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公开(公告)号：US09057108B2
公开(公告)日：2015-06-16
申请号：US13611584
申请日：2012-09-12
IPC分类号： C12Q1/68 , G01N33/574 , G06F19/20 , G06F19/24
CPC分类号： C12Q1/6886 , C12Q2600/112 , C12Q2600/158 , G01N33/574 , G01N33/57484 , G06F19/20 , G06F19/24
摘要： A two-tiered classification system that can be integrated with the current algorithm used by pathologists for identification of the site of origin for ‘malignancy with unknown primary’ is presented. In use, morphology, immunohistochemical (IHC) studies, and microarray-based top tier gene expression classifiers first subclassify cytokeratin positive carcinomas into adenocarcinoma, squamous cell carcinoma, neuroendocrine carcinoma and urothelial carcinoma. Subsequently, organ-specific IHC-markers, if available, are used in conjunction with microarray-based second tier gene expression classifiers to assign the primary site of origin to the sample. This new hybrid approach combines IHC with a hierarchy of quantitative gene expression based classifiers into an algorithmic method that can assist pathologists to further refine and support their decision making process.
摘要翻译： 提出了一种双层分类系统，可与病理学家使用的当前算法结合，用于鉴定“未知原发性恶性肿瘤”的起源部位。 在使用中，形态学，免疫组化（IHC）研究和基于微阵列的顶层基因表达分类器首先将细胞角蛋白阳性癌分为腺癌，鳞状细胞癌，神经内分泌癌和尿路上皮癌。 随后，器官特异性IHC标记（如果可用）与基于微阵列的第二层基因表达分类器结合使用，以将原始起始位点分配给样品。 这种新的混合方法将IHC与基于定量基因表达的分类器的层次结合成一种算法方法，可以帮助病理学家进一步完善和支持他们的决策过程。
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公开(公告)号：US20130172203A1
公开(公告)日：2013-07-04
申请号：US13611584
申请日：2012-09-12
IPC分类号： C12Q1/68 , G06F19/24 , G01N33/574
CPC分类号： C12Q1/6886 , C12Q2600/112 , C12Q2600/158 , G01N33/574 , G01N33/57484 , G06F19/20 , G06F19/24
摘要： A two-tiered classification system that can be integrated with the current algorithm used by pathologists for identification of the site of origin for ‘malignancy with unknown primary ’ is presented. In use, morphology, immunohistochemical (IHC) studies, and microarry-based top tier gene expression classifiers first subclassify cytokeratin positive carcinomas into adenocarcinoma, squamous cell carcinoma, neuroendocrine carcinoma and urothelial carcinoma. Subsequently, organ-specific IHC-markers, if available, are used in conjunction with microarray-based second tier gene expression classifiers to assign the primary site of origin to the sample. This new hybrid approach combines IHC with a hierarchy of quantitative gene expression based classifiers into an algorithmic method that can assist pathologists to further refine and support their decision making process.
摘要翻译： 提出了一种双层分类系统，可与病理学家使用的当前算法结合，用于鉴定“未知原发性恶性肿瘤”的起源部位。 在使用中，形态学，免疫组织化学（IHC）研究和基于微阵列的顶层基因表达分类器首先将细胞角蛋白阳性癌分类为腺癌，鳞状细胞癌，神经内分泌癌和尿路上皮癌。 随后，器官特异性IHC标记（如果可用）与基于微阵列的第二层基因表达分类器结合使用，以将原始起始位点分配给样品。 这种新的混合方法将IHC与基于定量基因表达的分类器的层次结合成一种算法方法，可以帮助病理学家进一步完善和支持他们的决策过程。
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3.发明申请公开(公告)号：US20110288890A1
公开(公告)日：2011-11-24
申请号：US13205536
申请日：2011-08-08
申请人： William S. Dalton , Timothy Yeatman
发明人： William S. Dalton , Timothy Yeatman
IPC分类号： G06Q50/00
摘要： Computers, computer program products, and methods for identifying a plurality of subjects for a clinical trial are provided. A candidate set of molecular profiles in a stored plurality of molecular profiles are identified. Each such profile has measurements for a discriminating set of cellular constituents that match the measurements of corresponding cellular constituents in a responder set of biological samples, thereby identifying the plurality of subjects for the trial from those subjects from which the candidate set of molecular profiles were derived. Each respective molecular profile in the stored plurality of profiles has measurements of a plurality of cellular constituents from a respective biological sample in a plurality of samples obtained from a first plurality of subjects. The discriminating set of cellular constituents is identified from those cellular constituents in the plurality of cellular constituents whose measurement values discriminates between the responder and nonresponder sets of biological samples.
