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1. 发明申请

WO2008131035A2 METHODS FOR DIAGNOSING, PROGNOSING, OR THERANOSING A CONDITION USING RARE CELLS 审中-公开
标题翻译：用于诊断，预处理或治疗使用稀有细胞的条件的方法
公开(公告)号：WO2008131035A2
公开(公告)日：2008-10-30
申请号：PCT/US2008/060527
申请日：2008-04-16
申请人： CELLPOINT DIAGNOTICS, INC. , KOPF-SILL, Anne, R. , WU, Lena , STOUGHTON, Roland
发明人： KOPF-SILL, Anne, R. , WU, Lena , STOUGHTON, Roland
IPC分类号： G01N33/569 , A61B5/00
CPC分类号： C12Q1/6883 , C12Q2600/118 , C12Q2600/156 , G01N1/31 , G01N33/5091 , G01N33/57484 , G01N33/57488 , G01N33/57492 , G01N2333/705

2. 发明申请

WO2004093644A3 METHODS AND APPARATUS FOR GENETIC EVALUATION 审中-公开
标题翻译：遗传评价的方法和装置
公开(公告)号：WO2004093644A3
公开(公告)日：2006-06-01
申请号：PCT/US2004011877
申请日：2004-04-16
申请人： ISIS PHARMACEUTICALS INC , SCIENCE APPLIC INT CORP , ECKER DAVID J , GRIFFEY RICHARD H , SAMPATH RANGARAJAN , HOFSTADLER STEVEN A , MCNEIL JOHN , CROOKE STANLEY T , SOFIANOS DINO J , RUDNICK KARL H , KNIZE DUANE J , STOUGHTON ROLAND B , BASHAM CECIL L JR , LEWIS CLIFFORD T , LARSON BRONS M , BAR-ON JONATHAN R , MURRAY DENNIS P , ROBBINS DAVID W , PENHUNE JOHN P
发明人： ECKER DAVID J , GRIFFEY RICHARD H , SAMPATH RANGARAJAN , HOFSTADLER STEVEN A , MCNEIL JOHN , CROOKE STANLEY T , SOFIANOS DINO J , RUDNICK KARL H , KNIZE DUANE J , STOUGHTON ROLAND B , BASHAM CECIL L JR , LEWIS CLIFFORD T , LARSON BRONS M , BAR-ON JONATHAN R , MURRAY DENNIS P , ROBBINS DAVID W , PENHUNE JOHN P
IPC分类号： C12Q1/68 , A61B20060101 , G01N33/48 , G01N33/50 , G06F19/00
CPC分类号： G06F19/22 , Y10T436/24
摘要： Rapid and definitive bioagent detection and identification can be carried out without nucleic acid sequencing. Analysis of a variety of bioagents and samples, such as air, fluid, and body samples, can be carried out to provide information useful for industrial, medical, and environmental purposes. Nucleic acid samples of unknown or suspected bioagents may be collected, optimal primer pairs may be selected, and the nucleic acid may be amplified. Expected mass spectra signal models may be generated and selected, the actual mass spectra of the amplicons may be obtained. The expected mass spectra most closely correlating with the actual mass spectra may be determined using a joint maximum likelihood analysis, and base counts for the actual mass spectra and the expected mass spectra may be obtained. The most likely candidate bioagents may then be determined.
摘要翻译：可以在不进行核酸测序的情况下进行快速和确定的生物鉴定检测和鉴定。可以对各种生物标本和样品（如空气，液体和身体样品）进行分析，以提供有用的工业，医疗和环境用途的信息。可以收集未知或疑似生物标记的核酸样品，可以选择最佳引物对，并且可以扩增核酸。可以生成和选择预期的质谱信号模型，可以获得扩增子的实际质谱。可以使用联合最大似然分析确定与实际质谱最密切相关的预期质谱，并且可以获得实际质谱和预期质谱的碱值。然后可能确定最可能的候选生物标签。

