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    Systems and methods for detecting the presence of a biological status using plot
    1.
    发明授权
    Systems and methods for detecting the presence of a biological status using plot 有权
    使用情节检测生物状态存在的系统和方法

    公开(公告)号：US09317655B2

    公开(公告)日：2016-04-19

    申请号：US13509347

    申请日：2010-11-11

    申请人： Jiuliu Lu ,  Zihua Wang ,  Antonio Arevalo Reyes ,  Erik Alan Gustafson ,  John Steven Riley

    发明人： Jiuliu Lu ,  Zihua Wang ,  Antonio Arevalo Reyes ,  Erik Alan Gustafson ,  John Steven Riley

    IPC分类号： G01N33/48 ,  G01N33/50 ,  G06F19/26 ,  G06F19/12 ,  G06F19/18 ,  G06T11/20 ,  G06F19/24

    CPC分类号： G06F19/26 ,  G06F19/12 ,  G06F19/18 ,  G06F19/24 ,  G06T11/206

    摘要： Systems and methods for identifying Methicillin resistant strains of Staphylococcus aureus (MRSA) in a sample are used that are based on the fact that an MRSA positive sample should have roughly the same copy numbers of mecA, SCCmec, and a Staphylococcus aureus-specific target gene sequence. The systems and methods may further present the three assays simultaneously on a 2-D plot with each axis of the plot 120 degrees apart. According to one embodiment, a Y plot is used for the 2-D display. If a given sample has similar readings of mecA, SCCmec, and a Staphylococcus aureus-specific target gene sequence, the sample's measured copy numbers of mecA, SCCmec, and the Staphylococcus aureus-specific target gene sequence can plot close to the origin regardless of the sample's absolute assay readings. With the help of this transformation, a boundary function can be defined that can be used to distinguish MRSA-positive samples from MRSA-negative samples.

    摘要翻译： 使用用于鉴定样品中的甲氧西林抗性金黄色葡萄球菌（MRSA）的系统和方法，其基于以下事实：MRSA阳性样品应具有与mecA，SCCmec和金黄色葡萄球菌特异性靶基因大致相同的拷贝数 序列。 系统和方法可以进一步在2-D图上同时进行三个测定，其中每个图的每个轴分开120度。 根据一个实施例，Y图被用于2-D显示。 如果给定的样品具有类似的mecA，SCCmec和金黄色葡萄球菌特异性靶基因序列的读数，则样本的mecA，SCCmec和金黄色葡萄球菌特异性靶基因序列的拷贝数可以靠近原点绘图，不管 样品的绝对测定读数。 在这种转化的帮助下，可以定义可用于区分MRSA阳性样本与MRSA阴性样本的边界函数。

    SYSTEMS AND METHODS FOR DETECTING THE PRESENCE OF A BIOLOGICAL STATUS USING PLOT
    2.
    发明申请
    SYSTEMS AND METHODS FOR DETECTING THE PRESENCE OF A BIOLOGICAL STATUS USING PLOT 有权
    用于检测生物状态存在的系统和方法

    公开(公告)号：US20120283957A1

    公开(公告)日：2012-11-08

    申请号：US13509347

    申请日：2010-11-11

    申请人： Jiuliu Lu ,  Zihua Wang ,  Antonio Arevalo Reyes ,  Erik Alan Gustafson ,  John Steven Riley

    发明人： Jiuliu Lu ,  Zihua Wang ,  Antonio Arevalo Reyes ,  Erik Alan Gustafson ,  John Steven Riley

    IPC分类号： G06F19/10 ,  G06G7/60 ,  G06F19/12 ,  G06F19/00

    CPC分类号： G06F19/26 ,  G06F19/12 ,  G06F19/18 ,  G06F19/24 ,  G06T11/206

    摘要： Systems and methods for identifying Methicillin resistant strains of Staphylococcus aureus (MRSA) in a sample are used that are based on the fact that an MRSA positive sample should have roughly the same copy numbers of mecA, SCCmec, and a Staphylococcus aureus-specific target gene sequence. The systems and methods may further present the three assays simultaneously on a 2-D plot with each axis of the plot 120 degrees apart. According to one embodiment, a Y plot is used for the 2-D display. If a given sample has similar readings of mecA, SCCmec, and a Staphylococcus aureus-specific target gene sequence, the sample's measured copy numbers of mecA, SCCmec, and the Staphylococcus aureus-specific target gene sequence can plot close to the origin regardless of the sample's absolute assay readings. With the help of this transformation, a boundary function can be defined that can be used to distinguish MRSA-positive samples from MRSA-negative samples.