摘要翻译： 提供了计算机，计算机程序产品和用于识别用于临床试验的多个对象的方法。 鉴定存储的多个分子谱中的候选分子谱集。 每个这样的简档具有与生物样本的响应者组中的相应细胞成分的测量相匹配的细胞成分鉴别组的测量结果，从而从衍生出候选分子谱的集合的那些受试者中鉴定出试验的多个受试者 。 存储的多个轮廓中的每个相应分子轮廓具有来自从第一组多个受试者获得的多个样本中的相应生物样品的多个细胞成分的测量。 从多个细胞组分中的细胞成分鉴别细胞组分的鉴别集，其测量值区分应答者和生物样品的无应答组。
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4.发明申请公开(公告)号：US20080033658A1
公开(公告)日：2008-02-07
申请号：US11879387
申请日：2007-07-16
申请人： William Dalton , Timothy Yeatman
发明人： William Dalton , Timothy Yeatman
IPC分类号： G06F19/00
摘要： Computers, computer program products, and methods for identifying a plurality of subjects for a clinical trial are provided. A candidate set of molecular profiles in a stored plurality of molecular profiles are identified. Each such profile has measurements for a discriminating set of cellular constituents that match the measurements of corresponding cellular constituents in a responder set of biological samples, thereby identifying the plurality of subjects for the trial from those subjects from which the candidate set of molecular profiles were derived. Each respective molecular profile in the stored plurality of profiles has measurements of a plurality of cellular constituents from a respective biological sample in a plurality of samples obtained from a first plurality of subjects. The discriminating set of cellular constituents is identified from those cellular constituents in the plurality of cellular constituents whose measurement values discriminates between the responder and nonresponder sets of biological samples.
摘要翻译： 提供了计算机，计算机程序产品和用于识别用于临床试验的多个对象的方法。 鉴定存储的多个分子谱中的候选分子谱集。 每个这样的简档具有与生物样本的响应者组中的相应细胞成分的测量相匹配的细胞成分鉴别组的测量结果，从而从衍生出候选分子谱的集合的那些受试者中鉴定出试验的多个受试者 。 存储的多个轮廓中的每个相应分子轮廓具有来自从第一组多个受试者获得的多个样本中的相应生物样品的多个细胞成分的测量。 从多个细胞组分中的细胞成分鉴别细胞组分的鉴别集，其测量值区分应答者和生物样品的无应答组。
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5.发明申请公开(公告)号：US20060195266A1
公开(公告)日：2006-08-31
申请号：US11065794
申请日：2005-02-25
申请人： Timothy Yeatman
发明人： Timothy Yeatman
IPC分类号： G06F19/00
CPC分类号： G16B25/00 , C12Q1/6886 , C12Q2600/106 , C12Q2600/118 , G16B40/00
摘要： The present invention pertains to specific gene signatures for cancer that are used to predict survival and novel processes for identifying such gene signatures. In one embodiment, gene signatures for human colorectal cancer are identified and outcomes are linked to the specific gene signatures using significance analysis of microarrays (SAM) and support vector machines (SVM) to provide a prognosis/survival classifier.
摘要翻译： 本发明涉及用于预测存活的癌症的特异性基因特征以及鉴定这种基因特征的新方法。 在一个实施方案中，使用微阵列（SAM）和支持向量机（SVM）的显着性分析来鉴定人结肠直肠癌的基因特征，并将结果与特定基因特征相关联，以提供预后/生存分类器。
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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。
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7.发明授权公开(公告)号：US08175896B2
公开(公告)日：2012-05-08
申请号：US13205536
申请日：2011-08-08
申请人： William S. Dalton , Timothy Yeatman
发明人： William S. Dalton , Timothy Yeatman
摘要： Computers, computer program products, and methods for identifying a plurality of subjects for a clinical trial are provided. A candidate set of molecular profiles in a stored plurality of molecular profiles are identified. Each such profile has measurements for a discriminating set of cellular constituents that match the measurements of corresponding cellular constituents in a responder set of biological samples, thereby identifying the plurality of subjects for the trial from those subjects from which the candidate set of molecular profiles were derived. Each respective molecular profile in the stored plurality of profiles has measurements of a plurality of cellular constituents from a respective biological sample in a plurality of samples obtained from a first plurality of subjects. The discriminating set of cellular constituents is identified from those cellular constituents in the plurality of cellular constituents whose measurement values discriminates between the responder and nonresponder sets of biological samples.