3. 发明申请

WO0202741A3 METHODS FOR GENETIC INTERPRETATION AND PREDICTION OF PHENOTYPE 审中-公开
标题翻译：用于遗传解释和预测的方法
公开(公告)号：WO0202741A3
公开(公告)日：2002-04-04
申请号：PCT/US0120931
申请日：2001-07-02
申请人： ROSETTA INPHARMATICS INC , STOUGHTON ROLAND , MARTON MATTHEW J
发明人： STOUGHTON ROLAND , MARTON MATTHEW J
IPC分类号： C12N15/10 , C12Q1/68 , G06F19/18 , A61B5/00 , G01N33/53 , G01N33/543 , G01N33/557
CPC分类号： C12N15/1079 , C12Q2600/158 , G06F19/18
摘要： The present invention relates to methods for determining the genetic causes of certain phenotypes. The present invention further relates to methods for predicting the phenotype of a organism from its genotype. In particular, the methods of the invention relate to the use of compendia of biological response profiles of cells having known genetic mutations for comparisons with the biological response profiles of cells having unknown phenotypes and genotypes. The methods of the present invention are particularly useful for monitoring the success of genetic engineering and cross-breeding of crops and livestock. The present invention further relates to a computer system for comparing biological response profiles to a compendium of biological response profiles and to kits for relating the phenotype of a cell type to its genotype or for predicting the phenotype of a cell type.
摘要翻译：本发明涉及确定某些表型的遗传原因的方法。本发明还涉及从其基因型预测生物体的表型的方法。特别地，本发明的方法涉及使用具有已知基因突变的细胞的生物学应答谱的概要与具有未知表型和基因型的细胞的生物反应谱比较。本发明的方法对于监测作物和牲畜的遗传工程和杂交育种的成功特别有用。本发明还涉及用于将生物反应概况与生物反应概况纲要进行比较的计算机系统和用于将细胞类型的表型与其基因型相关联或用于预测细胞类型的表型的试剂盒。

4. 发明申请

WO9966024A9 METHODS OF MONITORING DISEASE STATES AND THERAPIES USING GENE EXPRESSION PROFILES 审中-公开
标题翻译：使用基因表达谱来监测疾病状态和治疗方法
公开(公告)号：WO9966024A9
公开(公告)日：2000-03-23
申请号：PCT/US9913750
申请日：1999-06-17
申请人： ROSETTA INPHARMATICS INC , FRIEND STEPHEN H , STOUGHTON ROLAND
发明人： FRIEND STEPHEN H , STOUGHTON ROLAND
IPC分类号： G01D1/16 , A01N43/04 , A01N61/00 , C07H21/04 , C12M20060101 , C12M1/34 , C12M3/00 , C12N15/09 , C12P21/06 , C12Q1/02 , C12Q1/68 , G01N33/48 , G01N33/53 , G01N37/00 , G06G7/48
CPC分类号： C12Q1/6886 , C12Q2600/156 , C12Q2600/158
摘要： The present invention provides methods for monitoring disease states in a subject, as well as methods for monitoring the levels of effect of therapies upon a subject having one or more disease states. The methods involve: (i) measuring abundances of cellular constituents in a cell from a subject so that a diagnostic profile is obtained, (ii) measuring abundances of cellular constituents in a cell of one or more analogous subjects so that perturbation response profiles are obtained which correlate to a particular disease or therapy, and (iii) determining the interpolated perturbation response profile or profiles which best fit the diagnostic profile according to some objective measure. In other aspects, the invention also provides a computer system capable of performing the methods of the invention, data bases comprising perturbation response profiles for one or more diseases and/or therapies, and kits for determining levels of disease states and/or therapeutic effects according to the methods of the invention.
摘要翻译：本发明提供了用于监测受试者的疾病状态的方法，以及用于监测治疗对具有一种或多种疾病状态的受试者的疗效水平的方法。方法包括：（i）测量来自受试者的细胞中细胞成分的丰度，从而获得诊断分布，（ii）测量一个或多个类似受试者的细胞中细胞成分的丰度，从而获得扰动反应曲线其与特定疾病或治疗相关，以及（iii）根据一些客观测量来确定最适合于诊断谱的内插扰动响应曲线或轮廓。在其它方面，本发明还提供一种能够执行本发明方法的计算机系统，包括用于一种或多种疾病和/或疗法的扰动响应曲线的数据库，以及用于确定疾病状态和/或治疗效果水平的试剂盒，涉及本发明的方法。

