequencing data for a subset of the nucleic acid molecule colonies, calling preliminary sequences for the subset of the nucleic acid colonies, mapping the called preliminary sequences to a known reference sequence, and updating the pre-trained sequencer-specific machine-learning model. Also described herein are systems for carrying out such methods and computer readable memory for storing such methods.

    METHODS AND SYSTEMS FOR DETERMINNG SEQUENCING READ DISTANCES
    2.
    发明公开
    METHODS AND SYSTEMS FOR DETERMINNG SEQUENCING READ DISTANCES 审中-公开

    公开(公告)号：US20240043918A1

    公开(公告)日：2024-02-08

    申请号：US18035081

    申请日：2021-11-03

    Applicant: Ultima Genomics, Inc.

    Inventor： Omer BARAD ,  Yoav ETZIONI

    IPC: C12Q1/6869 ,  C12Q1/6809

    CPC classification number: C12Q1/6869 ,  C12Q1/6809

    Abstract: 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.

    METHODS AND SYSTEMS FOR INCREASING SEQUENCING QUALITY
    3.
    发明公开
    METHODS AND SYSTEMS FOR INCREASING SEQUENCING QUALITY 审中-公开

    公开(公告)号：US20240153583A1

    公开(公告)日：2024-05-09

    申请号：US18417825

    申请日：2024-01-19

    Applicant: Ultima Genomics, Inc.

    Inventor： Yoav ETZIONI ,  Edward PERELMAN

    IPC: G16B30/00 ,  G16B40/30

    CPC classification number: G16B30/00 ,  G16B40/30

    Abstract: Described herein are methods and systems for improving nucleic acid sequencing read quality. An exemplary method comprises receiving, at one or more processors, sequencing data comprising a plurality of sequencing reads; filtering the sequencing data, using the one or more processors, to remove sequencing reads for which an absence of an incorporated nucleotide was detected at three or more consecutive sequencing flow steps, thereby generating filtered sequencing data; determining, using the one or more processors, for each sequencing flow step of each sequencing read, a read quality metric based on one or more homopolymer probability values other than a highest homopolymer probability value; and trimming the terminus of one or more sequencing reads in the sequencing data based on the read quality metrics for a respective sequencing read, thereby generating trimmed sequencing data.

    FAST-FORWARD SEQUENCING BY SYNTHESIS METHODS
    6.
    发明申请
    FAST-FORWARD SEQUENCING BY SYNTHESIS METHODS 有权

    公开(公告)号：US20210054442A1

    公开(公告)日：2021-02-25

    申请号：US17086203

    申请日：2020-10-30

    Applicant: Ultima Genomics, Inc.

    Inventor： Mark PRATT ,  Gilad ALMOGY ,  Dumitru BRINZA ,  Eliane TREPAGNIER ,  Omer BARAD ,  Yoav ETZIONI ,  Florian OBERSTRASS

    IPC: C12Q1/6827 ,  C12Q1/6869 ,  G16B30/00

    Abstract: 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.

    FAST-FORWARD SEQUENCING BY SYNTHESIS METHODS
    7.
    发明申请
    FAST-FORWARD SEQUENCING BY SYNTHESIS METHODS 审中-公开

    公开(公告)号：US20200377937A1

    公开(公告)日：2020-12-03

    申请号：US16864971

    申请日：2020-05-01

    Applicant: Ultima Genomics, Inc.

    Inventor： Mark PRATT ,  Gilad ALMOGY ,  Dumitru BRINZA ,  Eliane TREPAGNIER ,  Omer BARAD ,  Yoav ETZIONI ,  Florian OBERSTRASS

    IPC: C12Q1/6869 ,  G16B30/00

    Abstract: 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.

    METHODS AND SYSTEMS FOR PHASING SEQUENCING STRANDS AND LONG-RANGE SEQUENCING
    10.
    发明公开
    METHODS AND SYSTEMS FOR PHASING SEQUENCING STRANDS AND LONG-RANGE SEQUENCING 审中-公开

    公开(公告)号：US20230407385A1

    公开(公告)日：2023-12-21

    申请号：US18035073

    申请日：2021-11-03

    Applicant: Ultima Genomics, Inc.

    Inventor： Omer BARAD ,  Mark PRATT ,  Eliane TREPAGNIER ,  Yoav ETZIONI ,  Florian OBERSTRASS ,  Gilad ALMOGY ,  Dumitru BRINZA

    IPC: C12Q1/6874

    CPC classification number: C12Q1/6874

    Abstract: 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.

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