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    RNA sequencing methods
    71.
    发明授权
    RNA sequencing methods 有权

    公开(公告)号：US11220709B2

    公开(公告)日：2022-01-11

    申请号：US17158953

    申请日：2021-01-26

    Applicant: Ultima Genomics, Inc.

    Inventor： Florian Oberstrass ,  Gilad Almogy

    IPC: C12Q1/6874 ,  C12Q1/6869 ,  C12N15/10

    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.

    IMPLEMENTING BARRIERS FOR CONTROLLED ENVIRONMENTS DURING SAMPLE PROCESSING AND DETECTION
    72.
    发明申请
    IMPLEMENTING BARRIERS FOR CONTROLLED ENVIRONMENTS DURING SAMPLE PROCESSING AND DETECTION 有权

    公开(公告)号：US20210354126A1

    公开(公告)日：2021-11-18

    申请号：US17336377

    申请日：2021-06-02

    Applicant: Ultima Genomics, Inc.

    Inventor： Nathan BECKETT ,  Nathan CASWELL

    IPC: B01L3/00 ,  G01N7/02

    Abstract: Provided herein are methods for processing and/or detecting a sample. A method can comprise providing a barrier between a first region and a second region, wherein the first region comprises the sample, wherein the barrier maintains the first region at a first atmosphere that is different than a second atmosphere of the second region, wherein a portion of the barrier comprises a fluid in coherent motion; and using a detector at least partially contained in the first region to detect one or more signals from the sample while the first region is maintained at the first atmosphere that is different than the second atmosphere of the second region. The portion of the barrier comprising fluid may have a pressure lower than the first atmosphere, the second atmosphere, or both.

    METHODS AND SYSTEMS FOR SEQUENCE CALLING
    74.
    发明申请
    METHODS AND SYSTEMS FOR SEQUENCE CALLING 有权

    公开(公告)号：US20210142869A1

    公开(公告)日：2021-05-13

    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.

    Methods, devices, and systems for analyte detection and analysis
    75.
    发明授权
    Methods, devices, and systems for analyte detection and analysis 有权

    公开(公告)号：US10830703B1

    公开(公告)日：2020-11-10

    申请号：US16677067

    申请日：2019-11-07

    Applicant: Ultima Genomics, Inc.

    Inventor： Gilad Almogy ,  Nathan Beckett ,  Nathan Caswell ,  Gene Polovy

    IPC: G01N21/65 ,  G02B21/00

    Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.

    IMPLEMENTING BARRIERS FOR CONTROLLED ENVIRONMENTS DURING SAMPLE PROCESSING AND DETECTION
    77.
    发明申请
    IMPLEMENTING BARRIERS FOR CONTROLLED ENVIRONMENTS DURING SAMPLE PROCESSING AND DETECTION 审中-公开

    公开(公告)号：US20200179926A1

    公开(公告)日：2020-06-11

    申请号：US16665559

    申请日：2019-10-28

    Applicant: Ultima Genomics, Inc.

    Inventor： Nathan BECKETT ,  Nathan CASWELL

    IPC: B01L3/00 ,  G01N33/487 ,  G01N7/02

    Abstract: Provided herein are methods for processing and/or detecting a sample. A method can comprise providing a barrier between a first region and a second region, wherein the first region comprises the sample, wherein the barrier maintains the first region at a first atmosphere that is different than a second atmosphere of the second region, wherein a portion of the barrier comprises a fluid in coherent motion; and using a detector at least partially contained in the first region to detect one or more signals from the sample while the first region is maintained at the first atmosphere that is different than the second atmosphere of the second region. The portion of the barrier comprising fluid may have a pressure lower than the first atmosphere, the second atmosphere, or both.

    Implementing barriers for controlled environments during sample processing and detection
    78.
    发明授权
    Implementing barriers for controlled environments during sample processing and detection 有权

    公开(公告)号：US10512911B1

    公开(公告)日：2019-12-24

    申请号：US16440026

    申请日：2019-06-13

    Applicant: Ultima Genomics, Inc.

    Inventor： Nathan Beckett ,  Nathan Caswell

    IPC: B01L3/00 ,  G01N7/02 ,  G01N33/487

    Abstract: Provided herein are methods for processing and/or detecting a sample. A method can comprise providing a barrier between a first region and a second region, wherein the first region comprises the sample, wherein the barrier maintains the first region at a first atmosphere that is different than a second atmosphere of the second region, wherein a portion of the barrier comprises a fluid in coherent motion; and using a detector at least partially contained in the first region to detect one or more signals from the sample while the first region is maintained at the first atmosphere that is different than the second atmosphere of the second region. The portion of the barrier comprising fluid may have a pressure lower than the first atmosphere, the second atmosphere, or both.

    Accelerated sequencing methods
    80.
    发明授权
    Accelerated sequencing methods 有权

    公开(公告)号：US12209278B2

    公开(公告)日：2025-01-28

    申请号：US17822760

    申请日：2022-08-26

    Applicant: Ultima Genomics, Inc.

    Inventor： Mark Pratt ,  Gilad Almogy ,  Dumitru Brinza ,  Eliane Trepagnier ,  Omer Barad ,  Yoav Etzioni ,  Florian Oberstrass

    IPC: C12Q1/68 ,  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.

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