5. 发明申请

WO2004093644A2 METHODS AND APPARATUS FOR GENETIC EVALUATION 审中-公开
标题翻译：遗传评价的方法和装置
公开(公告)号：WO2004093644A2
公开(公告)日：2004-11-04
申请号：PCT/US2004/011877
申请日：2004-04-16
申请人： ISIS PHARMACEUTICALS, INC. , SCIENCE APPLICATIONS INTERNATIONAL CORPORATION , ECKER, David, J. , GRIFFEY, Richard, H. , SAMPATH, Rangarajan , HOFSTADLER, Steven, A. , McNEIL, John , CROOKE, Stanley, T. , SOFIANOS, Dino, J. , RUDNICK, Karl, H. , KNIZE, Duane, J. , STOUGHTON, Roland, B. , BASHAM, Cecil, L., Jr. , LEWIS, Clifford, T. , LARSON, Brons, M. , BAR-ON, Jonathan, R. , MURRAY, Dennis, P. , ROBBINS, David, W. , PENHUNE, John, P.
发明人： ECKER, David, J. , GRIFFEY, Richard, H. , SAMPATH, Rangarajan , HOFSTADLER, Steven, A. , McNEIL, John , CROOKE, Stanley, T. , SOFIANOS, Dino, J. , RUDNICK, Karl, H. , KNIZE, Duane, J. , STOUGHTON, Roland, B. , BASHAM, Cecil, L., Jr. , LEWIS, Clifford, T. , LARSON, Brons, M. , BAR-ON, Jonathan, R. , MURRAY, Dennis, P. , ROBBINS, David, W. , PENHUNE, John, P.
IPC分类号： A61B
CPC分类号： G06F19/22 , Y10T436/24
摘要： Rapid and definitive bioagent detection and identification can be carried out without nucleic acid sequencing. Analysis of a variety of bioagents and samples, such as air, fluid, and body samples, can be carried out to provide information useful for industrial, medical, and environmental purposes. Nucleic acid samples of unknown or suspected bioagents may be collected, optimal primer pairs may be selected, and the nucleic acid may be amplified. Expected mass spectra signal models may be generated and selected, the actual mass spectra of the amplicons may be obtained. The expected mass spectra most closely correlating with the actual mass spectra may be determined using a joint maximum likelihood analysis, and base counts for the actual mass spectra and the expected mass spectra may be obtained. The most likely candidate bioagents may then be determined.
摘要翻译：可以在不进行核酸测序的情况下进行快速和确定的生物鉴定检测和鉴定。可以对各种生物标本和样品（如空气，液体和身体样品）进行分析，以提供有用的工业，医疗和环境用途的信息。可以收集未知或疑似生物标记的核酸样品，可以选择最佳引物对，并且可以扩增核酸。可以生成和选择预期的质谱信号模型，可以获得扩增子的实际质谱。可以使用联合最大似然分析来确定与实际质谱最密切相关的预期质谱，并且可以获得实际质谱和预期质谱的碱值。然后可能确定最可能的候选生物标签。

6. 发明申请

WO0003039A9 METHODS FOR DETERMINING CROSS-HYBRIDIZATION 审中-公开
标题翻译：确定交叉杂交的方法
公开(公告)号：WO0003039A9
公开(公告)日：2000-05-25
申请号：PCT/US9915813
申请日：1999-07-13
申请人： ROSETTA INPHARMATICS INC , BURCHARD JULJA , STOUGHTON ROLAND , FRIEND STEPHEN H
发明人： BURCHARD JULJA , STOUGHTON ROLAND , FRIEND STEPHEN H
IPC分类号： C07H21/04 , C12M1/34 , C12Q1/68 , G06F17/00
CPC分类号： C12Q1/6832 , C07B2200/11 , C12Q2527/107
摘要： The present invention provides methods for distinguishing the fractions of polynucleotide sequences which hybridize to any given probe, including probes on microarrays such as those described herein. In particular, the present invention enables users to identify the fraction of sequences which are perfectly complementary to a probe, thereby correcting for effects of cross-hybridization in a hybridization assay. The methods of the invention work by monitoring the kinetics of dissociation of sequences from the probe so that a resulting "dissociation curve" may be compared to a combination of the individual "dissociation profiles" for each sequence which hybridizes. In alternative embodiments, the invention also provides computer systems for performing the present methods, as well as databases of the dissociation profiles.
摘要翻译：本发明提供了区分与任何给定探针杂交的多核苷酸序列部分的方法，包括微阵列上的探针，例如本文所述的那些。具体而言，本发明使用户能够鉴定与探针完全互补的序列部分，由此校正杂交测定中的交叉杂交效应。本发明的方法通过监测来自探针的序列的解离动力学进行工作，以使得到的“解离曲线”可以与每个杂交序列的单个“解离曲线”的组合相比较。在替代实施例中，本发明还提供用于执行本发明方法的计算机系统以及解离曲线的数据库。

