公开(公告)号：US20100284915A1

公开(公告)日：2010-11-11

申请号：US12307114

申请日：2007-06-28

申请人： Hongyue Dai ,  Chunsheng Zhang ,  Andrey Loboda

发明人： Hongyue Dai ,  Chunsheng Zhang ,  Andrey Loboda

IPC分类号： A61K49/00 ,  C12Q1/68 ,  C40B30/00 ,  A61K31/713 ,  A61K31/7105 ,  A61K38/02 ,  A61K39/395 ,  A61K31/513 ,  A61K31/675 ,  A61K31/337 ,  A61K31/7048 ,  A61K31/282 ,  C12N5/07 ,  C12N5/071 ,  C40B40/08 ,  A61K31/7088 ,  A61P35/00

CPC分类号： G01N33/57415 ,  C12Q1/6886 ,  C12Q2600/106 ,  C12Q2600/118 ,  C12Q2600/136 ,  C12Q2600/158 ,  G01N33/57449 ,  G01N33/57484 ,  G16B20/00 ,  G16B25/00 ,  Y02A90/26

摘要： The invention provides molecular markers that are associated with responsiveness of a cancer patient to a chemotherapy treatment, and methods and computer systems for determining such responsiveness based on measurements of these molecular markers. The present invention also provides methods and compositions for enhancing the efficacy of chemotherapies in patients by modulating the expression or activity of genes encoding these molecular markers and/or their encoded proteins.

摘要翻译： 本发明提供与癌症患者对化疗治疗的反应性相关的分子标记，以及基于这些分子标记的测量来确定这种反应性的方法和计算机系统。 本发明还提供了通过调节编码这些分子标记和/或其编码蛋白的基因的表达或活性来增强患者化学疗法功效的方法和组合物。

公开(公告)号：US20140031251A1

公开(公告)日：2014-01-30

申请号：US13883478

申请日：2011-11-02

申请人： Timothy Yeatman ,  Andrey Loboda ,  Michael Nebozhyn ,  Hongyue Dai

发明人： Timothy Yeatman ,  Andrey Loboda ,  Michael Nebozhyn ,  Hongyue Dai

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6886 ,  C12Q2600/106 ,  C12Q2600/112 ,  C12Q2600/118 ,  C12Q2600/158 ,  C12Q2600/178

摘要： In one aspect, methods, markers, and expression signatures are disclosed for assessing the degree to which a cell sample has epithelial cell-like properties or mesenchymal cell-like properties. In another aspect, methods are provided for predicting cancer patient prognosis based on whether the cancer is classified as having a high or low EMT Signature Score.

摘要翻译： 一方面，公开了用于评估细胞样品具有上皮细胞样特性或间充质细胞样特性的程度的方法，标记和表达特征。 在另一方面，提供了用于基于癌症是否被分类为具有高或低EMT签名评分来预测癌症患者预后的方法。

公开(公告)号：US20140030255A1

公开(公告)日：2014-01-30

申请号：US13883485

申请日：2011-11-02

申请人： Andrey Loboda ,  Michael Nebozhyn ,  Hongyue Dai

发明人： Andrey Loboda ,  Michael Nebozhyn ,  Hongyue Dai

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6886 ,  C12Q2600/106 ,  C12Q2600/112 ,  C12Q2600/118 ,  C12Q2600/158 ,  C12Q2600/178

摘要： In one aspect, methods, markers, and expression signatures are disclosed for assessing the degree to which a cell sample has epithelial cell-like properties or mesenchymal cell-like properties. In another aspect, methods are provided for predicting whether a subject with cancer will respond to treatment with an agent, based on whether the cancer is classified as having a high or low EMT Signature Score.

