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1. 发明申请

WO2007084618A3 METHOD FOR DETERMINING RESISTANCE OF HIV TO PROTEASE INHIBITOR TREATMENT 审中-公开
标题翻译：用于确定HIV对蛋白酶抑制剂治疗的抗性的方法
公开(公告)号：WO2007084618A3
公开(公告)日：2008-07-17
申请号：PCT/US2007001338
申请日：2007-01-19
申请人： MONOGRAM BIOSCIENCES INC , PARKIN NEIL T , CHAPPEY COLOMBE
发明人： PARKIN NEIL T , CHAPPEY COLOMBE
IPC分类号： C12Q1/70 , C12Q1/68
CPC分类号： C12Q1/703 , G06F19/18 , G06F19/24
摘要： The present invention provides methods and devices for predicting whether an HIV-I is likely to have a reduced susceptibility to an antiviral drug based on the HIV- I 's genotype. In one aspect, the invention provides methods comprising determining whether a mutation or combination of mutations associated with altered susceptibility to protease inhibitors are present, as disclosed herein, thereby assessing the effectiveness of tipranavir therapy in the HIV-infected subject. Computer implemented methods comprising determining HIV-I 's altered susceptibility are provided.
摘要翻译：本发明提供了用于预测HIV-1是否可能对HIV-1基因型具有降低的抗病毒药物敏感性的方法和装置。一方面，本发明提供了如本文所公开的确定突变或与蛋白酶抑制剂的易感性相关的突变的组合是否存在的方法，从而评估了在HIV感染的受试者中替诺韦韦治疗的有效性。提供了确定HIV-1改变的易感性的计算机实施方法。

2. 发明申请

WO2005076893A2 COMPOSITIONS AND METHODS FOR DETERMINING THE REPLICATION CAPACITY OF A PATHOGENIC VIRUS 审中-公开
标题翻译：用于确定致病病毒的复制能力的组合物和方法
公开(公告)号：WO2005076893A2
公开(公告)日：2005-08-25
申请号：PCT/US2005003392
申请日：2005-02-04
申请人： VIROLOGIC INC , PARKIN NEIL T , CHAPPEY COLOMBE , BATES MICHAEL
发明人： PARKIN NEIL T , CHAPPEY COLOMBE , BATES MICHAEL
IPC分类号： C12Q1/68 , C12Q1/70 , G01N33/48 , G01N33/50 , G01N33/569 , G06F19/00
CPC分类号： G01N33/56988 , C12Q1/703
摘要： This invention relates to methods for predicting replication capacity of a virus based on genotype and identifying targets for antiviral therapy by identifying mutations associated with altered replication capacity. The methods are useful, for example, for identifying previously unknown interactions among viral molecules or between viral molecules and host cell molecules that are essential to viral infection and/or replication. By identifying such interactions, novel targets for antiviral therapy can be identified. In another aspect, the invention provides a method for determining that an HIV has an altered replication capacity. In certain embodiments, the method comprises detecting a mutation in a codon of gag that is selected from the group consisting of 437, 439, 441, 442, 454, 478, 479, and 484. In certain embodiments, the mutation is selected from the group consisting of I437L, P439S, E454V, P478L, and I479K. In certain embodiments, the mutation is in a codon of gag that is selected from the group consisting of 418, 456, 456, 453, 418, 483, 481, 465, 429, 484, 481, 483, 484, 465, 454, 442, 479, 418, 479, and 486.
摘要翻译：本发明涉及用于基于基因型预测病毒的复制能力的方法，并且通过鉴定与改变的复制能力相关的突变来鉴定抗病毒治疗的靶标。该方法例如用于鉴定病毒分子之间或病毒分子与病毒感染和/或复制必需的宿主细胞分子之间的先前未知的相互作用是有用的。通过鉴定这种相互作用，可以鉴定抗病毒治疗的新靶点。另一方面，本发明提供了确定HIV具有改变的复制能力的方法。在某些实施方案中，该方法包括检测gag密码子中的突变，其选自437,439,441,442,454,478,479和484.在某些实施方案中，突变选自由I437L，P439S，E454V，P478L和I479K组成的组。在某些实施方案中，突变是gag的密码子，其选自418,456,465,463,418,483,481,465,489,484,481,483,448,465,454,448,448,448,448,448,448,448,448,448,448,448,448,448,454,454,454,454,454,454,454,454,454,454,454,454,454,454,454,454,454,454,454,454,448,454,454,454,454,454 442,479,418,479和486。