    摘要翻译： 使用用于鉴定样品中的甲氧西林抗性金黄色葡萄球菌（MRSA）的系统和方法，其基于以下事实：MRSA阳性样品应具有与mecA，SCCmec和金黄色葡萄球菌特异性靶基因大致相同的拷贝数 序列。 系统和方法可以进一步在2-D图上同时进行三个测定，每个图的每个轴分开120度。 根据一个实施例，Y图被用于2-D显示。 如果给定的样品具有类似的mecA，SCCmec和金黄色葡萄球菌特异性靶基因序列的读数，则样本的mecA，SCCmec和金黄色葡萄球菌特异性靶基因序列的拷贝数可以靠近原点绘图，不管 样品的绝对测定读数。 在这种转化的帮助下，可以定义可用于区分MRSA阳性样本与MRSA阴性样本的边界函数。

    SYSTEMS AND METHODS FOR DETECTING THE PRESENCE OF A BIOLOGICAL STATUS USING CLUSTERING
    5.
    发明申请
    SYSTEMS AND METHODS FOR DETECTING THE PRESENCE OF A BIOLOGICAL STATUS USING CLUSTERING 有权
    用于检测使用聚类的生物状态存在的系统和方法

    公开(公告)号：US20110131159A1

    公开(公告)日：2011-06-02

    申请号：US12944992

    申请日：2010-11-12

    申请人： Jiuliu Lu ,  Zihua Wang ,  Antonio Arevalo Reyes ,  Erik Alan Gustafson ,  John Steven Riley

    发明人： Jiuliu Lu ,  Zihua Wang ,  Antonio Arevalo Reyes ,  Erik Alan Gustafson ,  John Steven Riley

    IPC分类号： G06F15/18 ,  G06N5/02

    CPC分类号： G06F19/24 ,  C12Q1/689 ,  C12Q2600/112 ,  G06F19/12 ,  G06F19/18

    摘要： A method for determining the presence of a biological entity. The method may include entering into a digital computer, at least a plurality of first input values associated with a first genetic element (e.g., mecA), a plurality of second input values associated with a second genetic element (femA), and a plurality of third input values associated with a third genetic element (e.g., orfX) associated with a plurality of samples. Each sample includes a first input value in the plurality of first input values, a second input value in the plurality of second input values, and a third input value in the plurality of third input values. The method also includes determining a threshold value associated with the third genetic element, separating the samples using the threshold value into a first set of samples and a second set of samples, clustering the first set of samples in a feature space defined by the first genetic element and the second genetic element, defining a first boundary space using the first set of samples, and defining a second boundary space using the second set of samples. The first and second boundary spaces differentiate a biological entity from other biological statuses. Other embodiments may also include the use of a genetic element such as SCCmec.

    摘要翻译： 用于确定生物实体的存在的方法。 该方法可以包括进入数字计算机，与第一遗传元素（例如，mecA）相关联的至少多个第一输入值，与第二遗传元件（femA）相关联的多个第二输入值，以及多个 与与多个样本相关联的第三遗传元素（例如，orfX）相关联的第三输入值。 每个样本包括多个第一输入值中的第一输入值，多个第二输入值中的第二输入值和多个第三输入值中的第三输入值。 该方法还包括确定与第三遗传元件相关联的阈值，使用阈值将样本分离成第一组样本和第二组样本，将第一组样本聚集在由第一遗传学定义的特征空间中 元素和第二遗传元素，使用第一组样本定义第一边界空间，以及使用第二组样本定义第二边界空间。 第一和第二边界空间将生物体与其他生物状态区分开来。 其他实施方案还可以包括遗传元件如SCCmec的使用。

