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1. 发明申请

WO2016197028A1 DETERMINING THE LIMIT OF DETECTION OF RARE TARGETS USING DIGITAL PCR 审中-公开
标题翻译：使用数字PCR测定稀有目标检测的限度
公开(公告)号：WO2016197028A1
公开(公告)日：2016-12-08
申请号：PCT/US2016/035870
申请日：2016-06-03
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： MAJUMDAR, Nivedita Sumi , WESSEL, Thomas
IPC分类号： G06F19/24 , G06F19/20
CPC分类号： G06F19/24 , G06N7/005
摘要： A method for determining false positives calls in a biological data plot is provided. The method includes identifying a first data cluster as non-amplification data points within the biological data plot and identifying a second data cluster as wild-type positives within the biological data plot. The method further includes estimating a position in the biological data plot of a center of the first and second data clusters. The method further includes determining, for each data point within the first data cluster, a probability of belonging to the first data cluster and determining, for each data point within the second data cluster, a probability of belonging to the second data cluster. The method includes applying a probability threshold for each data point within the first and second data cluster to identify false positives.
摘要翻译：提供了一种用于在生物数据图中确定假阳性呼叫的方法。该方法包括将第一数据簇识别为生物数据图中的非扩增数据点，并将第二数据簇识别为生物数据图中的野生型阳性。该方法还包括估计第一和第二数据簇的中心的生物数据图中的位置。该方法还包括为第一数据簇内的每个数据点确定属于第一数据簇的概率，并且针对第二数据簇内的每个数据点确定属于第二数据簇的概率。该方法包括对第一和第二数据簇内的每个数据点应用概率阈值以识别误报。

2. 发明申请

WO2014074735A2 VISUALIZATION TOOLS FOR DIGITAL PCR DATA 审中-公开
标题翻译：数字PCR数据可视化工具
公开(公告)号：WO2014074735A2
公开(公告)日：2014-05-15
申请号：PCT/US2013/068984
申请日：2013-11-07
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： LEONG, Harrison , MAJUMDAR, Nivedita Sumi , MARKS, Jeffrey , STRAUB, Theodore , TALBOT, Ryan , BODNER, Kevin , HOARD, David
IPC分类号： G06F19/26
CPC分类号： G06T11/206 , G06F19/26 , G06T11/203
摘要： A method for generating a data visualization is provided. The method includes displaying a representation of a portion of detected data from a substrate to a user. The method further includes generating a data quality value for the portion of detected data and displaying, along with the representation of the portion of detected data, an indication of data quality value for the portion of detected data. The method further includes selecting, by the user, a quality value threshold, and displaying an adjusted indication of data quality value for the portion of detected data meeting the quality value threshold.
摘要翻译：提供了一种用于生成数据可视化的方法。该方法包括将检测到的数据的一部分从衬底显示给用户。该方法还包括为检测到的数据的部分生成数据质量值，以及与检测到的数据的部分的表示一起显示检测到的数据的部分的数据质量值的指示。该方法还包括由用户选择质量值阈值，并且显示对于满足质量值阈值的检测数据的部分的数据质量值的调整指示。

3. 发明申请

WO2017205796A9 METHODS AND SYSTEMS FOR GRAPHICAL USER INTERFACES FOR BIOLOGICAL DATA 审中-公开
公开(公告)号：WO2017205796A9
公开(公告)日：2017-11-30
申请号：PCT/US2017/034776
申请日：2017-05-26
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： MAJUMDAR, Nivedita Sumi
IPC分类号： G06F19/26
摘要： In one exemplary embodiment, a method computer-implemented method of generating an outlier wheel data visualization for a graphical user interface, GUI, is provided. The method includes receiving emission data from a plurality of amplification reactions. The method further includes generating an outlier wheel data visualization using the emission data including a plurality of lines, where each line included in the outlier wheel data visualization represents emission data from an amplification reaction of the plurality of amplification reactions, and each line having a length and a visual indicator. The length of each line represents growth of intensity of fluorescence of the emission data and the visual indicator indicates the associated cycle number of the emission data. Further, each line is associated with an angular position so that the plurality of lines is configured in a circular shape. The method includes displaying the outlier wheel data visualization on a GUI.