3. 发明申请

WO2006084018A3 METHODS FOR DETERMINING RESPONSIVENESS TO CANCER THERAPY 审中-公开
标题翻译：确定对癌症治疗的反应的方法
公开(公告)号：WO2006084018A3
公开(公告)日：2006-09-21
申请号：PCT/US2006003660
申请日：2006-02-01
申请人： MONOGRAM BIOSCIENCES INC , TANG MENGXIANG , CAO LICHING , DUA RAJIV , MUKHERJEE ALI , PANNU HERJIT , PANNU JAGRUP , SHI YINING , TAN YUPING , SINGH SHARAT , CHAPPEY COLOMBE
发明人： TANG MENGXIANG , CAO LICHING , DUA RAJIV , MUKHERJEE ALI , PANNU HERJIT , PANNU JAGRUP , SHI YINING , TAN YUPING , SINGH SHARAT , CHAPPEY COLOMBE
IPC分类号： C12Q1/68 , G01N33/567
CPC分类号： G01N33/57484 , G01N33/5748 , G01N2333/82
摘要： In certain aspects, the present invention provides methods and compositions for determining whether a cancer cells is likely to respond to treatment with a Her 1 -acting agent. In one aspect, the invention provides a method for determining whether a cancer cell is likely to respond to treatment with a Her 1 -acting agent, comprising detecting on the cancer cell at least about 600 Her 1 -Her 1 dimers, wherein the presence of the at least about 600 Her 1 -Her 1 dimers indicates that the cancer is likely to respond to treatment with the Her 1 -acting agent. In another aspect, the invention provides a method for determining whether a cancer cell is likely to respond to treatment with a Her 1 -acting agent, comprising detecting on a cell of the cancer at least about 600 Her 1 -Her 1 dimers, at least about 1000 Herl-Her2 dimers, and fewer than about 1000 Her2-Her3 dimers, wherein the presence of the at least about 600 Her 1 -Her 1 dimers, the at least about 1000 Herl-Her2 dimers, and the fewer than about 1000 Her2-Her3 dimers indicates that the cancer cell is likely to respond to treatment with the Her 1 -acting agent. Preferably, methods of the invention are implemented by using sets of binding compounds having releasable molecular tags that are specific for multiple components of one or more types of receptor dimers. After binding, molecular tags are released and separated from the assay mixture for analysis.
摘要翻译：在某些方面，本发明提供了用于确定癌细胞是否可能响应Her 1作用剂治疗的方法和组合物。在一个方面，本发明提供了用于确定癌细胞是否可能对用Her 1作用剂治疗有反应的方法，包括在癌细胞上检测至少约600个Her 1 --Her 1二聚体，其中存在该至少约600个Her 1 -Her 1二聚体表明癌症可能对用Her 1作用剂治疗有反应。另一方面，本发明提供了用于确定癌细胞是否可能响应用Her 1作用剂治疗的方法，包括在癌细胞上检测至少约600个Her 1 --Her 1二聚体，至少约1000个Her1-Her2二聚体和少于约1000个Her2-Her3二聚体，其中所述至少约600个Her1-Her1二聚体，所述至少约1000个Her1-Her2二聚体和少于约1000个Her2 -Her3二聚体表明癌细胞可能对Her-1作用剂的治疗有反应。优选地，本发明的方法通过使用具有对一种或多种类型的受体二聚体的多种组分特异的可释放分子标签的结合化合物组来实施。结合后，分子标签被释放并从测定混合物中分离出来用于分析。