摘要翻译： 一方面，公开了用于评估细胞样品具有上皮细胞样特性或间充质细胞样特性的程度的方法，标记和表达特征。 在另一方面，提供了用于基于癌症是否被分类为具有高或低EMT签名积分来预测癌症受试者是否将对药物治疗反应的方法。

公开(公告)号：US20100169025A1

公开(公告)日：2010-07-01

申请号：US12641486

申请日：2009-12-18

申请人： William T. Arthur ,  Brian Roberts ,  Rachel Needham ,  Hongyue Dai

发明人： William T. Arthur ,  Brian Roberts ,  Rachel Needham ,  Hongyue Dai

IPC分类号： G06F19/00 ,  C12Q1/68 ,  G06N5/02

CPC分类号： C12Q1/6876 ,  C12Q2600/158 ,  G16B25/00

摘要： Methods, biomarkers, and expression signatures are disclosed for assessing the regulation status of Wnt/β-catenin signaling pathway in a cell sample or subject. More specifically, several aspects of the invention provide a set of genes which can be used as biomarkers and gene signatures for evaluating Wnt/β-catenin pathway deregulation status in a sample; classifying a cell sample as having a deregulated or regulated Wnt/β-catenin signaling pathway; determining whether an agent modulates the Wnt/β-catenin signaling pathway in sample; predicting response of a subject to an agent that modulates the Wnt/β-catenin signaling pathway; assigning treatment to a subject; and evaluating the pharmacodynamic effects of therapies designed to regulate Wnt/β-catenin pathway signaling.

摘要翻译： 公开了方法，生物标志物和表达特征，用于评估细胞样品或受试者中Wnt / / bgr-catenin信号通路的调节状态。 更具体地，本发明的几个方面提供了一组基因，其可以用作用于评估样品中Wnt / bgr-连接蛋白通路去调节状态的生物标志物和基因特征; 将细胞样品分类为具有失调或调节的Wnt / / bgr-catenin信号通路; 确定试剂是否调节样品中的Wnt / bgr-catenin信号通路; 预测受试者对调节Wnt / bgr-catenin信号通路的药剂的反应; 为受试者分配治疗; 并评估旨在调节Wnt / bgr-catenin途径信号传导的疗法的药效学作用。

公开(公告)号：US20050084872A1

公开(公告)日：2005-04-21

申请号：US10764420

申请日：2004-01-23

申请人： Pek Lum ,  Yejun Tan ,  Hongyue Dai ,  Eric Muise ,  Joel Berger ,  John Thompson

发明人： Pek Lum ,  Yejun Tan ,  Hongyue Dai ,  Eric Muise ,  Joel Berger ,  John Thompson

IPC分类号： G01N33/48 ,  G01N33/50 ,  G06F19/00 ,  C12Q1/68

CPC分类号： G01N33/5014 ,  G01N33/48 ,  G01N2333/70567 ,  G16B25/00

摘要： In one aspect, the present invention provides methods for determining whether an agent (e.g., candidate drug) possesses a biological activity. In another aspect, the present invention provides populations of nucleic acid molecules useful in the practice of the present invention as probes for measuring the level of expression of populations of genes.

摘要翻译： 一方面，本发明提供了用于确定试剂（例如候选药物）是否具有生物活性的方法。 另一方面，本发明提供了可用于本发明实践的核酸分子群体，作为用于测量基因群体表达水平的探针。

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：US07171311B2

公开(公告)日：2007-01-30

申请号：US10342887

申请日：2003-01-15

申请人： Hongyue Dai ,  Yudong He ,  Peter S. Linsley ,  Mao Mao ,  Christopher J. Roberts ,  Laura Johanna Van't Veer ,  Marc J. Van de Vijver ,  Rene Bernards ,  A. A. M. Hart

发明人： Hongyue Dai ,  Yudong He ,  Peter S. Linsley ,  Mao Mao ,  Christopher J. Roberts ,  Laura Johanna Van't Veer ,  Marc J. Van de Vijver ,  Rene Bernards ,  A. A. M. Hart

IPC分类号： G01N33/48 ,  C12Q1/68

CPC分类号： C12Q1/6886 ,  C12Q2600/106 ,  C12Q2600/112 ,  C12Q2600/118 ,  C12Q2600/136 ,  C12Q2600/158

摘要： The present invention relates to genetic markers whose expression is correlated with breast cancer. Specifically, the invention provides sets of markers whose expression patterns can be used to differentiate clinical conditions associated with breast cancer, such as the presence or absence of the estrogen receptor ESR1, and BRCA1 and sporadic tumors, and to provide information on the likelihood of tumor distant metastases within five years of initial diagnosis. The invention relates to methods of using these markers to distinguish these conditions. The invention also provides methods of classifying and treating patients based on prognosis. The invention also relates to kits containing ready-to-use microarrays and computer software for data analysis using the diagnostic, prognostic and statistical methods disclosed herein.