4. 发明申请

WO2017015133A1 TOOL FOR VISUALIZING PCR RESULTS 审中-公开
标题翻译：可视化PCR结果的工具
公开(公告)号：WO2017015133A1
公开(公告)日：2017-01-26
申请号：PCT/US2016/042553
申请日：2016-07-15
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： MAJUMDAR, Nivedita Sumi
IPC分类号： G06F19/26
CPC分类号： G06F19/26
摘要： In some embodiments, a method or system for visualizing data generated from one or more reaction devices, chips, or reaction sites may be provided. On a scatter plot, data points may be displayed indicative of results from nucleic amplification, wherein the nucleic acid amplification comprises a first target and a second target and the data points are designated as being indicative of amplification of the first target, the second target, both targets, or neither target. In response to user input, an adjustable threshold may be varied used to designate the data points. And, in response to the varying, designations and a display of the designations may be altered for one or more of the data points whose designation is changed based on the varied threshold.
摘要翻译：在一些实施例中，可以提供用于可视化从一个或多个反应装置，芯片或反应部位产生的数据的方法或系统。在散点图上，可以显示指示来自核酸扩增的结果的数据点，其中所述核酸扩增包括第一靶和第二靶，并且所述数据点被指定为指示所述第一靶，第二靶，两个目标，或既不是目标。响应于用户输入，可以改变用于指定数据点的可调阈值。并且，响应于变化的指定，并且可以基于变化的阈值改变其指定被改变的一个或多个数据点来改变指定的显示。

5. 发明申请

WO2017205796A2 METHODS AND SYSTEMS FOR GRAPHICAL USER INTERFACES FOR BIOLOGICAL DATA 审中-公开
标题翻译：用于生物数据的图形用户界面的方法和系统
公开(公告)号：WO2017205796A2
公开(公告)日：2017-11-30
申请号：PCT/US2017/034776
申请日：2017-05-26
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： MAJUMDAR, Nivedita Sumi
IPC分类号： G06F19/26
摘要： In one exemplary embodiment, a method computer-implemented method of generating an outlier wheel data visualization for a graphical user interface, GUI, is provided. The method includes receiving emission data from a plurality of amplification reactions. The method further includes generating an outlier wheel data visualization using the emission data including a plurality of lines, where each line included in the outlier wheel data visualization represents emission data from an amplification reaction of the plurality of amplification reactions, and each line having a length and a visual indicator. The length of each line represents growth of intensity of fluorescence of the emission data and the visual indicator indicates the associated cycle number of the emission data. Further, each line is associated with an angular position so that the plurality of lines is configured in a circular shape. The method includes displaying the outlier wheel data visualization on a GUI.
摘要翻译：在一个示例性实施例中，提供了一种为图形用户界面GUI生成离群轮数据可视化的方法计算机实现的方法。该方法包括从多个扩增反应中接收发射数据。该方法进一步包括使用包括多个线的发射数据生成离群轮数据可视化，其中包含在离群轮数据可视化中的每个线表示来自多个扩增反应的扩增反应的发射数据，并且每个线具有长度和一个视觉指示器。每条线的长度表示发射数据的荧光强度的增长，并且可视指示器指示发射数据的相关联的周期数。此外，每条线与角位置相关联，使得多条线配置成圆形。该方法包括在GUI上显示离群轮数据可视化。

6. 发明申请

WO2017059049A1 SYSTEMS AND METHODS FOR PERFORMING DIGITAL PCR 审中-公开
标题翻译：用于执行数字PCR的系统和方法
公开(公告)号：WO2017059049A1
公开(公告)日：2017-04-06
申请号：PCT/US2016/054406
申请日：2016-09-29
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： KEYS, David , MAJUMDAR, Nivedita Sumi , STRAUB, Theodore
IPC分类号： C12Q1/68 , B01L3/00
CPC分类号： C12Q1/686 , B01L7/52 , B01L2300/024 , B01L2300/0829 , C12Q1/6851 , C12Q2527/107 , C12Q2545/114 , C12Q2561/113 , C12Q2563/159
摘要： Systems and methods are described for quantifying a target nucleic acid. A sample comprising a target nucleic acid is segregated into a first plurality of the reaction volumes containing at least one target nucleic acid molecule and a second plurality of the reaction volumes containing no target nucleic acid molecules. The reaction volumes are subjected to an amplification assay, wherein the amplification assay is configured to amplify the target nucleic acid. An indicator of amplification is detected or measured in at least some of the plurality of reaction volumes. The target nucleic acid is quantified based on the detection or measurement. After discontinuing the amplification assay, the plurality of reaction volumes may be heated and changes in the indicators of amplification of two or more of the at least some of the reaction volumes may be detected or measured.
摘要翻译：描述了用于定量靶核酸的系统和方法。将包含靶核酸的样品分离成含有至少一个靶核酸分子的第一多个反应体积和不含靶核酸分子的第二多个反应体积。对反应体积进行扩增测定，其中扩增测定被配置为扩增靶核酸。在多个反应体积中的至少一些反应体积中检测或测量扩增指示物。基于检测或测量量化靶核酸。在停止扩增测定后，可以加热多个反应体积，并且可以检测或测量两种或更多种反应体积的扩增指标的变化。

