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    ENGINEERED POLYMERASES FOR IMPROVED SEQUENCING
    1.
    发明申请
    ENGINEERED POLYMERASES FOR IMPROVED SEQUENCING 有权

    公开(公告)号：US20220235336A1

    公开(公告)日：2022-07-28

    申请号：US17564500

    申请日：2021-12-29

    申请人： OMNIOME, INC.

    发明人： Pinar IYIDOGAN

    IPC分类号： C12N9/12 ,  C12P19/34 ,  C12Q1/6874

    摘要： Provided are nucleic acids encoding engineered polymerases comprising at least one modification in a motif A and/or at least one modification in a motif B of the polymerase and engineered polymerases encoded by the nucleic acids. Also provided are engineered DNA polymerases comprising a variant of SEQ ID NO:1, SEQ ID NO:2, or SEQ ID NO:3, the variant being at least 80% identical to SEQ ID NO:1, SEQ ID NO:2 or SEQ ID NO:3 and comprising an amino acid substitution at one or more positions selected from the group consisting of L408, Y409, P410, R484, A/L485, and I486. Methods, vectors, kits, and compositions comprising the nucleic acids and compositions, methods and kits comprising the engineered polymerases are also provided.

    METHODS AND COMPOSITIONS FOR CAPPING NUCLEIC ACIDS
    4.
    发明申请
    METHODS AND COMPOSITIONS FOR CAPPING NUCLEIC ACIDS 审中-公开

    公开(公告)号：US20200032322A1

    公开(公告)日：2020-01-30

    申请号：US16657051

    申请日：2019-10-18

    申请人： Omniome, Inc.

    发明人： Hari SUBRAMANIAN ,  Chad FLEISCHER ,  Denis MALYSHEV

    IPC分类号： C12Q1/6811 ,  C12Q1/682

    摘要： A method for identifying a nucleic acid template that include (a) providing a plurality of primer-template hybrids, wherein a first hybrid of the plurality includes a first template hybridized to a first primer, and wherein a second hybrid of the plurality includes a second template hybridized to a second primer, the second primer having a ternary complex inhibitor moiety at the 3′ end; (b) delivering polymerases and nucleotides to the plurality, whereby the first hybrid binds a polymerase and nucleotide to form a stabilized ternary complex and whereby the second hybrid does not bind a polymerase and nucleotide to form a stabilized ternary complex; and (c) detecting the stabilized ternary complex to identify the first template.

    ACCURACY OF BASE CALLS IN NUCLEIC ACID SEQUENCING METHODS
    5.
    发明申请
    ACCURACY OF BASE CALLS IN NUCLEIC ACID SEQUENCING METHODS 审中-公开

    公开(公告)号：US20190338352A1

    公开(公告)日：2019-11-07

    申请号：US16361034

    申请日：2019-03-21

    申请人： Omniome, Inc.

    发明人： Alex NEMIROSKI ,  Sean STROMBERG ,  John VIECELI

    IPC分类号： C12Q1/6874 ,  G16B30/00

    摘要： A method of determining nucleic acid sequences can include steps of (a) obtaining signal data from a nucleic acid sequencing procedure carried out on an array of nucleic acid features; (b) extracting signals from each nucleic acid feature to produce multiple extracted signal traces that each correlate signal characteristics with sequencing cycle for a particular nucleotide type at a particular nucleic acid feature; (c) comparing the series of signals for different nucleotide types at each of the features to distinguish a candidate base call from background signals for each cycle at each feature; (d) applying a baseline adjustment to each series of signals based on the extracted background signals; and (e) comparing the adjusted signal traces for different nucleotide types at each of the features, thereby distinguishing adjusted signals having characteristics of a base call from adjusted background signals for each cycle at each feature.

