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    Methods and apparatus that increase sequencing-by-binding efficiency
    31.
    发明授权
    Methods and apparatus that increase sequencing-by-binding efficiency 有权

    公开(公告)号：US12180545B2

    公开(公告)日：2024-12-31

    申请号：US17876893

    申请日：2022-07-29

    Applicant: Pacific Biosciences of California, Inc.

    Inventor： Sean Stromberg ,  John Vieceli ,  Kandaswamy Vijayan ,  Arnold Oliphant

    IPC: C12Q1/68 ,  C12Q1/6832 ,  C12Q1/6853 ,  C12Q1/6869 ,  C12Q1/6874

    Abstract: A method of determining a nucleic acid sequence that includes steps of: (a) contacting a primed template nucleic acid with a series of mixtures for forming ternary complexes, wherein each of the mixtures includes a polymerase and nucleotide cognates for at least two different base types suspected of being present at the next template position of the template nucleic acid; (b) monitoring the next template position for ternary complexes formed by the series of mixtures, wherein a signal state indicates presence or absence of ternary complex formed at the next template position by each individual mixture, thereby determining a series of signal states that encodes a base call for the next template position; and (c) decoding the series of signal states to distinguish a correct base call for the next template position from an error in the base call.

    METHODS AND SYSTEMS FOR GENETIC ANALYSIS
    33.
    发明申请
    METHODS AND SYSTEMS FOR GENETIC ANALYSIS 有权

    公开(公告)号：US20240425920A1

    公开(公告)日：2024-12-26

    申请号：US18824319

    申请日：2024-09-04

    Applicant: Personalis, Inc.

    Inventor： Gabor T. Bartha ,  Gemma Chandratillake ,  Richard Chen ,  Sarah Garcia ,  Hugo Yu Kor Lam ,  Mark R. Pratt ,  John West

    IPC: C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6869 ,  G16B20/00 ,  G16B20/10 ,  G16B20/20 ,  G16B30/00 ,  G16B35/00 ,  G16B35/10 ,  G16B99/00 ,  G16C20/60

    Abstract: This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

    EPITRANSCRIPTOME EVALUATION
    34.
    发明申请
    EPITRANSCRIPTOME EVALUATION 有权

    公开(公告)号：US20240425914A1

    公开(公告)日：2024-12-26

    申请号：US18687476

    申请日：2022-08-29

    Applicant: HTG Molecular Diagnostics, Inc.

    Inventor： Debrah Thompson

    IPC: C12Q1/6869 ,  C12Q1/6804 ,  C12Q1/6876

    Abstract: The present disclosure provides methods of using quantitative nuclease protection sequencing (qNPS) methods to evaluate epitranscriptomes. The disclosed methods capture nucleic acid molecules that are modified as a result of exposure to an agent, such as stress, a mutagen, a microbe (such as a pathogen), or therapeutic agent. The resulting modified nucleic acid molecules are then directly or indirectly sequenced using nuclease protection probes (NPPs) and qNPS, allowing for the detection of target and off-target modifications of an epitranscriptome.

    Sequencing using non-natural nucleotides
    35.
    发明授权
    Sequencing using non-natural nucleotides 有权

    公开(公告)号：US12173365B2

    公开(公告)日：2024-12-24

    申请号：US17713934

    申请日：2022-04-05

    Applicant: Ultima Genomics, Inc.

    Inventor： Gilad Almogy ,  Linda Lee

    IPC: C12Q1/6869 ,  C12Q1/6806

    Abstract: The present disclosure provides methods and systems for nucleic acid sequencing. Such systems and methods may achieve context-independent incorporation, have reduced context-dependence or have context-dependence that is amenable to calibration and modeling. Such systems and methods may also reduce misincorporation.

    SYSTEMS, DEVICES, AND METHODS OF A DATA PIPELINE
    37.
    发明申请
    SYSTEMS, DEVICES, AND METHODS OF A DATA PIPELINE 有权

    公开(公告)号：US20240417752A1

    公开(公告)日：2024-12-19

    申请号：US18742805

    申请日：2024-06-13

    Applicant: Regeneron Pharmaceuticals, Inc. ,  Intellia Therapeutics, Inc.

    Inventor： Ayush Saxena ,  Rong-sen Calvin Chen

    IPC: C12N15/86 ,  C12Q1/6869

    Abstract: Disclosed are data pipelines for string extraction, clustering, and comparison. A method may include extracting, from each plasmid genome sequence sequenced from genomes of plasmids, based on the presence of fixed flanking sequence markers (FFSMs) in the plasmid genome sequence, sequence regions. Each sequence region is within the FFSMs and includes a candidate inverted terminal repeat (ITR) sequence. The example method further includes clustering, based on perfect sequence identity, two or more sequence regions of the sequence regions to generate a clusters, merging, based on an alignment between their corresponding sequence regions, two or more clusters of the clusters; when a single cluster remains, identifying, based on a local alignment, a genotype of a candidate ITR sequence of the single cluster, and manufacturing, based on the genotype of the candidate ITR sequence, a plurality of AAV vectors using plasmids having ITR sequences with the genotype of the candidate ITR sequence.

    Methods and systems for evaluating microsatellite instability status
    38.
    发明授权
    Methods and systems for evaluating microsatellite instability status 有权

    公开(公告)号：US12168800B2

    公开(公告)日：2024-12-17

    申请号：US18529188

    申请日：2023-12-05

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Sameh El-Difrawy

    IPC: G16B40/20 ,  C12Q1/6809 ,  C12Q1/6869 ,  C12Q1/6886 ,  G16B20/00 ,  G16B50/00

    Abstract: Methods for evaluating microsatellite instability (MSI) analyze nucleic acid sequence reads corresponding to a plurality of marker regions for MSI. The marker regions may include long homopolymers and/or short tandem repeats (STRs). For a target homopolymer, a histogram of homopolymer signal values is calculated based on flow space signal measurements for the homopolymer region in the sequence reads. A score per marker based on features of the histogram of homopolymer signal values is determined for each marker region corresponding to the target homopolymers. For a target STR, the method includes calculating a histogram of repeat lengths for sequence reads corresponding to the marker region of the target STR. A score per STR marker is calculated based on features of the histogram of repeat lengths. A plurality of per marker scores may be combined to form a total MSI score for the sample.

    Recombinant KOD polymerase
    39.
    发明授权
    Recombinant KOD polymerase 有权

    公开(公告)号：US12168785B2

    公开(公告)日：2024-12-17

    申请号：US17270489

    申请日：2018-09-03

    Applicant: BGI SHENZHEN

    Inventor： Lili Zhai ,  Lin Wang ,  Wenwei Zhang ,  Yuliang Dong ,  Yue Zheng ,  Fen Liu

    IPC: C12Q1/68 ,  C12N9/12 ,  C12Q1/6806 ,  C12Q1/6869

    Abstract: Provided is a recombinant KOD polymerase, which is the following A) or B): the polymerase shown in A) is a protein having DNA polymerase activity that is obtained by modifying amino acid residues in at least one of the following 18 positions in a wild-type KOD DNA polymerase amino acid sequence: 675th, 385th, 710th, 674th, 735th, 736th, 606th, 709th, 347th, 349th, 590th, 676th, 389th, 589th, 680th, 384th, 496th and 383rd; the polymerase described by B) is a protein having DNA polymerase activity that is derived from A) by adding a tag sequence to an end of the amino acid sequence of the protein shown in A).

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