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    Expression data analysis systems and methods
    1.
    发明申请
    Expression data analysis systems and methods 有权
    表达数据分析系统和方法

    公开(公告)号：US20060129331A1

    公开(公告)日：2006-06-15

    申请号：US11341699

    申请日：2006-01-26

    申请人： Shreeram Akilesh ,  Kevin Mills ,  Derry Roopenian ,  Daniel Shaffer

    发明人： Shreeram Akilesh ,  Kevin Mills ,  Derry Roopenian ,  Daniel Shaffer

    IPC分类号： C12Q1/68 ,  G06F19/00

    CPC分类号： G16B25/00 ,  G16B20/00 ,  G16B40/00

    摘要： Systems and methods for performing rapid genomic DNA analysis of samples, such as control samples and experimental samples. In one aspect, the system makes use of genomic DNA input, rather than gene expression input such as mRNA and/or cDNA associated with mRNA. The systems and methods perform statistical analyses on data generated from the samples to determine which DNA sequences in an identified set of DNA sequences have a basis of variation in an experimental sample when compared to a control sample, and additionally provide a quantitative measure of this variation. The quantitative measure may be based on metrics such as copy number and/or fold-change. The systems and methods employ this statistical framework in DNA-based evaluation settings, including the evaluation/diagnosis of a pathological condition such as cancer or transgenic analysis of transgenic plants and animals. The systems and methods also provide means to select and refine the selection of DNA sequences, such as genes, known to undergo copy change for a particular pathological condition. This leads to the creation of stock gene sets catered to individual application areas and/or clinical uses, which may be used with the systems and methods described in this application for the purpose of, for example, a clinical kit for rapid DNA-based evaluation.

    摘要翻译： 用于进行样品快速基因组DNA分析的系统和方法，如对照样品和实验样品。 在一个方面，该系统利用基因组DNA输入，而不是基因表达输入，例如与mRNA相关的mRNA和/或cDNA相关的基因表达输入。 系统和方法对从样本产生的数据执行统计分析，以确定当与对照样品相比时，确定的DNA序列集合中的哪些DNA序列具有实验样品的变化基础，并另外提供该变化的定量测量 。 定量测量可以基于诸如拷贝数和/或折叠变化之类的度量。 系统和方法在基于DNA的评估设置中采用这种统计框架，包括病理条件如癌症或转基因植物和动物的转基因分析的评估/诊断。 系统和方法还提供了选择和改进DNA序列选择的方法，例如已知对特定病理状况进行复制变化的基因。 这导致创建适合于个体应用领域和/或临床应用的库存基因组，其可以与本申请中描述的系统和方法一起使用，用于例如用于快速基于DNA的评估的临床试剂盒 。

    Expression data analysis systems and methods
    2.
    发明授权
    Expression data analysis systems and methods 有权
    表达数据分析系统和方法

    公开(公告)号：US07822556B2

    公开(公告)日：2010-10-26

    申请号：US12511493

    申请日：2009-07-29

    申请人： Shreeram Akilesh ,  Derry Roopenian ,  Daniel J. Shaffer

    发明人： Shreeram Akilesh ,  Derry Roopenian ,  Daniel J. Shaffer

    IPC分类号： G01N33/50

    CPC分类号： G06F19/20 ,  G06F19/24

    摘要： Methods and applications of Global Patter Recognition (GPR), including a system for analyzing the results of real-time polymerase chain reaction (RT-PCR) experiments employing micro-titer and/or microarray plates and robotic plate readers is described. The system employs a set of self-normalizing housekeeping primers or oligonucleotides on the plates/arrays and an algorithmic approach to normalizing expression data from all primers on the plate based on the reaction products of several of the self-normalizing gene primers oligonucleotides. Normalization is accomplished using simplex reactions involving these self-normalizing primers/oligonucleotides; the normalization parameters are then useable across all control and experimental reactions of the plate/array. A ranked list of genes whose amount of change is statistically significant can be determined. The accuracy of this list is enhanced by the data normalization aspect of the system. Other applications of GPR are also disclosed herein.

    摘要翻译： 描述了全球散射识别（GPR）的方法和应用，包括用于分析使用微滴度和/或微阵列板和机器人读板器的实时聚合酶链反应（RT-PCR）实验的结果的系统。 该系统在板/阵列上采用一套自标准化管家引物或寡核苷酸，以及基于几个自归一化基因引物寡核苷酸的反应产物，从板上所有引物标准化表达数据的算法方法。 使用涉及这些自标准化引物/寡核苷酸的单纯形反应来实现标准化; 标准化参数随后可用于板/阵列的所有控制和实验反应。 可以确定其变化量具有统计学显着性的基因的排名列表。 该列表的准确性由系统的数据归一化方面增强。 本文还公开了GPR的其它应用。

