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    Systems and Methods for Error Correction in DNA Sequencing
    13.
    发明申请
    Systems and Methods for Error Correction in DNA Sequencing 审中-公开
    DNA测序中错误校正的系统和方法

    公开(公告)号：US20160188794A1

    公开(公告)日：2016-06-30

    申请号：US14951964

    申请日：2015-11-25

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Marcin Sikora ,  Alan Blanchard

    IPC: G06F19/20

    CPC classification number: G16B25/00 ,  C12Q1/6869 ,  C12Q1/6874 ,  G16B30/00 ,  G16B99/00 ,  C12Q2565/102 ,  C12Q2521/501

    Abstract: Disclosed are systems and methods for polynucleotide sequencing where detection and correction of base calling errors can be achieved without reliance on a reference sequence. In certain embodiments, redundant information can be introduced during measurement so as to allow such detection of errors. Such redundant information and measurements can be facilitated by encoding of nucleotide sequence being measured. Various examples of such encoding, redundancy introduction, and decoding are provided.

    Abstract translation: 公开了用于多核苷酸测序的系统和方法，其中可以在不依赖参考序列的情况下实现基本呼叫错误的检测和校正。 在某些实施例中，可以在测量期间引入冗余信息，以允许这种错误检测。 可以通过编码被测量的核苷酸序列来促进这种冗余信息和测量。 提供了这种编码，冗余引入和解码的各种示例。

    Methods and systems for modeling phasing effects in sequencing using termination chemistry
    15.
    发明授权
    Methods and systems for modeling phasing effects in sequencing using termination chemistry 有权

    公开(公告)号：US11636922B2

    公开(公告)日：2023-04-25

    申请号：US16550374

    申请日：2019-08-26

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Christian Koller ,  Marcin Sikora ,  Peter Vander Horn

    IPC: G16B40/10 ,  G16B20/00 ,  G16B25/00 ,  G16B30/00 ,  C12Q1/6869 ,  G16B5/00

    Abstract: A method for nucleic acid sequencing includes receiving observed or measured nucleic acid sequencing data from a sequencing instrument that receives and processes a sample nucleic acid in a termination sequencing-by-synthesis process. The method also includes generating a set of candidate sequences of bases for the observed or measured nucleic acid sequencing data by determining a predicted signal for candidate sequences using a simulation framework. The simulation framework incorporates an estimated carry forward rate (CFR), an estimated incomplete extension rate (IER), an estimated droop rate (DR), an estimated reactivated molecules rate (RMR), and an estimated termination failure rate (TFR), the RMR being greater than or equal to zero and the TFR being lesser than one. The method also includes identifying, from the set of candidate sequences of bases, one candidate sequence leading to optimization of a solver function as corresponding to the sequence for the sample nucleic acid.

    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR MAKING BASE CALLS IN NUCLEIC ACID SEQUENCING
    17.
    发明申请
    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR MAKING BASE CALLS IN NUCLEIC ACID SEQUENCING 审中-公开

    公开(公告)号：US20190170680A1

    公开(公告)日：2019-06-06

    申请号：US16196502

    申请日：2018-11-20

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Marcin Sikora ,  Melville Davey ,  Christian Koller ,  Simon Cawley ,  Alan Williams ,  David Kulp

    IPC: G01N27/414 ,  G16B30/00

    Abstract: A method for nucleic acid sequencing includes receiving a plurality of observed or measured signals indicative of a parameter observed or measured for a plurality of defined spaces; determining, for at least some of the defined spaces, whether the defined space comprises one or more sample nucleic acids; processing, for at least some of the defined spaces, the observed or measured signal to improve a quality of the observed or measured signal; generating, for at least some of the defined spaces, a set of candidate sequences of bases for the defined space using one or more metrics adapted to associate a score or penalty to the candidate sequences of bases; and selecting the candidate sequence leading to a highest score or a lowest penalty as corresponding to the correct sequence for the one or more sample nucleic acids in the defined space.

