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    Systems and Methods for Detecting Homopolymer Insertions/Deletions
    2.
    发明申请
    Systems and Methods for Detecting Homopolymer Insertions/Deletions 审中-公开
    用于检测均聚物插入/缺失的系统和方法

    公开(公告)号：US20140052381A1

    公开(公告)日：2014-02-20

    申请号：US13966378

    申请日：2013-08-14

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Sowmi UTIRAMERUR ,  Dumitru BRINZA ,  Marcin SIKORA ,  Christian KOLLER ,  Earl HUBBELL ,  Chantal ROTH ,  Rajesh GOTTIMUKKALA

    IPC: G06F19/22

    CPC classification number: G16B30/00

    Abstract: Systems and method for determining variants can receive mapped reads and determine a distribution of matched-filter residuals distribution from a plurality of reads at a homopolymer region. The distribution of matched-filter residuals can be fit to uni-modal and bi-modal models. Based on the model that best fits the distribution of matched-filter residuals, the heterozygosity of the sample and the absence or presence of an insertion/deletion in the homopolymer can be determined.

    Abstract translation: 用于确定变体的系统和方法可以接收映射读取并且从均聚物区域的多次读取确定匹配滤波器残差分布的分布。 匹配滤波器残差的分布可以适用于单模和双模态模型。 基于最适合匹配滤波器残差分布的模型，可以确定样品的杂合度和均聚物中插入/缺失的不存在或不存在。

    CONTROL NUCLEIC ACID SEQUENCES FOR USE IN SEQUENCING-BY-SYNTHESIS AND METHODS FOR DESIGNING THE SAME
    3.
    发明申请
    CONTROL NUCLEIC ACID SEQUENCES FOR USE IN SEQUENCING-BY-SYNTHESIS AND METHODS FOR DESIGNING THE SAME 有权

    公开(公告)号：US20210102249A1

    公开(公告)日：2021-04-08

    申请号：US16999001

    申请日：2020-08-20

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Marcin SIKORA

    IPC: C12Q1/6874 ,  G16B30/00

    Abstract: A method for designing test or control sequences may include identifying, using a variant caller, loci with systematic errors present in a plurality of sequencing runs included in a training set of sequencing runs obtained using sequencing-by-synthesis; and selecting a representative set of loci, including selecting from the identified loci an approximately equal number of loci involving errors in A, T, C, and G homopolymers and selecting from the identified loci an approximately equal number of loci involving homopolymers having a length of two, three, and four.

    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR MAKING BASE CALLS IN NUCLEIC ACID SEQUENCING
    5.
    发明申请
    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR MAKING BASE CALLS IN NUCLEIC ACID SEQUENCING 审中-公开
    方法，系统和计算机可读介质，用于在核酸序列中进行基准测量

    公开(公告)号：US20130090860A1

    公开(公告)日：2013-04-11

    申请号：US13645058

    申请日：2012-10-04

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Marcin SIKORA ,  Earl HUBBELL ,  Simon CAWLEY ,  Christian KOLLER

    IPC: G06F19/20

    CPC classification number: G16B25/00 ,  G01N27/27 ,  G01N27/4145 ,  G16B30/00

    Abstract: A method for nucleic acid sequencing includes: receiving a signal comprising measurements of a parameter measured in response to a plurality of nucleotide flows flowed in a space comprising a sample nucleic acid; normalizing the signal to obtain a normalized signal; adaptively normalizing the normalized signal to obtain an adaptively normalized signal; and predicting a sequence of base calls corresponding to the sample nucleic acid using the adaptively normalized signal.

    Abstract translation: 用于核酸测序的方法包括：接收包含响应于在包含样品核酸的空间中流动的多个核苷酸流测量的参数的测量值的信号; 对信号进行归一化以获得归一化信号; 自适应地归一化归一化信号以获得自适应归一化信号; 以及使用自适应归一化信号来预测对应于样本核酸的碱基呼叫序列。

    CONTROL NUCLEIC ACID SEQUENCES FOR USE IN SEQUENCING-BY-SYNTHESIS AND METHODS FOR DESIGNING THE SAME
    6.
    发明申请
    CONTROL NUCLEIC ACID SEQUENCES FOR USE IN SEQUENCING-BY-SYNTHESIS AND METHODS FOR DESIGNING THE SAME 有权
    按顺序合成使用的控制核酸序列及其设计方法

    公开(公告)号：US20150031551A1

    公开(公告)日：2015-01-29

    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.

