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    SYSTEMS AND METHODS FOR RUN-TIME SEQUENCING RUN QUALITY MONITORING
    2.
    发明申请
    SYSTEMS AND METHODS FOR RUN-TIME SEQUENCING RUN QUALITY MONITORING 有权

    公开(公告)号：US20220072681A1

    公开(公告)日：2022-03-10

    申请号：US17478096

    申请日：2021-09-17

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Yerramalli Subramaniam ,  Puneet Suri ,  Sylvia Chang ,  Chengyong Yang

    IPC: B24B41/06 ,  G16B30/00 ,  G05B11/01 ,  B24B5/04

    Abstract: Systems and methods of providing run-time quality control and monitoring of a single or multiple sequencing runs are provided herein. In some embodiments, the run-time system includes or is in communication with a processor capable of determining various types of run-time information relating to the quality, progress, etc. of various sequencing runs. In some embodiments, the system can also be in communication with a user interface, for example, a GUI, capable of representing and communicating various types of information to a user regarding the quality of the individual or multiple runs, the functioning of the instrument, an error event, etc. Additionally, the system can capable of receiving actionable information from a user via the GUI thereby allowing the user to terminate or repeat various sequencing steps in a particular run, terminate a entire run, terminate all runs, allow a run to proceed, etc.

    Methods, Systems, and Computer Readable Media for Improving Base Calling Accuracy
    3.
    发明申请
    Methods, Systems, and Computer Readable Media for Improving Base Calling Accuracy 审中-公开
    方法，系统和计算机可读媒体，以提高基本呼叫精度

    公开(公告)号：US20140316716A1

    公开(公告)日：2014-10-23

    申请号：US14255528

    申请日：2014-04-17

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Ming Jiang ,  Chengyong Yang ,  Jianxin Zhang

    IPC: G06F19/22

    CPC classification number: G16B30/00

    Abstract: A method includes exposing template polynucleotide strands, sequencing primers, and polymerase to flows of nucleotide species; obtaining a series of measured intensity values and randomly selecting a training subset therefrom; generating series of base calls using a base caller and aligning the series of base calls to a reference genome or sequence using an aligner; determining intensity value thresholds and parameters of a linear transformation corresponding to different homopolymer lengths and nucleotide species; generating series of base calls corresponding to the series of measured intensity values using at least some of the parameters of a linear transformation; and recalibrating the series of base calls corresponding to the plurality of series of measured intensity values using at least some of the intensity value thresholds.

    Abstract translation: 一种方法包括将模板多核苷酸链，测序引物和聚合酶暴露于核苷酸物种的流动; 获得一系列测量的强度值并随机选择训练子集; 使用基本呼叫者产生一系列基本呼叫，并使用对准器将一系列基本呼叫对准参考基因组或序列; 确定对应于不同均聚物长度和核苷酸种类的线性转化的强度值阈值和参数; 使用线性变换的至少一些参数来生成对应于所述一系列测量的强度值的一系列基本呼叫; 以及使用至少一些所述强度值阈值来重新校准对应于所述多个测量强度值序列的一系列基本呼叫。

    Robust Detection Of Variablility In Multiple Sets Of Data
    4.
    发明申请
    Robust Detection Of Variablility In Multiple Sets Of Data 审中-公开
    在多组数据中的可变性的鲁棒检测

    公开(公告)号：US20170046308A1

    公开(公告)日：2017-02-16

    申请号：US15213237

    申请日：2016-07-18

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Chengyong Yang ,  David Woo

    IPC: G06F17/18 ,  G01N21/64

    CPC classification number: G06F17/18 ,  G01D1/14 ,  G01N21/6428 ,  G01N2021/6439

    Abstract: The present teachings comprise systems and methods for calibrating the background or baseline signal in a PCR or other reaction. The background signal derived from detected emissions of sample wells can be subjected to a normalized statistical metric, and be compared to a threshold or other standard to discard outlier cycles or other extraneous data. According to various embodiments, a relative standard deviation (relativeSTD) for the background component can be generated by dividing the standard deviation by the median of differences across all wells, where the difference is defined as the difference between maximum and minimum pixel values of a well. The relativeSTD as a metric is not sensitive to machine-dependent variations in absolute signal output that can be caused by different gain settings, different LED draw currents, different optical paths, or other instrumental variations. More accurate background characterization can be achieved.

