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    Methods and systems for instrument validation
    1.
    发明授权
    Methods and systems for instrument validation 有权

    公开(公告)号：US10648912B2

    公开(公告)日：2020-05-12

    申请号：US15016485

    申请日：2016-02-05

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Thomas Wessel ,  Yong Chu ,  Jacob Freudenthal ,  David Woo

    IPC: G01N21/64 ,  G01N21/27 ,  G16B40/00

    Abstract: In one exemplary embodiment, a method for validating an instrument is provided. The method includes receiving amplification data from a validation plate to generate a plurality of amplification curves. The validation plate includes a sample of a first quantity and a second quantity, and each amplification curve includes an exponential region. The method further includes determining a set of fluorescence thresholds based on the exponential regions of the plurality of amplification curves and determining, for each fluorescence threshold of the set, a first set of cycle threshold (Ct) values of amplification curves generated from the samples of the first quantity and a second set of Ct values of amplification curves generated from the samples of the second quantity. The method includes calculating if the first and second quantities are sufficiently distinguishable based on Ct values at each of the plurality of fluorescence thresholds.

    BASECALLER WITH DILATED CONVOLUTIONAL NEURAL NETWORK
    3.
    发明申请
    BASECALLER WITH DILATED CONVOLUTIONAL NEURAL NETWORK 有权

    公开(公告)号：US20210398615A1

    公开(公告)日：2021-12-23

    申请号：US16899545

    申请日：2020-06-11

    Applicant: Life Technologies Corporation

    Inventor： Yong Chu ,  Stephanie Jo Schneider ,  Rylan Schaeffer ,  David Woo

    IPC: G16B30/00 ,  G16B25/00 ,  G16B40/00 ,  G06N3/08 ,  G06N5/04 ,  G06K9/62 ,  C12Q1/6869

    Abstract: A method of automatically sequencing or basecalling one or more DNA (deoxyribonucleic acid) molecules of a biological sample is described. The method comprises using a capillary electrophoresis genetic analyzer to measure the biological sample to obtain at least one input trace comprising digital data corresponding to fluorescence values for a plurality of scans. Scan labelling probabilities for the plurality of scans are generated using a trained artificial neural network comprising a plurality of layers including convolutional layers. A basecall sequence comprising a plurality of basecalls for the one or more DNA molecules based on the scan labelling probabilities for the plurality of scans is determined.

    METHODS AND SYSTEMS FOR INSTRUMENT VALIDATION
    5.
    发明申请
    METHODS AND SYSTEMS FOR INSTRUMENT VALIDATION 审中-公开
    仪器验证的方法和系统

    公开(公告)号：US20160231245A1

    公开(公告)日：2016-08-11

    申请号：US15016485

    申请日：2016-02-05

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Thomas Wessel ,  Yong Chu ,  Jacob Freudenthal ,  David Woo

    IPC: G01N21/64

    CPC classification number: G01N21/6428 ,  G01N21/274 ,  G01N21/6452 ,  G01N21/6456 ,  G01N2021/6439 ,  G16B40/00

    Abstract: In one exemplary embodiment, a method for validating an instrument is provided. The method includes receiving amplification data from a validation plate to generate a plurality of amplification curves. The validation plate includes a sample of a first quantity and a second quantity, and each amplification curve includes an exponential region. The method further includes determining a set of fluorescence thresholds based on the exponential regions of the plurality of amplification curves and determining, for each fluorescence threshold of the set, a first set of cycle threshold (Ct) values of amplification curves generated from the samples of the first quantity and a second set of Ct values of amplification curves generated from the samples of the second quantity. The method includes calculating if the first and second quantities are sufficiently distinguishable based on Ct values at each of the plurality of fluorescence thresholds.

    Abstract translation: 在一个示例性实施例中，提供了用于验证仪器的方法。 该方法包括从验证板接收放大数据以产生多个扩增曲线。 验证板包括第一数量和第二数量的样本，并且每个扩增曲线包括指数区域。 该方法还包括基于多个扩增曲线的指数区域来确定一组荧光阈值，并且针对该组的每个荧光阈值确定从样品中产生的扩增曲线的第一组循环阈值（Ct）值 从第二数量的样本产生的第一数量和第二组扩增曲线的Ct值。 该方法包括基于多个荧光阈值中的每个荧光阈值处的Ct值来计算第一和第二量是否足够可区分。