摘要翻译： 本发明涉及其表达与乳腺癌相关的遗传标记。 具体地，本发明提供了一组标志物，其表达模式可用于区分与乳腺癌相关的临床病症，例如雌激素受体ESR1和BRCA1和散发性肿瘤的存在或不存在，并提供关于肿瘤可能性的信息 初步诊断五年内远处转移。 本发明涉及使用这些标记来区分这些条件的方法。 本发明还提供了基于预后对患者进行分类和治疗的方法。 本发明还涉及包含即用型微阵列的试剂盒和用于使用本文公开的诊断，预后和统计学方法进行数据分析的计算机软件。

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：US08105777B1

公开(公告)日：2012-01-31

申请号：US12370264

申请日：2009-02-12

申请人： Hongyue Dai ,  Laura J. Van't Veer ,  Yudong He

发明人： Hongyue Dai ,  Laura J. Van't Veer ,  Yudong He

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6886 ,  C12Q2600/118 ,  C12Q2600/158

摘要： The present invention relates to genetic markers whose expression is correlated with colon cancer. In one aspect, the invention provides sets of markers whose expression can be used for classifying colon cancer patients into different prognostic categories. In another aspect, the invention provides kits containing marker sets for determining prognosis of colon cancer. In another aspect, the invention provides methods of classifying cancer patients with regard to prognosis.

摘要翻译： 本发明涉及其表达与结肠癌相关的遗传标记。 一方面，本发明提供了一组标志物，其表达可用于将结肠癌患者分类为不同的预后类别。 另一方面，本发明提供了包含用于确定结肠癌预后的标记物组的试剂盒。 另一方面，本发明提供了关于预后的癌症患者分类方法。

公开(公告)号：US08014957B2

公开(公告)日：2011-09-06

申请号：US11640517

申请日：2006-12-14

申请人： Jerald P. Radich ,  Hongyue Dai ,  Mao Mao ,  Janell M. Schelter ,  Peter S. Linsley

发明人： Jerald P. Radich ,  Hongyue Dai ,  Mao Mao ,  Janell M. Schelter ,  Peter S. Linsley

IPC分类号： G01N33/48

CPC分类号： C12Q1/6886 ,  C12Q2600/106 ,  C12Q2600/112 ,  C12Q2600/136 ,  C12Q2600/158 ,  Y02A90/26

摘要： The invention provides molecular markers that are associated with the progression of chronic myeloid leukemia (CML), and methods and computer systems for monitoring the progression of CML in a patient based on measurements of these molecular markers. The present invention also provides CML target genes, and methods and compositions for treating CML patients by modulating the expression or activity of these CML target genes and/or their encoded proteins. The invention also provides genes that are associated with resistance to imatinib mesylate (Gleevec™) treatment in CML patients, and methods and compositions for determining the responsiveness of a CML patient to imatinib mesylate treatment based on measurements of these genes and/or their encoded proteins. The invention also provides methods and compositions for enhancing the effect of Gleevec™ by modulating the expression or activity of these genes and/or their encoded proteins.

摘要翻译： 本发明提供了与慢性骨髓性白血病（CML）进展相关的分子标记，以及用于基于这些分子标记物的测量来监测患者中CML进展的方法和计算机系统。 本发明还提供CML靶基因，以及通过调节这些CML靶基因和/或其编码蛋白的表达或活性来治疗CML患者的方法和组合物。 本发明还提供了与CML患者中对伊马替尼甲磺酸盐（Gleevec TM）治疗有关的基因，以及基于这些基因和/或其编码蛋白质的测量来确定CML患者对甲磺酸伊马替尼治疗的反应性的方法和组合物 。 本发明还提供了通过调节这些基因和/或其编码的蛋白质的表达或活性来增强Gleevec TM的作用的方法和组合物。