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    BARCODE SEQUENCES, AND RELATED SYSTEMS AND METHODS
    1.
    发明申请
    BARCODE SEQUENCES, AND RELATED SYSTEMS AND METHODS 审中-公开
    条形码序列及相关系统和方法

    公开(公告)号：US20160333402A1

    公开(公告)日：2016-11-17

    申请号：US15154499

    申请日：2016-05-13

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Christian KOLLER ,  Michael D. ALLEN

    IPC: C12Q1/68 ,  G06F19/22

    CPC classification number: C12Q1/6874 ,  G16B30/00

    Abstract: Methods, system, and kits are provided for sample identification, and, more specifically, for designing, and/or making, and/or using sample discriminating codes or barcodes for identifying sample nucleic acids or other biomolecules or polymers. For example, a plurality of flowspace codewords may be generated, the codewords comprising a string of characters. A location for at least one padding character within the flowspace codewords may be determined. The padding character may be inserted into the flowspace codewords at the determined location. After the inserting, a plurality of the flowspace codewords may be selected based on satisfying a predetermined minimum distance criteria, wherein the selected codewords correspond to valid base space sequences according to a predetermined flow order. And the barcode sequences corresponding to the selected codewords may be manufactured.

    Abstract translation: 提供方法，系统和试剂盒用于样品鉴定，更具体地说，用于设计和/或制作和/或使用用于鉴定样品核酸或其它生物分子或聚合物的样品鉴别代码或条形码。 例如，可以生成多个流空间码字，码字包括一串字符。 可以确定流行空间码字内的至少一个填充字符的位置。 填充字符可以被插入到确定位置处的流空间码字中。 在插入之后，可以基于满足预定的最小距离标准来选择多个流空间码字，其中所选择的码字根据预定的流顺序对应于有效的基本空间序列。 并且可以制造对应于所选择的码字的条形码序列。

    METHODS AND SYSTEMS FOR MODELING PHASING EFFECTS IN SEQUENCING USING TERMINATION CHEMISTRY
    2.
    发明申请
    METHODS AND SYSTEMS FOR MODELING PHASING EFFECTS IN SEQUENCING USING TERMINATION CHEMISTRY 审中-公开

    公开(公告)号：US20200043571A1

    公开(公告)日：2020-02-06

    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 ,  G16B5/00 ,  G16B20/00 ,  G16B25/00 ,  G16B30/00 ,  C12Q1/6869

    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.

    BARCODE SEQUENCES, AND RELATED SYSTEMS AND METHODS
    3.
    发明申请
    BARCODE SEQUENCES, AND RELATED SYSTEMS AND METHODS 有权

    公开(公告)号：US20210304843A1

    公开(公告)日：2021-09-30

    申请号：US17202408

    申请日：2021-03-16

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Christian KOLLER ,  Michael D. ALLEN

    IPC: G16B30/00 ,  C12Q1/6869 ,  C12Q1/6874

    Abstract: Methods, system, and kits are provided for sample identification, and, more specifically, for designing, and/or making, and/or using sample discriminating codes or barcodes for identifying sample nucleic acids or other biomolecules or polymers. For example, a plurality of flowspace codewords may be generated, the codewords comprising a string of characters. A location for at least one padding character within the flowspace codewords may be determined. The padding character may be inserted into the flowspace codewords at the determined location. After the inserting, a plurality of the flowspace codewords may be selected based on satisfying a predetermined minimum distance criteria, wherein the selected codewords correspond to valid base space sequences according to a predetermined flow order. And the barcode sequences corresponding to the selected codewords may be manufactured.

    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR MAKING BASE CALLS IN NUCLEIC ACID SEQUENCING
    4.
    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。

    Systems and Methods for Detecting Homopolymer Insertions/Deletions
    6.
    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。

    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR REPEAT SEQUENCING
    7.
    发明申请
    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR REPEAT SEQUENCING 有权

    公开(公告)号：US20250019759A1

    公开(公告)日：2025-01-16

    申请号：US18782286

    申请日：2024-07-24

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Earl HUBBELL ,  Christian KOLLER ,  Nils HOMER

    IPC: C12Q1/6869 ,  G16B30/00

    Abstract: A method for sequencing a nucleic acid template includes: (a) performing a first sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a first predetermined ordering of nucleotides and/or reagents to obtain a first sequencing result; (b) after the first sequencing process, performing a second sequencing process including flowing nucleotides and/or reagents to the nucleic acid template according to a second predetermined ordering of nucleotides and/or reagents to obtain a second sequencing result, the second predetermined ordering of nucleotides and/or reagents being different from the first predetermined ordering of nucleotides and/or reagents and at least one of the first and second predetermined orderings of nucleotides and/or reagents being designed for repeat sequencing; and (c) determining a sequence of bases corresponding to at least a portion of the nucleic acid template using both the first sequencing result and the second sequencing result.

    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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