公开(公告)号：US20050033520A1

公开(公告)日：2005-02-10

申请号：US10475960

申请日：2002-04-24

申请人： Hongyue Dai ,  Michael Meyer ,  Roland Stoughton

发明人： Hongyue Dai ,  Michael Meyer ,  Roland Stoughton

IPC分类号： C12Q1/68 ,  G06F19/20 ,  G06F19/00

CPC分类号： C12Q1/6816 ,  C12Q1/6837 ,  G16B25/00 ,  C12Q2527/113

摘要： The present invention provides methods for utilizing the changes of hybridization levels in time during approach to equilibrium duplex formation for identifying specific hybridization to polynucleotide probes. In the invention, the changes of hybridization levels at one or more polynucleotide probes by a sample comprising a plurality of nucleic acid molecules having different sequences are monitored during their progress towards equilibrium and the continuing increase of hybridization signals beyond cross-hybridization is used as an indication of specific binding. The invention also provides methods of comparing specificities of different polynucleotides probes. The invention further provides methods for ranking and selecting polynucleotide probes that are specific to particular nucleic acids and methods for enhancing the detection of nucleic acids. The invention further provides methods for determining the orientation of nucleotide sequences.

摘要翻译： 本发明提供了在平衡双相形成过程中利用杂交水平随时间变化的方法，用于鉴定与多核苷酸探针的特异性杂交。 在本发明中，在包含具有不同序列的多个核酸分子的样品的一个或多个多核苷酸探针处的杂交水平的变化在其进展到平衡期间被监测，并且超越交叉杂交的杂交信号的持续增加用作 指示具体绑定。 本发明还提供了比较不同多核苷酸探针的特异性的方法。 本发明还提供了用于评估和选择对特定核酸特异性的多核苷酸探针的方法和用于增强核酸检测的方法。 本发明还提供了确定核苷酸序列取向的方法。

公开(公告)号：US07565251B2

公开(公告)日：2009-07-21

申请号：US11303121

申请日：2005-12-12

申请人： Roland Stoughton ,  Hongyue Dai

发明人： Roland Stoughton ,  Hongyue Dai

IPC分类号： G01N33/50

CPC分类号： G06F19/20 ,  C12Q1/6837 ,  Y10T436/10

摘要： A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.

摘要翻译： 用于微阵列实验对中的荧光团的微阵列实验中的荧光团偏置去除方法是相反的。 此外，一种用于计算与名义上重复的微阵列实验中进行的每个测量相关联的各个错误的方法。 该误差测量可选地与基于秩的方法耦合，以便确定响应于扰动的细胞成分向上或向下调节的概率。 最后，在名义上重复的微阵列实验中确定细胞成分的表达水平的加权平均的置信度的方法。

公开(公告)号：US20060190191A1

公开(公告)日：2006-08-24

申请号：US11303121

申请日：2005-12-12

申请人： Roland Stoughton ,  Hongyue Dai

发明人： Roland Stoughton ,  Hongyue Dai

IPC分类号： G06F19/00

CPC分类号： G06F19/20 ,  C12Q1/6837 ,  Y10T436/10

摘要： A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.

公开(公告)号：US20050164273A1

公开(公告)日：2005-07-28

申请号：US11042654

申请日：2005-01-24

申请人： Roland Stoughton ,  Hongyue Dai

发明人： Roland Stoughton ,  Hongyue Dai

IPC分类号： G01N33/53 ,  C12N15/09 ,  C12Q1/68 ,  G01N33/48 ,  G01N33/566 ,  G01N33/58 ,  G01N37/00 ,  G06F17/18 ,  G06F19/20 ,  G01N33/50 ,  G06F19/00

CPC分类号： G06F19/20 ,  C12Q1/6837 ,  Y10T436/10

摘要： A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.