    Control nucleic acid sequences for use in sequencing-by-synthesis and methods for designing the same
    18.
    发明授权
    Control nucleic acid sequences for use in sequencing-by-synthesis and methods for designing the same 有权

    公开(公告)号：US09926597B2

    公开(公告)日：2018-03-27

    申请号：US14338682

    申请日：2014-07-23

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Marcin Sikora

    IPC: C12Q1/68 ,  G06F19/22

    CPC classification number: C12Q1/6874 ,  G06F19/22 ,  C12Q2537/157 ,  C12Q2545/101

    Abstract: A method for nucleic acid sequencing includes (a) disposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands comprising a test or control sequence; (b) exposing a plurality of the template polynucleotide strands in the defined spaces to a series of flows of nucleotide species flowed according to a predetermined ordering; and (c) determining sequence information for a plurality of the template polynucleotide strands in the defined spaces based on the flows of nucleotide species to generate a plurality of sequencing reads corresponding to the template polynucleotide strands, wherein the test or control sequence comprises a sequence determined by identifying, using a variant caller, loci with systematic errors present in a plurality of sequencing runs included in a training set of sequencing runs.

    SYSTEM AND METHOD FOR DETERMINING COPIES-PER-UNIT-VOLUME USING PCR AND FLOW CONTROL OF DROPLETS
    19.
    发明申请
    SYSTEM AND METHOD FOR DETERMINING COPIES-PER-UNIT-VOLUME USING PCR AND FLOW CONTROL OF DROPLETS 审中-公开
    使用PCR和流量控制法确定复制单位体积的系统和方法

    公开(公告)号：US20160208342A1

    公开(公告)日：2016-07-21

    申请号：US15080801

    申请日：2016-03-25

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Gordon A. Janaway ,  Mark Andersen ,  Kornelija Zgonc ,  Michael C. Pallas ,  Marcin Sikora ,  Casey R. McFarland ,  Ferrier N. Le ,  Haopeng Wang ,  Jian Gong ,  Gothami Padmabandu

    IPC: C12Q1/68 ,  G01N21/64

    CPC classification number: C12Q1/6886 ,  C12Q1/686 ,  C12Q2600/158 ,  C12Q2600/178 ,  G01N21/6486 ,  C12Q2537/16 ,  C12Q2563/143 ,  C12Q2563/159 ,  C12Q2565/626

    Abstract: Methods and systems for quantification of a target nucleic acid in a sample are provided. The method includes forming a plurality of discrete sample portions. Each of the plurality of discrete sample portions comprising a portion of the sample, and a reaction mixture. The method further includes amplifying the plurality of discrete sample portions to form a plurality of discrete processed sample portions. At least one discrete processed sample portion containing nucleic acid amplification reaction products. Fluorescence signals are detected from the at least one of the plurality of discrete processed sample portions to determine a presence of the at least one target nucleic acid. The method also includes determining the respective volumes of the plurality of the plurality of discrete processed sample portions, and estimating the number of copies-per-unit-volume of the at least one target nucleic acid in the sample. Estimating the number of copies-per-unit-volume is based on the number of discrete processed sample portions determined to contain the at least one target nucleic acid therein.

    Abstract translation: 提供了用于定量样品中靶核酸的方法和系统。 该方法包括形成多个离散的样本部分。 多个离散样品部分中的每一个包含样品的一部分和反应混合物。 该方法还包括放大多个离散样本部分以形成多个离散处理的样本部分。 至少一个离散加工的样品部分含有核酸扩增反应产物。 从所述多个离散处理样品部分中的至少一个检测荧光信号以确定所述至少一种靶核酸的存在。 该方法还包括确定多个多个离散处理的样本部分的相应体积，以及估计样品中至少一个靶核酸的每单位体积的拷贝数。 估计每单位体积的拷贝数是基于确定为在其中含有至少一种靶核酸的离散加工样品部分的数量。

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