    Abstract translation: 用于核酸测序的方法包括（a）在设置在传感器阵列上的多个限定的空间中设置多个模板多核苷酸链，至少一些模板多核苷酸链包含测试或对照序列; （b）将限定空间中的多个模板多核苷酸链在暴露于根据预定顺序流动的一系列核苷酸类型的流中; 基于核苷酸物种的流量，确定多个定义空间中的模板多核苷酸链的序列信息，以产生对应于模板多核苷酸链的多个测序读数，其中测试或控制序列包含确定的序列 通过识别，使用变体呼叫者，具有存在于测序运行的训练集中的多个测序运行中的系统误差的基因座。

    Methods and Apparatuses for Estimating Parameters in a Predictive Model for Use in Sequencing-by-Synthesis
    7.
    发明申请
    Methods and Apparatuses for Estimating Parameters in a Predictive Model for Use in Sequencing-by-Synthesis 审中-公开
    用于按序排序合成的预测模型中估计参数的方法和装置

    公开(公告)号：US20140051584A1

    公开(公告)日：2014-02-20

    申请号：US13967665

    申请日：2013-08-15

    Applicant: Life Technologies Corporation

    Inventor： Melville DAVEY ,  Michael MEYER ,  Marcin SIKORA ,  Simon CAWLEY ,  Kirk PASTORIAN

    IPC: C12Q1/68

    CPC classification number: C12Q1/6874 ,  G06F19/10 ,  C12Q2537/165

    Abstract: A method of estimating a parameter related to sequencing of a sample nucleic acid template includes: receiving signal data relating to nucleotide incorporation events resulting from a series of flows of nucleotides onto an array of wells including (i) a first well containing the sample nucleic acid template and (ii) a plurality of other sample-containing wells; determining sequence information for the sample nucleic acid template using signal data from the first well; and constructing a phase-state model for a set of nucleotide flows that contributed at least in part to the sequence information, wherein the model includes a signal correction parameter that is determined using signal data from the plurality of other sample-containing wells.

    Abstract translation: 估计与样品核酸模板的测序有关的参数的方法包括：接收与一系列核苷酸产生的核苷酸掺入事件相关的信号数据，其包含（i）包含样品核酸的第一阱 模板和（ii）多个其他含样品的孔; 使用来自第一孔的信号数据确定样品核酸模板的序列信息; 以及构建至少部分地对所述序列信息贡献的一组核苷酸流的相态模型，其中所述模型包括使用来自所述多个其它含样品孔的信号数据确定的信号校正参数。

    METHODS AND SYSTEMS FOR MODELING PHASING EFFECTS IN SEQUENCING USING TERMINATION CHEMISTRY
    10.
    发明申请
    METHODS AND SYSTEMS FOR MODELING PHASING EFFECTS IN SEQUENCING USING TERMINATION CHEMISTRY 审中-公开
    使用终止化学序列建模相关效应的方法和系统

    公开(公告)号：US20150100247A1

    公开(公告)日：2015-04-09

    申请号：US14506520

    申请日：2014-10-03

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Christian KOLLER ,  Marcin SIKORA ,  Peter VANDER HORN

    IPC: G06F19/22 ,  G06F19/12 ,  G06F19/18

    CPC classification number: G16B40/10 ,  C12Q1/6869 ,  G16B5/00 ,  G16B20/00 ,  G16B25/00 ,  G16B30/00

    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.

    Abstract translation: 用于核酸测序的方法包括接收来自测序仪器的观测或测量的核酸测序数据，所述测序仪器在终止测序合成过程中接收和处理样品核酸。 该方法还包括通过使用模拟框架确定候选序列的预测信号来产生用于观察或测量的核酸测序数据的一组候选碱基序列。 模拟框架包含估计结转率（CFR），估计不完全扩展率（IER），估计下降率（DR），估计的再活化分子率（RMR）和估计的终止失败率（TFR）， RMR大于或等于零，TFR小于1。 该方法还包括从候选碱基序列的集合中鉴定出一个候选序列，导致解析函数的优化对应于样品核酸的序列。

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