7. 发明申请

WO9959037A9 METHODS OF DETERMINING PROTEIN ACTIVITY LEVELS USING GENE EXPRESSION PROFILES 审中-公开
标题翻译：使用基因表达谱分析蛋白质活性水平的方法
公开(公告)号：WO9959037A9
公开(公告)日：2000-03-02
申请号：PCT/US9910027
申请日：1999-05-07
申请人： ROSETTA INPHARMATICS INC , FRIEND STEPHEN H , STOUGHTON ROLAND
发明人： FRIEND STEPHEN H , STOUGHTON ROLAND
IPC分类号： G01N33/68 , A61K38/00 , C07K14/47 , C12Q1/68 , G01N33/15 , G01N33/50 , G01N33/53 , G05B1/03
CPC分类号： C07K14/4702 , A61K38/00
摘要： The present invention provides methods for determining the level of protein activity in a cell by: (i) measuring abundances of cellular constituents in a cell in which the activity of a specific protein is to be determined so that a diagnostic profile is thus obtained; (ii) measuring abundances of cellular constituents that occur in a cell in response to perturbations in the activity of said protein to obtain response profiles and interpolating said response profiles to generate response curves; and (iii) determining a protein activity level at which the response profile extracted from the response curves best fits the measured diagnostic profile, according to some objective measure. In alternative embodiments, the present invention also provides methods for identifying individuals having genetic mutations or polymorphisms that disrupt protein activity, and methods for identifying drug activity in vivo by determining the activity levels of proteins which interact with said drugs.
摘要翻译：本发明提供了通过以下步骤确定细胞中蛋白质活性水平的方法：（i）测量要确定特定蛋白质的活性的细胞中细胞成分的丰度，从而获得诊断特征; （ii）测量在细胞中发生的细胞成分的丰度以响应所述蛋白质的活动中的扰动以获得反应谱并内插所述响应谱以产生响应曲线; 和（iii）根据一些客观的测定，确定从响应曲线提取的反应曲线最适合测量的诊断谱的蛋白质活性水平。在替代实施方案中，本发明还提供了用于鉴定具有破坏蛋白质活性的遗传突变或多态性的个体的方法，以及通过测定与所述药物相互作用的蛋白质的活性水平来鉴定体内药物活性的方法。

8. 发明申请

WO9946367A8 METHODS OF DIAGNOSIS AND TRIAGE USING CELL ACTIVATION MEASURES 审中-公开
标题翻译：使用细胞激活措施的诊断和治疗方法
公开(公告)号：WO9946367A8
公开(公告)日：2000-01-13
申请号：PCT/US9905247
申请日：1999-03-11
申请人： CELL ACTIVATION INC , UNIV CALIFORNIA , SCRIPPS RESEARCH INST , STOUGHTON ROLAND B , SCHMID SCHONBEIN GEERT W , HUGLI TONY E , KISTLER ERIK
发明人： STOUGHTON ROLAND B , SCHMID-SCHONBEIN GEERT W , HUGLI TONY E , KISTLER ERIK
IPC分类号： A61K35/39 , A61K38/55 , A61K38/57 , A61K49/00 , A61M1/14 , A61P3/10 , A61P9/00 , A61P9/10 , A61P25/28 , A61P27/02 , A61P37/02 , A61P37/06 , A61P43/00 , C07K14/47 , C12N5/06 , C12N5/08 , C12Q1/02 , C12Q1/26 , G01N33/15 , G01N33/50 , A61K31/235
CPC分类号： A61K38/57 , C07K14/4705 , C12Q1/26 , G01N33/5091
摘要： Diagnostic methods that rely on the use of one or more assays that assess cellular activation are provided. The assays are performed on whole blood or leukocytes (neutrophils), and indicate individually or in combination the level of cardiovascular cell activation, which is pivotal in many chronic and acute disease states. These results of the assays are used within a clinical framework to support therapeutic decisions such as: further testing for infectious agents, anti-oxidant or anti-adhesion therapy, postponement and optimal re-scheduling of high-risk surgeries, classifying susceptibility to and progression rates of chronic disease such as diabetes, organ rejection, atherogenesis, and venous insufficiency; extreme interventions in trauma cases of particularly high risk and activation-lowering therapies. Also provided is composition derived from a pancreatic homogenate that contains circulating cell activating factors, which can serve as targets for drug screening to identify drug candidates for use in activation lowering therapies. Methods for lowering cell activation by administering protease inhibitors, particularly serine protease inhibitors, are also provided. Kits for performing the methods are also provided.
摘要翻译：提供依赖于使用一种或多种评估细胞活化的测定法的诊断方法。对全血或白细胞（嗜中性粒细胞）进行测定，并且单独地或组合地表示许多慢性和急性疾病状态中关键的心血管细胞活化水平。这些测定结果在临床框架内用于支持治疗决定，例如：进一步测试感染因子，抗氧化剂或抗粘连治疗，推迟和最佳重新调度高风险手术，分类易感性和进展慢性疾病如糖尿病，器官排斥，动脉粥样硬化和静脉功能不全的发生率; 极度干预创伤病例特别高风险和降低激活的疗法。还提供衍生自包含循环细胞活化因子的胰脏匀浆的组合物，其可以用作药物筛选的靶标，以鉴定用于活化降低疗法的药物候选物。还提供了通过施用蛋白酶抑制剂，特别是丝氨酸蛋白酶抑制剂来降低细胞活化的方法。还提供了用于执行方法的工具包。