    METHODS AND SYSTEMS FOR DETERMINING OPTICAL REGIONS OF INTEREST
    8.
    发明申请
    METHODS AND SYSTEMS FOR DETERMINING OPTICAL REGIONS OF INTEREST 有权
    用于确定光学区域的方法和系统

    公开(公告)号：US20160231250A1

    公开(公告)日：2016-08-11

    申请号：US15016564

    申请日：2016-02-05

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Yong Chu

    IPC: G01N21/76 ,  G06K9/00 ,  G01N21/77 ,  G06K9/32

    CPC classification number: G01N21/763 ,  G01N21/274 ,  G01N21/6428 ,  G01N21/6452 ,  G01N21/6456 ,  G01N21/77 ,  G01N2021/7786 ,  G01N2201/127 ,  G06K9/00134 ,  G06K9/0014 ,  G06K9/3233

    Abstract: The present teachings relate to a method and system for determining Regions of Interest (ROI) for one or more biological samples in a laboratory instrument. The method can include an optical system capable of imaging florescence emission from a plurality of sample wells. An initial ROI, its center location and size can be estimated from the fluorescence detected from each well. From this information the average size of the ROIs can be determined and global gridding models can be derived to better locate each of the ROIs. The global gridding models can then be applied to the ROIs to improve the precision of the ROI center locations. Sample wells not originally providing fluorescence ROIs can be recovered through the use of mapping functions. The radius of each ROI can then be adjusted to improve the signal-to-noise ratio of the optical system.

    Abstract translation: 本教导涉及用于确定实验室仪器中的一个或多个生物样品的感兴趣区域（ROI）的方法和系统。 该方法可以包括能够成像来自多个样品孔的荧光发射的光学系统。 初始ROI，其中心位置和大小可以从每个孔中检测到的荧光估计。 从该信息可以确定ROI的平均大小，并且可以导出全局网格化模型以更好地定位每个ROI。 然后，可以将全局网格模型应用于ROI，以提高ROI中心位置的精度。 原始提供荧光ROI的样品孔可以通过使用映射函数来恢复。 然后可以调整每个ROI的半径以提高光学系统的信噪比。

    METHODS AND SYSTEMS FOR BIOLOGICAL INSTRUMENT CALIBRATION
    9.
    发明申请
    METHODS AND SYSTEMS FOR BIOLOGICAL INSTRUMENT CALIBRATION 有权
    生物仪器校准的方法和系统

    公开(公告)号：US20160231246A1

    公开(公告)日：2016-08-11

    申请号：US15017249

    申请日：2016-02-05

    Applicant: LIFE TECHNOLOGIES CORPORATION

    Inventor： Yong Chu ,  Jeffrey Marks ,  Jacob Freudenthal ,  Thomas Wessel ,  David Woo

    IPC: G01N21/64 ,  C12Q1/68

    CPC classification number: G01N21/6428 ,  C12Q1/6851 ,  C12Q1/686 ,  G01N21/274 ,  G01N21/278 ,  G01N21/6452 ,  G01N21/6456 ,  G01N2021/6439 ,  G01N2021/6471 ,  G01N2201/127 ,  G01N2201/13 ,  G01N2333/922

    Abstract: In one exemplary embodiment, a method for calibrating an instrument is provided. The instrument includes an optical system capable of imaging florescence emission from a plurality of reaction sites. The method includes performing a region-of-interest (ROI) calibration to determine reaction site positions in an image. The method further includes performing a pure dye calibration to determine the contribution of a fluorescent dye used in each reaction site by comparing a raw spectrum of the fluorescent dye to a pure spectrum calibration data of the fluorescent dye. The method further includes performing an instrument normalization calibration to determine a filter normalization factor. The method includes performing an RNase P validation to validate the instrument is capable of distinguishing between two different quantities of sample.

    Abstract translation: 在一个示例性实施例中，提供了一种用于校准仪器的方法。 该仪器包括能够成像来自多个反应位点的荧光发射的光学系统。 该方法包括执行感兴趣区域（ROI）校准以确定图像中的反应位置位置。 该方法还包括进行纯染料校准，以通过将荧光染料的原始光谱与荧光染料的纯光谱校准数据进行比较来确定每个反应位点中使用的荧光染料的贡献。 该方法还包括执行仪器归一化校准以确定滤波器归一化因子。 该方法包括执行RNase P验证以验证仪器能够区分两种不同数量的样品。

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