    Systems and methods for statistical genomic DNA based analysis and evaluation
    4.
    发明授权
    Systems and methods for statistical genomic DNA based analysis and evaluation 有权
    用于统计基因组DNA分析和评估的系统和方法

    公开(公告)号：US07881873B2

    公开(公告)日：2011-02-01

    申请号：US11341699

    申请日：2006-01-27

    申请人： Shreeram Akilesh ,  Kevin D. Mills ,  Derry Charles Roopenian ,  Daniel J. Shaffer

    发明人： Shreeram Akilesh ,  Kevin D. Mills ,  Derry Charles Roopenian ,  Daniel J. Shaffer

    IPC分类号： G01N33/48

    CPC分类号： G06F19/20 ,  G06F19/18 ,  G06F19/24

    摘要： Systems and methods for performing rapid genomic DNA analysis of samples, such as control samples and experimental samples. In one aspect, the system makes use of genomic DNA input, rather than gene expression input such as mRNA and/or cDNA associated with mRNA. The systems and methods perform statistical analyses on data generated from the samples to determine which DNA sequences in an identified set of DNA sequences have a basis of variation in an experimental sample when compared to a control sample, and additionally provide a quantitative measure of this variation. The quantitative measure may be based on metrics such as copy number and/or fold-change. The systems and methods employ this statistical framework in DNA-based evaluation settings, including the evaluation/diagnosis of a pathological condition such as cancer or transgenic analysis of transgenic plants and animals. The systems and methods also provide means to select and refine the selection of DNA sequences, such as genes, known to undergo copy change for a particular pathological condition. This leads to the creation of stock gene sets catered to individual application areas and/or clinical uses, which may be used with the systems and methods described in this application for the purpose of, for example, a clinical kit for rapid DNA-based evaluation.

    摘要翻译： 用于进行样品快速基因组DNA分析的系统和方法，如对照样品和实验样品。 在一个方面，该系统利用基因组DNA输入，而不是基因表达输入，例如与mRNA相关的mRNA和/或cDNA相关的基因表达输入。 系统和方法对从样本产生的数据执行统计分析，以确定当与对照样品相比时，确定的DNA序列集合中的哪些DNA序列具有实验样品的变化基础，并另外提供该变化的定量测量 。 定量测量可以基于诸如拷贝数和/或折叠变化之类的度量。 系统和方法在基于DNA的评估设置中采用这种统计框架，包括病理条件如癌症或转基因植物和动物的转基因分析的评估/诊断。 系统和方法还提供了选择和改进DNA序列选择的方法，例如已知对特定病理状况进行复制变化的基因。 这导致创建适合于个体应用领域和/或临床应用的库存基因组，其可以与本申请中描述的系统和方法一起使用，用于例如用于快速基于DNA的评估的临床试剂盒 。

    Expression Data Analysis Systems and Methods
    5.
    发明申请
    Expression Data Analysis Systems and Methods 有权
    表达数据分析系统与方法

    公开(公告)号：US20100023272A1

    公开(公告)日：2010-01-28

    申请号：US12511493

    申请日：2009-07-29

    申请人： Shreeram Akilesh ,  Derry Roopenian ,  Daniel J. Shaffer

    发明人： Shreeram Akilesh ,  Derry Roopenian ,  Daniel J. Shaffer

    IPC分类号： G06F19/00 ,  G06F17/18

    CPC分类号： G06F19/20 ,  G06F19/24

    摘要： Methods and applications of Global Patter Recognition (GPR), including a system for analyzing the results of real-time polymerase chain reaction (RT-PCR) experiments employing micro-titer and/or microarray plates and robotic plate readers is described. The system employs a set of self-normalizing housekeeping primers or oligonucleotides on the plates/arrays and an algorithmic approach to normalizing expression data from all primers on the plate based on the reaction products of several of the self-normalizing gene primers oligonucleotides. Normalization is accomplished using simplex reactions involving these self-normalizing primers/oligonucleotides; the normalization parameters are then useable across all control and experimental reactions of the plate/array. A ranked list of genes whose amount of change is statistically significant can be determined. The accuracy of this list is enhanced by the data normalization aspect of the system. Other applications of GPR are also disclosed herein.

    摘要翻译： 描述了全球散射识别（GPR）的方法和应用，包括用于分析使用微滴度和/或微阵列板和机器人读板器的实时聚合酶链反应（RT-PCR）实验的结果的系统。 该系统在板/阵列上采用一套自标准化管家引物或寡核苷酸，以及基于几个自归一化基因引物寡核苷酸的反应产物，从板上所有引物标准化表达数据的算法方法。 使用涉及这些自标准化引物/寡核苷酸的单纯形反应来实现标准化; 标准化参数随后可用于板/阵列的所有控制和实验反应。 可以确定其变化量具有统计学显着性的基因的排名列表。 该列表的准确性由系统的数据归一化方面增强。 本文还公开了GPR的其它应用。