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    Methods and systems for sequence calling
    41.
    发明授权
    Methods and systems for sequence calling 有权

    公开(公告)号：US11107554B2

    公开(公告)日：2021-08-31

    申请号：US17090176

    申请日：2020-11-05

    Applicant: ULTIMA GENOMICS, INC.

    Inventor： Mark Pratt ,  Gilad Almogy ,  Avishai Bartov

    IPC: G16B40/10 ,  G16B30/10 ,  G16B45/00 ,  C12Q1/6806 ,  C12Q1/6869

    Abstract: The present disclosure provides methods and systems for accurate and efficient context-aware base calling of sequences. In an aspect, disclosed herein is a method for sequencing a nucleic acid molecule, comprising: (a) sequencing the nucleic acid molecule to generate a plurality of sequence signals; and (b) determining base calls of the nucleic acid molecule based at least in part on (i) the plurality of sequence signals and (ii) quantified context dependency for at least a portion of the plurality of sequence signals.

    NUCLEIC ACID CLONAL AMPLIFICATION AND SEQUENCING METHODS, SYSTEMS, AND KITS
    42.
    发明申请
    NUCLEIC ACID CLONAL AMPLIFICATION AND SEQUENCING METHODS, SYSTEMS, AND KITS 有权

    公开(公告)号：US20210230669A1

    公开(公告)日：2021-07-29

    申请号：US17150659

    申请日：2021-01-15

    Applicant: Ultima Genomics, Inc.

    Inventor： Abizar LAKDAWALLA ,  Florian OBERSTRASS ,  Chandan SHEE

    IPC: C12Q1/6806 ,  C12Q1/6855

    Abstract: 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.

    RNA SEQUENCING METHODS
    43.
    发明申请
    RNA SEQUENCING METHODS 有权

    公开(公告)号：US20210147930A1

    公开(公告)日：2021-05-20

    申请号：US17158953

    申请日：2021-01-26

    Applicant: Ultima Genomics, Inc.

    Inventor： Florian OBERSTRASS ,  Gilad ALMOGY

    IPC: C12Q1/6874

    Abstract: 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.

    METHODS OF SEQUENCING NUCLEIC ACID MOLECULES
    45.
    发明申请
    METHODS OF SEQUENCING NUCLEIC ACID MOLECULES 有权

    公开(公告)号：US20210079465A1

    公开(公告)日：2021-03-18

    申请号：US17032023

    申请日：2020-09-25

    Applicant: ULTIMA GENOMICS, INC.

    Inventor： Gilad ALMOGY ,  Linda LEE

    IPC: C12Q1/6874

    Abstract: 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.

    SYSTEMS AND METHODS FOR SEQUENCING ERROR CORRECTION VIA DOUBLE STRAND PRESERVATION
    46.
    发明申请
    SYSTEMS AND METHODS FOR SEQUENCING ERROR CORRECTION VIA DOUBLE STRAND PRESERVATION 有权

    公开(公告)号：US20250154582A1

    公开(公告)日：2025-05-15

    申请号：US18959350

    申请日：2024-11-25

    Applicant: Ultima Genomics, Inc.

    Inventor： Florian OBERSTRASS ,  Tyson CLARK ,  Caterina SCHWEIDENBACK ,  Daniel MAZUR

    IPC: C12Q1/6869 ,  C12Q1/6844

    Abstract: The present disclosure provides compositions, methods, and systems for preparing nucleic acid samples for sequencing, including attaching adapters to a template nucleic acid molecule having a first and second strands; attaching the template nucleic acid molecule to a support; detaching the first and second strands from each other; generating a reverse complement copy of the second strand using a primer coupled to the support; generating amplified copies of the first strand and the reverse complement copy of the second strand using primers coupled to the support; and identifying the sequences of the first strand and the reverse complement copy of the second strand. Further provided herein are methods of error correction by preserving both strands of a template nucleic acid molecule during amplification.

    METHODS AND SYSTEMS FOR DETECTING RESIDUAL DISEASE
    47.
    发明申请
    METHODS AND SYSTEMS FOR DETECTING RESIDUAL DISEASE 有权

    公开(公告)号：US20250101533A1

    公开(公告)日：2025-03-27

    申请号：US18910965

    申请日：2024-10-09

    Applicant: Ultima Genomics, Inc.

    Inventor： Gilad ALMOGY ,  Mark PRATT ,  Omer BARAD ,  Simchon FAIGLER ,  Florian OBERSTRASS

    IPC: C12Q1/6886 ,  C12Q1/6809 ,  C12Q1/6869 ,  G06F17/18 ,  G16B20/00

    Abstract: 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.

    Sequencer machine
    49.
    外观设计
    Sequencer machine 有权

    公开(公告)号：USD1048460S1

    公开(公告)日：2024-10-22

    申请号：US29795241

    申请日：2021-06-17

    Applicant: Ultima Genomics, Inc.

    Designer： Joseph Anthony ,  Nathan Beckett ,  Ryan Rosenfeld

    Abstract: FIG. 1 is a front perspective view of a sequencer machine, according to a new design;
    FIG. 2 is a top back perspective view thereof;
    FIG. 3 is a front view of thereof;
    FIG. 4 is a left view of thereof;
    FIG. 5 is a back view of thereof;
    FIG. 6 is a right side view of thereof; and,
    FIG. 7 is a top view of thereof.
    FIG. 8 is a close-up view of an area of the front of the sequencer machine as indicated by a circle in FIG. 3.
    FIG. 9 is a close-up view of the area of the rear of the sequencer machine as indicated by a circle in FIG. 5; and,
    FIG. 10 is a close-up view of the area of the side of the sequencer machine as indicated by a circle in FIG. 6.
    In the drawings, the equal-length broken lines depict portions of the sequencer machine and form no part of the claimed design. The dash-dot-dash broken lines define the limits of the enlarged portions shown. All broken lines form no part of the claim.

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