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    METHODS AND SYSTEMS FOR DETECTING RESIDUAL DISEASE
    1.
    发明公开
    METHODS AND SYSTEMS FOR DETECTING RESIDUAL DISEASE 审中-公开

    公开(公告)号：US20240018599A1

    公开(公告)日：2024-01-18

    申请号：US18035075

    申请日：2021-11-17

    Applicant: Ultima Genomics, Inc.

    Inventor： Omer BARAD ,  Itai RUSINEK ,  Ilya SOIFER

    IPC: C12Q1/6886 ,  C12Q1/6827

    CPC classification number: C12Q1/6886 ,  C12Q1/6827 ,  C12Q2600/112

    Abstract: 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.

    METHODS AND SYSTEMS FOR DETERMINNG SEQUENCING READ DISTANCES
    3.
    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.

    METHYLATION SEQUENCING METHODS AND COMPOSITIONS
    4.
    发明申请
    METHYLATION SEQUENCING METHODS AND COMPOSITIONS 有权

    公开(公告)号：US20240368686A1

    公开(公告)日：2024-11-07

    申请号：US18657167

    申请日：2024-05-07

    Applicant: ULTIMA GENOMICS, INC.

    Inventor： Zohar SHIPONY ,  Florian OBERSTRASS ,  Doron LIPSON ,  Eti MEIRI ,  Omer BARAD

    IPC: C12Q1/6874 ,  C12Q1/6876

    Abstract: Described herein is a composition, comprising: a first strand comprising a first portion and a first copy portion, wherein the first copy portion is a copy of the first portion except that substantially all cytosine bases in the first copy portion are methylated; and a second strand comprising a second portion and a second copy portion, wherein the second copy portion is a copy of the second portion except that substantially all cytosine bases in the second copy portion are methylated. In some implementations, at least one cytosine base in the first portion or the second portion is not methylated.

    FAST-FORWARD SEQUENCING BY SYNTHESIS METHODS
    5.
    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
    6.
    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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