摘要翻译： 提供了计算机，计算机程序产品和用于识别用于临床试验的多个对象的方法。 鉴定存储的多个分子谱中的候选分子谱集。 每个这样的简档具有与生物样本的响应者组中的相应细胞成分的测量相匹配的细胞成分鉴别组的测量结果，从而从衍生出候选分子谱的集合的那些受试者中鉴定出试验的多个受试者 。 存储的多个轮廓中的每个相应分子轮廓具有来自从第一组多个受试者获得的多个样本中的相应生物样品的多个细胞成分的测量。 从多个细胞组分中的细胞成分鉴别细胞组分的鉴别集，其测量值区分应答者和生物样品的无应答组。
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公开(公告)号：US08095389B2
公开(公告)日：2012-01-10
申请号：US11879387
申请日：2007-07-16
申请人： William S. Dalton , Timothy Yeatman
发明人： William S. Dalton , Timothy Yeatman
摘要： Computers, computer program products, and methods for identifying a plurality of subjects for a clinical trial are provided. A candidate set of molecular profiles in a stored plurality of molecular profiles are identified. Each such profile has measurements for a discriminating set of cellular constituents that match the measurements of corresponding cellular constituents in a responder set of biological samples, thereby identifying the plurality of subjects for the trial from those subjects from which the candidate set of molecular profiles were derived. Each respective molecular profile in the stored plurality of profiles has measurements of a plurality of cellular constituents from a respective biological sample in a plurality of samples obtained from a first plurality of subjects. The discriminating set of cellular constituents is identified from those cellular constituents in the plurality of cellular constituents whose measurement values discriminates between the responder and nonresponder sets of biological samples.
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公开(公告)号：US20060195269A1
公开(公告)日：2006-08-31
申请号：US11134688
申请日：2005-05-19
申请人： Timothy Yeatman , Steven Eschrich , Gregory Bloom
发明人： Timothy Yeatman , Steven Eschrich , Gregory Bloom
IPC分类号： G06F19/00
CPC分类号： G06F19/20 , C12Q1/6886 , C12Q2600/106 , C12Q2600/118 , G06F19/24
摘要： The invention provides a molecular marker set that can be used for prognosis of colorectal cancer in a colorectal cancer patient. The invention also provides methods and computer systems for evaluating prognosis of colorectal cancer in a colorectal cancer patient based on the molecular marker set. The invention also provides methods and computer systems for determining chemotherapy for a colorectal cancer patient and for enrolling patients in clinical trials.
摘要翻译： 本发明提供可用于结肠直肠癌患者结肠直肠癌预后的分子标记物。 本发明还提供了基于分子标记物组来评估结直肠癌患者的结肠直肠癌预后的方法和计算机系统。 本发明还提供了用于确定结肠直肠癌患者的化学疗法的方法和计算机系统，并且用于在临床试验中招募患者。
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公开(公告)号：US20110046002A1
公开(公告)日：2011-02-24
申请号：US12744027
申请日：2008-11-20
申请人： Timothy Yeatman , Dung-Tsa Chen , Aejaz Nasir
发明人： Timothy Yeatman , Dung-Tsa Chen , Aejaz Nasir
CPC分类号： C12Q1/6886 , C12Q2600/118 , C12Q2600/158
摘要： The invention provides a molecular marker set that can be used for prognosis of breast cancer in a patient using histologically normal tissue. The invention also provides methods for evaluating prognosis of breast cancer in a patient based on a molecular molecular signature.
摘要翻译： 本发明提供了可以用于使用组织学正常组织的患者乳腺癌预后的分子标记物组。 本发明还提供了基于分子分子特征评估患者乳腺癌预后的方法。
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