摘要翻译： 用于微阵列实验对中的荧光团的微阵列实验中的荧光团偏置去除方法是相反的。 此外，一种用于计算与名义上重复的微阵列实验中进行的每个测量相关联的各个错误的方法。 该误差测量可选地与基于秩的方法耦合，以便确定响应于扰动的细胞成分向上或向下调节的概率。 最后，在名义上重复的微阵列实验中确定细胞成分的表达水平的加权平均的置信度的方法。

公开(公告)号：US08521441B2

公开(公告)日：2013-08-27

申请号：US11042654

申请日：2005-01-24

申请人： Roland Stoughton ,  Hongyue Dai

发明人： Roland Stoughton ,  Hongyue Dai

IPC分类号： G06F19/00

CPC分类号： G06F19/20 ,  C12Q1/6837 ,  Y10T436/10

摘要： A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.

摘要翻译： 用于微阵列实验对中的荧光团的微阵列实验中的荧光团偏置去除方法是相反的。 此外，一种用于计算与名义上重复的微阵列实验中进行的每个测量相关联的各个错误的方法。 该误差测量可选地与基于秩的方法耦合，以便确定响应于扰动的细胞成分向上或向下调节的概率。 最后，在名义上重复的微阵列实验中确定细胞成分的表达水平的加权平均的置信度的方法。

公开(公告)号：US07966130B2

公开(公告)日：2011-06-21

申请号：US10287130

申请日：2002-11-04

申请人： Roland Stoughton ,  Hongyue Dai

发明人： Roland Stoughton ,  Hongyue Dai

IPC分类号： G06F19/00 ,  G06F7/38 ,  G01N33/48

CPC分类号： G06F19/20 ,  C12Q1/6837 ,  Y10T436/10

摘要： A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.

摘要翻译： 用于微阵列实验对中的荧光团的微阵列实验中的荧光团偏置去除方法是相反的。 此外，一种用于计算与名义上重复的微阵列实验中进行的每个测量相关联的各个错误的方法。 该误差测量可选地与基于秩的方法耦合，以便确定响应于扰动的细胞成分向上或向下调节的概率。 最后，在名义上重复的微阵列实验中确定细胞成分的表达水平的加权平均的置信度的方法。

公开(公告)号：US06351712B1

公开(公告)日：2002-02-26

申请号：US09222596

申请日：1998-12-28

申请人： Roland Stoughton ,  Hongyue Dai

发明人： Roland Stoughton ,  Hongyue Dai

IPC分类号： G01N3348

CPC分类号： G06F19/20 ,  C12Q1/6837 ,  Y10T436/10

摘要： A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.

公开(公告)号：US08019552B2

公开(公告)日：2011-09-13

申请号：US10591800

申请日：2005-03-07

申请人： Hongyue Dai ,  Laura J. Van't Veer ,  John Lamb ,  Roland Stoughton ,  Stephen H. Friend ,  Yudong He

发明人： Hongyue Dai ,  Laura J. Van't Veer ,  John Lamb ,  Roland Stoughton ,  Stephen H. Friend ,  Yudong He

IPC分类号： G01N33/48 ,  G01N33/50

CPC分类号： G01N33/57415 ,  C12Q1/6886 ,  C12Q2600/106 ,  C12Q2600/112 ,  C12Q2600/118 ,  Y10T436/143333

摘要： The present invention provides prognostic methods for conditions such as cancer, for example, breast cancer, comprising classifying an individual by a plurality of phenotypic, genotypic or clinical characteristics of the condition into a plurality of patient subsets, and analyzing the pattern of expression of prognosis-informative genes identified for that subset in a sample from the individual. The present invention also provides methods for constructing such patient subsets and of identifying prognosis-informative genesets for such subsets. The invention further provides methods of assigning a therapeutic regimen to an individual, microarrays useful for performing prognosis, kits comprising these microarrays, and computer systems and programs for implementing the methods of the invention.