    Methods and apparatus that increase sequencing-by-binding efficiency
    8.
    发明授权
    Methods and apparatus that increase sequencing-by-binding efficiency 有权

    公开(公告)号：US09951385B1

    公开(公告)日：2018-04-24

    申请号：US15712632

    申请日：2017-09-22

    申请人： OMNIOME, INC.

    发明人： Kandaswamy Vijayan ,  Arnold Oliphant

    IPC分类号： C12Q1/68

    CPC分类号： C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6853 ,  C12Q1/6869 ,  C12Q2525/186 ,  C12Q2565/101

    摘要： A method of nucleic acid detection including (a) contacting a primed template with a polymerase, nucleotide cognate of a first base type and nucleotide cognate of a second base type under ternary complex stabilizing conditions; (b) contacting the primed template nucleic acid with a polymerase, nucleotide cognate of the first base type and nucleotide cognate of a third base type under ternary complex stabilizing conditions; (c) examining products of (a) and (b) for signals produced by a ternary complex that includes the primed template nucleic acid, polymerase and next correct nucleotide, wherein signals for the product of (a) are ambiguous for the first and second base type, and signals for the product of (b) are ambiguous for the first and third base type; (d) disambiguating signals acquired in (c) to identify the next correct nucleotide.

    NUCLEIC ACID SEQUENCING METHODS AND SYSTEMS
    9.
    发明申请
    NUCLEIC ACID SEQUENCING METHODS AND SYSTEMS 审中-公开
    核酸序列测序方法和系统

    公开(公告)号：US20170022553A1

    公开(公告)日：2017-01-26

    申请号：US14805381

    申请日：2015-07-21

    申请人： Omniome, Inc.

    发明人： Kandaswamy Vijayan ,  Eugene Tu ,  Mark A. Bernard

    IPC分类号： C12Q1/68

    CPC分类号： C12Q1/6869 ,  C12Q2563/103 ,  C12Q2565/607

    摘要： The present disclosure provides compositions, methods and systems for sequencing a template nucleic acid using a polymerase based, nucleic acid binding reaction involving examination of the interaction between a polymerase and template nucleic acid in the presence of one or more unlabeled nucleotides. The methods rely, in part, on identifying a base of a template nucleic acid during nucleic acid synthesis by controlling the sequencing reaction conditions. Template nucleic acid bases may be identified during an examination step followed by an optional incorporation step.

    摘要翻译： 本公开提供了使用基于聚合酶的核酸结合反应来测序模板核酸的组合物，方法和系统，所述核酸结合反应涉及在一个或多个未标记的核苷酸存在下检测聚合酶和模板核酸之间的相互作用。 该方法部分地依赖于通过控制测序反应条件在核酸合成中鉴定模板核酸的碱基。 模板核酸碱基可以在检查步骤之后，然后是任选的掺入步骤。

    Mitigating adverse impacts of detection systems on nucleic acids and other biological analytes
    10.
    发明授权
    Mitigating adverse impacts of detection systems on nucleic acids and other biological analytes 有权

    公开(公告)号：US11499189B2

    公开(公告)日：2022-11-15

    申请号：US16783488

    申请日：2020-02-06

    申请人： OMNIOME, INC.

    发明人： Min-Jui Richard Shen

    IPC分类号： C12Q1/6869 ,  C12Q1/6876 ,  G01N21/64

    摘要： A method for sequencing a population of nucleic acids, which includes (a) binding the population of nucleic acids with a fractionally labeled mixture of nucleotides, thereby forming a fractionally labeled population of nucleic acids, wherein the mixture includes nucleotide cognates for a common base type in the templates, and wherein a fraction of the nucleotide cognates for the common base type in the mixture are exogenously labeled nucleotides that produce a signal that is not produced by other nucleotide cognates for the common base type in the mixture; (b) detecting the signal from the fractionally labeled population of nucleic acids; and (c) repeating (a) and (b) using a second mixture of the fractionally labeled nucleotides, wherein the fraction of the exogenously labeled nucleotides is higher in the second mixture.