9. 发明申请

WO2009035447A1 DIAGNOSIS OF FETAL ABNORMALITIES BY COMPARATIVE GENOMIC HYBRIDIZATION ANALYSIS 审中-公开
标题翻译：通过比较基因组杂交分析诊断不典型性
公开(公告)号：WO2009035447A1
公开(公告)日：2009-03-19
申请号：PCT/US2007/071255
申请日：2007-06-14
申请人： LIVING MICROSYSTEMS, INC. , STOUGHTON, Roland , KAPUR, Ravi
发明人： STOUGHTON, Roland , KAPUR, Ravi
IPC分类号： C07H21/04 , C12P19/34
CPC分类号： C12Q1/6809 , C12Q1/6827 , C12Q1/6883 , C12Q2600/156 , C12Q2600/158 , G01N2015/1006 , G01N2015/1087
摘要： The present invention provides systems, apparatuses, and methods to detect the presence of fetal cells when mixed with a population of maternal cells in a sample and to test fetal abnormalities, e.g. aneuploidy. The present invention involves performing comparative genomic hybridization (CGH) analysis when fetal cells are present in a mixed population of cells. The present invention involves detecting the presence of fetal cells in a mixed maternal sample by detecting the presence of non-maternal alleles in said sample. Furthermore, the present invention also involves correlating the presence of fetal cells in a mixed sample with CGH analysis results to detect a fetal abnormality or declare a test non- informative.
摘要翻译：本发明提供了当与样品中的母体细胞群混合时检测胎儿细胞的存在并测试胎儿异常的系统，装置和方法，例如，非整倍体。当胎儿细胞存在于混合细胞群体中时，本发明涉及进行比较基因组杂交（CGH）分析。本发明涉及通过检测所述样品中非母体等位基因的存在来检测混合母体样品中胎儿细胞的存在。此外，本发明还涉及将混合样品中的胎儿细胞的存在与CGH分析结果相关联以检测胎儿异常或者宣布非信息性测试。

10. 发明申请

WO2007149065A3 METHODS AND APPARATUSES FOR DETECTING CHEMICAL OR BIOLOGICAL AGENTS 审中-公开
标题翻译：检测化学或生物学试剂的方法和装置
公开(公告)号：WO2007149065A3
公开(公告)日：2008-09-25
申请号：PCT/US2006013246
申请日：2006-04-10
申请人： STOUGHTON ROLAND B , MEYER MICHAEL R , SHOEMAKER DANIEL D
发明人： STOUGHTON ROLAND B , MEYER MICHAEL R , SHOEMAKER DANIEL D
IPC分类号： C12M1/00 , C12Q1/68
CPC分类号： C12Q1/6813 , B82Y5/00 , B82Y10/00
摘要： The present invention provides methods and apparatuses for detection of pathogens or toxins in a sample. The invention also provides kits comprises reagents, including probes sets, and other consumables, such as surfaces, which can be used for detection of pathogens or toxins in a sample.
摘要翻译：本发明提供了用于检测样品中病原体或毒素的方法和装置。本发明还提供了包括试剂，包括探针组和其它可用于检测样品中的病原体或毒素的消耗品，例如表面的试剂盒。

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