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    Control nucleic acid sequences for use in sequencing-by-synthesis and methods for designing the same
    11.
    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
    12.
    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。

    Systems and methods for genotyping by angle configuration search
    16.
    发明授权
    Systems and methods for genotyping by angle configuration search 有权

    公开(公告)号：US11227668B2

    公开(公告)日：2022-01-18

    申请号：US15889177

    申请日：2018-02-05

    Applicant: Life Technologies Corporation

    Inventor： Marcin Sikora

    IPC: G16B20/20 ,  G06F16/24 ,  G16B20/00 ,  G16B40/30 ,  G16B40/20 ,  G16B40/00 ,  G16B20/40

    Abstract: Methods and systems for the analysis of genotyping data are presented. According to various embodiments of methods and systems, an angle configuration search may be performed. In various embodiments, an exhaustive search over the entirety of an angle configuration space may be performed to provide a fit to a plurality of angles determined for a plurality of points in a data set generated from a plurality of biological samples. For various embodiments, the angle configuration space may be defined to ensure that a global fit may be determined. According to various methods and systems, a data base of possible angle configurations may be searched, in which each angle configuration may include three angles. According to various methods and systems, a data base of possible angle configurations may include for each angle configuration a probability that the angle configuration may occur.

    Methods and Systems for a Digital PCR Experiment Designer
    17.
    发明申请
    Methods and Systems for a Digital PCR Experiment Designer 审中-公开
    数字PCR实验设计器的方法和系统

    公开(公告)号：US20150278437A1

    公开(公告)日：2015-10-01

    申请号：US14428312

    申请日：2013-09-13

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Nivedita Sumi Majumdar ,  Thomas Wessel ,  David C. Woo ,  Marcin Sikora ,  Gordon A. Janaway ,  Shweta Raizada ,  Joanna Lankester ,  Jeffrey A. Marks ,  Daniel Wessel

    IPC: G06F19/20 ,  C12Q1/68

    CPC classification number: G16B25/00 ,  C12Q1/686 ,  G16B40/00

    Abstract: A computer-implemented method for designing a digital PCR (dPCR) experiment is provided. The method includes receiving, from a user, a selection of optimization type. The optimization type may be maximizing the dynamic range, minimizing the number of substrates including reaction sites needed for the experiment, determining a dilution factor, or determining the lower limit of detection, for example. The method further includes receiving, from the user, a precision measure for an experiment, and a minimum concentration of a target in a reaction site for the experiment. The method also includes determining a set of dPCR experiment design factors for the experiment based on the optimization type. The set of dPCR experiment design factors is then displayed to the user.

    Abstract translation: 提供了一种用于设计数字PCR（dPCR）实验的计算机实现方法。 该方法包括从用户接收优化类型的选择。 优化类型可以使动态范围最大化，例如最小化包括实验所需的反应位点，确定稀释因子或确定检测下限的底物数量。 该方法还包括从用户接收实验的精确度量，以及用于实验的反应部位中靶的最小浓度。 该方法还包括基于优化类型确定实验的一组dPCR实验设计因子。 然后将该组dPCR实验设计因子显示给用户。

    Systems and Methods for Genotyping by Angle Configuration Search
    18.
    发明申请
    Systems and Methods for Genotyping by Angle Configuration Search 审中-公开
    通过角度配置搜索进行基因分型的系统和方法

    公开(公告)号：US20140365141A1

    公开(公告)日：2014-12-11

    申请号：US14463536

    申请日：2014-08-19

    Applicant: Life Technologies Corporation

    Inventor： Marcin Sikora

    IPC: G06F19/18 ,  G06F17/30

    CPC classification number: G16B20/00 ,  G06F16/24 ,  G16B40/00

    Abstract: Methods and systems for the analysis of genotyping data are presented. According to various embodiments of methods and systems, an angle configuration search may be performed. In various embodiments, an exhaustive search over the entirety of an angle configuration space may be performed to provide a fit to a plurality of angles determined for a plurality of points in a data set generated from a plurality of biological samples. For various embodiments, the angle configuration space may be defined to ensure that a global fit may be determined. According to various methods and systems, a data base of possible angle configurations may be searched, in which each angle configuration may include three angles. According to various methods and systems, a data base of possible angle configurations may include for each angle configuration a probability that the angle configuration may occur.

    Abstract translation: 提出了分析基因分型数据的方法和系统。 根据方法和系统的各种实施例，可以执行角度配置搜索。 在各种实施例中，可以执行整个角度配置空间的详尽搜索，以提供对从多个生物样本产生的数据集中的多个点确定的多个角度的拟合。 对于各种实施例，可以定义角度配置空间以确保可以确定全局拟合。 根据各种方法和系统，可以搜索可能的角度配置的数据库，其中每个角度配置可以包括三个角度。 根据各种方法和系统，可能的角度配置的数据库可以包括对于每个角度配置可能发生角度配置的概率。

    System and method for determining copies-per-unit-volume using PCR and flow control of droplets
    19.
    发明授权
    System and method for determining copies-per-unit-volume using PCR and flow control of droplets 有权

    公开(公告)号：US12275997B2

    公开(公告)日：2025-04-15

    申请号：US17976128

    申请日：2022-10-28

    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: C12Q1/6886 ,  C12Q1/686 ,  G01N21/64

    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.

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