摘要翻译： 本发明提供了诸如癌症例如乳腺癌的病症的预后方法，包括将个体的多个表型，基因型或临床特征分类为多个患者子集，并分析预后表达模式 在来自个体的样品中识别该子集的信息基因。 本发明还提供了用于构建这样的患者子集以及鉴定这样的子集的预后信息性基因组的方法。 本发明进一步提供了将个体的治疗方案分配给用于进行预后的微阵列，包括这些微阵列的试剂盒以及用于实施本发明的方法的计算机系统和程序的方法。

公开(公告)号：US20080187909A1

公开(公告)日：2008-08-07

申请号：US10591800

申请日：2005-03-07

申请人： Hongyue Dai ,  Laura J. Van't Veer ,  John Lamb ,  Roland Stoughton ,  Stephen H. Friend ,  Yudong He

发明人： Hongyue Dai ,  Laura J. Van't Veer ,  John Lamb ,  Roland Stoughton ,  Stephen H. Friend ,  Yudong He

IPC分类号： C12Q1/68 ,  C40B40/06

CPC分类号： G01N33/57415 ,  C12Q1/6886 ,  C12Q2600/106 ,  C12Q2600/112 ,  C12Q2600/118 ,  Y10T436/143333

摘要： The present invention provides prognostic methods for conditions such as cancer, for example, breast cancer, comprising classifying an individual by a plurality of phenotypic, genotypic or clinical characteristics of the condition into a plurality of patient subsets, and analyzing the pattern of expression of prognosis-informative genes identified for that subset in a sample from the individual. The present invention also provides methods for constructing such patient subsets and of identifying prognosis-informative genesets for such subsets. The invention further provides methods of assigning a therapeutic regimen to an individual, microarrays useful for performing prognosis, kits comprising these microarrays, and computer systems and programs for implementing the methods of the invention.

摘要翻译： 本发明提供了诸如癌症例如乳腺癌的病症的预后方法，包括将个体的多个表型，基因型或临床特征分类为多个患者子集，并分析预后表达模式 在来自个体的样品中识别该子集的信息基因。 本发明还提供了用于构建这样的患者子集以及鉴定这样的子集的预后信息性基因组的方法。 本发明进一步提供了将个体的治疗方案分配给用于进行预后的微阵列，包括这些微阵列的试剂盒以及用于实施本发明的方法的计算机系统和程序的方法。

公开(公告)号：US20050130215A1

公开(公告)日：2005-06-16

申请号：US11042653

申请日：2005-01-24

申请人： Roland Stoughton ,  Hongyue Dai

发明人： Roland Stoughton ,  Hongyue Dai

IPC分类号： G01N33/53 ,  C12N15/09 ,  C12Q1/68 ,  C12Q1/6837 ,  G01N33/48 ,  G01N33/566 ,  G01N33/58 ,  G01N37/00 ,  G06F17/18 ,  G06F19/20 ,  G06F19/00 ,  G01N33/50

CPC分类号： C12Q1/6837 ,  G16B25/00 ,  Y10T436/10

摘要： A method for fluorophore bias removal in microarray experiments in which the fluorophores used in microarray experiment pairs are reversed. Further, a method for calculating the individual errors associated with each measurement made in nominally repeated microarray experiments. This error measurement is optionally coupled with rank based methods in order to determine a probability that a cellular constituent is up or down regulated in response to a perturbation. Finally, a method for determining the confidence in the weighted average of the expression level of a cellular constituent in nominally repeated microarray experiments.

摘要翻译： 用于微阵列实验对中的荧光团的微阵列实验中的荧光团偏置去除方法是相反的。 此外，一种用于计算与名义上重复的微阵列实验中进行的每个测量相关联的各个错误的方法。 该误差测量可选地与基于秩的方法耦合，以便确定响应于扰动的细胞成分向上或向下调节的概率。 最后，在名义上重复的微阵列实验中确定细胞成分的表达水平的加权平均的置信度的方法。