    Abstract translation: 本教导包括用于在PCR或其他反应中校准背景或基线信号的系统和方法。 从检测到的样本井的排放导出的背景信号可以经受归一化的统计度量，并与阈值或其他标准进行比较以丢弃异常周期或其他无关数据。 根据各种实施例，可以通过将标准偏差除以所有孔的差异中值来产生背景分量的相对标准偏差（relativeSTD），其中差被定义为井的最大和最小像素值之间的差 。 作为度量的relativeSTD对于可能由不同的增益设置，不同的LED绘制电流，不同的光路或其他工具变化引起的绝对信号输出的机器相关变化不敏感。 可以获得更准确的背景特征。

    SYSTEMS AND METHODS FOR RUN-TIME SEQUENCING RUN QUALITY MONITORING
    5.
    发明申请
    SYSTEMS AND METHODS FOR RUN-TIME SEQUENCING RUN QUALITY MONITORING 有权

    公开(公告)号：US20240391053A1

    公开(公告)日：2024-11-28

    申请号：US18672549

    申请日：2024-05-23

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Yerramalli Subramaniam ,  Chengyong Yang ,  Sylvia Chang ,  Puneet Suri

    IPC: B24B41/06 ,  B24B5/04 ,  G05B11/01 ,  G16B30/00

    Abstract: Systems and methods of providing run-time quality control and monitoring of a single or multiple sequencing runs are provided herein. In some embodiments, the run-time system includes or is in communication with a processor capable of determining various types of run-time information relating to the quality, progress, etc. of various sequencing runs. In some embodiments, the system can also be in communication with a user interface, for example, a GUI, capable of representing and communicating various types of information to a user regarding the quality of the individual or multiple runs, the functioning of the instrument, an error event, etc. Additionally, the system can capable of receiving actionable information from a user via the GUI thereby allowing the user to terminate or repeat various sequencing steps in a particular run, terminate a entire run, terminate all runs, allow a run to proceed, etc.

    Systems and methods for run-time sequencing run quality monitoring
    6.
    发明授权
    Systems and methods for run-time sequencing run quality monitoring 有权

    公开(公告)号：US11135699B2

    公开(公告)日：2021-10-05

    申请号：US15652425

    申请日：2017-07-18

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Yerramalli Subramaniam ,  Puneet Suri ,  Sylvia Chang ,  Chengyong Yang

    IPC: B24B41/06 ,  G16B30/00 ,  G05B11/01 ,  B24B5/04

    Abstract: Systems and methods of providing run-time quality control and monitoring of a single or multiple sequencing runs are provided herein. In some embodiments, the run-time system includes or is in communication with a processor capable of determining various types of run-time information relating to the quality, progress, etc. of various sequencing runs. In some embodiments, the system can also be in communication with a user interface, for example, a GUI, capable of representing and communicating various types of information to a user regarding the quality of the individual or multiple runs, the functioning of the instrument, an error event, etc. Additionally, the system can capable of receiving actionable information from a user via the GUI thereby allowing the user to terminate or repeat various sequencing steps in a particular run, terminate a entire run, terminate all runs, allow a run to proceed, etc.

    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR IMPROVING BASE CALLING ACCURACY
    8.
    发明申请
    METHODS, SYSTEMS, AND COMPUTER READABLE MEDIA FOR IMPROVING BASE CALLING ACCURACY 审中-公开

    公开(公告)号：US20190034584A1

    公开(公告)日：2019-01-31

    申请号：US16055315

    申请日：2018-08-06

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Ming Jiang ,  Chengyong Yang ,  Jianxin Zhang

    IPC: G06F19/22

    Abstract: A method includes exposing template polynucleotide strands, sequencing primers, and polymerase to flows of nucleotide species; obtaining a series of measured intensity values and randomly selecting a training subset therefrom; generating series of base calls using a base caller and aligning the series of base calls to a reference genome or sequence using an aligner; determining intensity value thresholds and parameters of a linear transformation corresponding to different homopolymer lengths and nucleotide species; generating series of base calls corresponding to the series of measured intensity values using at least some of the parameters of a linear transformation; and recalibrating the series of base calls corresponding to the plurality of series of measured intensity values using at least some of the intensity value thresholds.

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