7. 发明申请

WO2017205796A3 METHODS AND SYSTEMS FOR GRAPHICAL USER INTERFACES FOR BIOLOGICAL DATA 审中-公开
公开(公告)号：WO2017205796A3
公开(公告)日：2017-11-30
申请号：PCT/US2017/034776
申请日：2017-05-26
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： MAJUMDAR, Nivedita Sumi
IPC分类号： G06F19/26
摘要： In one exemplary embodiment, a method computer-implemented method of generating an outlier wheel data visualization for a graphical user interface, GUI, is provided. The method includes receiving emission data from a plurality of amplification reactions. The method further includes generating an outlier wheel data visualization using the emission data including a plurality of lines, where each line included in the outlier wheel data visualization represents emission data from an amplification reaction of the plurality of amplification reactions, and each line having a length and a visual indicator. The length of each line represents growth of intensity of fluorescence of the emission data and the visual indicator indicates the associated cycle number of the emission data. Further, each line is associated with an angular position so that the plurality of lines is configured in a circular shape. The method includes displaying the outlier wheel data visualization on a GUI.

8. 发明申请

WO2016172628A1 METHODS AND SYSTEMS FOR VOLUME VARIATION MODELING IN DIGITAL PCR 审中-公开
标题翻译：数字PCR中体积变异建模的方法与系统
公开(公告)号：WO2016172628A1
公开(公告)日：2016-10-27
申请号：PCT/US2016/029046
申请日：2016-04-22
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： MAJUMDAR, Nivedita Sumi , BANERJEE, Swapnonil
IPC分类号： G06F19/24
CPC分类号： C12Q1/6851 , G06F17/18 , G06F19/24
摘要： A method for performing digital polymerase chain reaction (dPCR) is provided. The method comprises partitioning a biological sample volume including a plurality of target nucleic acids into a plurality of partitions. At least one partition includes at least one target nucleic acid. The method further includes determining a model for volume variation of the plurality of partitions and determining a fraction of partitions including at least one target nucleic acid. The method includes generating a concentration of target nucleic acids in the biological sample based on the model for volume variation and the fraction of partitions including at least one target nucleic acid.
摘要翻译：提供了一种执行数字聚合酶链反应（dPCR）的方法。该方法包括将包括多个靶核酸的生物样品体积分成多个分区。至少一个分区包括至少一个靶核酸。该方法还包括确定多个分区的体积变化的模型并确定包括至少一个靶核酸的分区的一部分。该方法包括基于用于体积变化的模型和包括至少一种靶核酸的分区部分产生生物样品中靶核酸的浓度。

9. 发明申请

WO2015148546A1 METHODS AND SYSTEMS FOR KNOWLEDGE DISCOVERY USING BIOLOGICAL DATA 审中-公开
标题翻译：使用生物数据知识发现的方法和系统
公开(公告)号：WO2015148546A1
公开(公告)日：2015-10-01
申请号：PCT/US2015/022298
申请日：2015-03-24
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： MAJUMDAR, Nivedita Sumi , LEONG, Harrison , POTHINI, Shakila , HOARD, David , FONG, Christopher , SOARES, Pratik Simon , KUMAR, Salil , WESSEL, Thomas , ALIMINATI, Manjula , EGRY, Levente
IPC分类号： G06F19/28 , G06F19/22 , G06F19/26
CPC分类号： G06F19/28 , G06F17/30864 , G06F19/22 , G06F19/26
摘要： A system for analyzing biological data, comprising: a storage configured to store a plurality of data files containing biological data obtained from a plurality of devices; a server configured to: host a plurality of applications, each configured to be implemented on the server and to provide analysis, manipulation, comparison, visualization, or a combination thereof, of the biological data included in the data files, wherein the plurality of applications allow a user to analyze different data files related to the same sample and compare the results of the analysis.
摘要翻译：一种用于分析生物数据的系统，包括：存储器，被配置为存储包含从多个设备获得的生物数据的多个数据文件; 服务器，被配置为：托管多个应用，每个应用被配置为在服务器上实现并且提供包括在数据文件中的生物数据的分析，操作，比较，可视化或其组合，其中所述多个应用允许用户分析与相同样本相关的不同数据文件，并比较分析结果。

10. 发明申请

WO2014043581A1 METHODS AND SYSTEMS FOR A DIGITAL PCR EXPERIMENT DESIGNER 审中-公开
标题翻译：数字PCR实验设计者的方法和系统
公开(公告)号：WO2014043581A1
公开(公告)日：2014-03-20
申请号：PCT/US2013/059815
申请日：2013-09-13
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： MAJUMDAR, Nivedita Sumi , WESSEL, Thomas , WOO, David C. , SIKORA, Marcin , JANAWAY, Gordon , RAIZADA, Shweta , LANKESTER, Joanna , MARKS, Jeffrey , WESSEL, Daniel
IPC分类号： G06F19/24
CPC分类号： G06F19/20 , C12Q1/686 , G06F19/24
摘要： 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.
摘要翻译：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。

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