    Genetic Copy Number Determination Using High Throughput Multiplex Sequencing Of Smashed Nucleotides
    7.
    发明申请
    Genetic Copy Number Determination Using High Throughput Multiplex Sequencing Of Smashed Nucleotides 审中-公开

    公开(公告)号：US20170152548A1

    公开(公告)日：2017-06-01

    申请号：US15419878

    申请日：2017-01-30

    申请人： Michael H. Wigler ,  Dan Levy ,  Zihua Wang

    发明人： Michael H. Wigler ,  Dan Levy ,  Zihua Wang

    IPC分类号： C12Q1/68 ,  C12N15/10 ,  G06F19/22

    摘要： The present invention, SMASH (Short Multiply Aggregated Sequence Homologies), is a technique designed to pack multiple independent mappings into every read. Specifically, the invention relates to a composition comprising a first mixture of different chimeric genomic nucleic acid fragments, wherein each different fragment in the mixture comprises randomly ligated DNA segments, wherein each DNA segment in the fragment is a nucleic acid molecule at least 27 base pairs in length resulting from random fragmentation of a single genome. The invention also relates to methods for generating said composition and use of said composition to obtain genomic information, for example, copy number variation.

    Systems and methods for detecting the presence of a biological status using clustering
    9.
    发明授权
    Systems and methods for detecting the presence of a biological status using clustering 有权
    使用聚类检测生物状态存在的系统和方法

    公开(公告)号：US08442924B2

    公开(公告)日：2013-05-14

    申请号：US12944992

    申请日：2010-11-12

    申请人： Jiuliu Lu ,  Zihua Wang ,  Antonio Arevalo Reyes ,  Erik Alan Gustafson ,  John Steven Riley

    发明人： Jiuliu Lu ,  Zihua Wang ,  Antonio Arevalo Reyes ,  Erik Alan Gustafson ,  John Steven Riley

    IPC分类号： G06F15/18

    CPC分类号： G06F19/24 ,  C12Q1/689 ,  C12Q2600/112 ,  G06F19/12 ,  G06F19/18

    摘要： A method for determining the presence of a biological entity. The method may include entering into a digital computer, at least a plurality of first input values associated with a first genetic element (e.g., mecA), a plurality of second input values associated with a second genetic element (femA), and a plurality of third input values associated with a third genetic element (e.g., orfX) associated with a plurality of samples. Each sample includes a first input value in the plurality of first input values, a second input value in the plurality of second input values, and a third input value in the plurality of third input values. The method also includes determining a threshold value associated with the third genetic element, separating the samples using the threshold value into a first set of samples and a second set of samples, clustering the first set of samples in a feature space defined by the first genetic element and the second genetic element, defining a first boundary space using the first set of samples, and defining a second boundary space using the second set of samples. The first and second boundary spaces differentiate a biological entity from other biological statuses. Other embodiments may also include the use of a genetic element such as SCCmec.

    摘要翻译： 用于确定生物实体的存在的方法。 该方法可以包括进入数字计算机，与第一遗传元素（例如，mecA）相关联的至少多个第一输入值，与第二遗传元件（femA）相关联的多个第二输入值，以及多个 与与多个样本相关联的第三遗传元素（例如，orfX）相关联的第三输入值。 每个样本包括多个第一输入值中的第一输入值，多个第二输入值中的第二输入值和多个第三输入值中的第三输入值。 该方法还包括确定与第三遗传元件相关联的阈值，使用阈值将样本分离成第一组样本和第二组样本，将第一组样本聚集在由第一遗传学定义的特征空间中 元素和第二遗传元素，使用第一组样本定义第一边界空间，以及使用第二组样本定义第二边界空间。 第一和第二边界空间将生物体与其他生物状态区分开来。 其他实施方案还可以包括遗传元件如SCCmec的使用。