4. 发明申请

WO2006084018A2 METHODS FOR DETERMINING RESPONSIVENESS TO CANCER THERAPY 审中-公开
标题翻译：用于确定对癌症治疗的反应的方法
公开(公告)号：WO2006084018A2
公开(公告)日：2006-08-10
申请号：PCT/US2006/003660
申请日：2006-02-01
申请人： MONOGRAM BIOSCIENCES, INC. , TANG, Mengxiang , CAO, Liching , DUA, Rajiv , MUKHERJEE, Ali , PANNU, Herjit , PANNU, Jagrup , SHI, Yining , TAN, Yuping , SINGH, Sharat , CHAPPEY, Colombe
发明人： TANG, Mengxiang , CAO, Liching , DUA, Rajiv , MUKHERJEE, Ali , PANNU, Herjit , PANNU, Jagrup , SHI, Yining , TAN, Yuping , SINGH, Sharat , CHAPPEY, Colombe
IPC分类号： C12Q1/68
CPC分类号： G01N33/57484 , G01N33/5748 , G01N2333/82
摘要： In certain aspects, the present invention provides methods and compositions for determining whether a cancer cells is likely to respond to treatment with a Her 1 -acting agent. In one aspect, the invention provides a method for determining whether a cancer cell is likely to respond to treatment with a Her 1 -acting agent, comprising detecting on the cancer cell at least about 600 Her 1 -Her 1 dimers, wherein the presence of the at least about 600 Her 1 -Her 1 dimers indicates that the cancer is likely to respond to treatment with the Her 1 -acting agent. In another aspect, the invention provides a method for determining whether a cancer cell is likely to respond to treatment with a Her 1 -acting agent, comprising detecting on a cell of the cancer at least about 600 Her 1 -Her 1 dimers, at least about 1000 Herl-Her2 dimers, and fewer than about 1000 Her2-Her3 dimers, wherein the presence of the at least about 600 Her 1 -Her 1 dimers, the at least about 1000 Herl-Her2 dimers, and the fewer than about 1000 Her2-Her3 dimers indicates that the cancer cell is likely to respond to treatment with the Her 1 -acting agent. Preferably, methods of the invention are implemented by using sets of binding compounds having releasable molecular tags that are specific for multiple components of one or more types of receptor dimers. After binding, molecular tags are released and separated from the assay mixture for analysis.
摘要翻译：在某些方面，本发明提供了用于确定癌细胞是否可能对Her 1处理剂的治疗有反应的方法和组合物。一方面，本发明提供了一种用于确定癌细胞是否可能对Her1处理剂起反应的方法，包括在癌细胞上检测至少约600个Her 1 -Her 1二聚体，其中存在至少约600个Her 1 -Her 1二聚体表明癌症可能对她用1代谢剂的治疗有反应。在另一方面，本发明提供了一种用于确定癌细胞是否可能对Her 1处理剂有反应的方法，包括至少检测至少约600个Her 1 -Her 1二聚体的癌细胞约1000个Herl-Her2二聚体和少于约1000个Her2-Her3二聚体，其中存在至少约600个Her1-Her2二聚体，至少约1000个Her1-Her2二聚体，以及少于约1000个Her2-Her2二聚体 -Her3二聚体表明癌细胞很可能对Her1处理剂有反应。优选地，通过使用具有对一种或多种类型的受体二聚体的多种成分特异的可释放分子标签的组合化合物来实现本发明的方法。结合后，将分子标签从测定混合物中释放并分离出来进行分析。

5. 发明申请

WO2008103490A3 METHODS AND COMPOSITIONS FOR DETERMINING ALTERED SUSCEPTIBILITY OF HIV-1 TO PROTEASE INHIBITOR TREATMENT 审中-公开
标题翻译：用于确定HIV-1对蛋白酶抑制剂治疗的改变的易感性的方法和组合物
公开(公告)号：WO2008103490A3
公开(公告)日：2008-11-06
申请号：PCT/US2008002439
申请日：2008-02-25
申请人： MONOGRAM BIOSCIENCES INC , PARKIN NEIL T , CHAPPEY COLOMBE , STAWISKI ERIC
发明人： PARKIN NEIL T , CHAPPEY COLOMBE , STAWISKI ERIC
IPC分类号： A61K39/00
CPC分类号： C12Q1/18 , C12Q1/703 , G01N2333/16 , G01N2800/52
摘要： This invention relates to methods for determining altered susceptibility of HIV-I viruses to protease inhibitors (PIs) based on the viral genotypes. The methods generally comprise detecting, in a gene encoding protease and/or gag of the HIV-I, the presence of mutations correlated with altered susceptibility to amprenavir and/or darunavir.
摘要翻译：本发明涉及基于病毒基因型确定HIV-1病毒对蛋白酶抑制剂（PI）的易感性改变的方法。该方法通常包括在编码HIV-1蛋白酶和/或gag的基因中检测与对安普那韦和/或地瑞那韦的易感性改变相关的突变的存在。

6. 发明申请

WO2006130449A2 METHOD FOR DETERMINING RESISTANCE OF HIV TO NUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR TREATMENT 审中-公开
标题翻译：用于确定HIV对核苷酸逆转录酶抑制剂治疗的抗性的方法
公开(公告)号：WO2006130449A2
公开(公告)日：2006-12-07
申请号：PCT/US2006/020364
申请日：2006-05-25
申请人： MONOGRAM BIOSCIENCES, INC. , PARKIN, Neil, T. , CHAPPEY, Colombe , WHITCOMB, Jeannette
发明人： PARKIN, Neil, T. , CHAPPEY, Colombe , WHITCOMB, Jeannette
CPC分类号： C12Q1/6883 , C12Q2600/156
摘要： The present invention provides methods and devices for predicting whether an HIV-1 is resistant to an antiviral drug based on the HIV-1's genotype. In one aspect, the invention provides methods comprising determining whether a mutation or combination of mutations associated with NRTI resistance are present, as disclosed herein, thereby assessing the effectiveness of FTC therapy in the HIV-infected subject. Computer implemented methods comprising determining HIV-1 resistance are provided.
摘要翻译：本发明提供了用于预测HIV-1是否对基于HIV-1的基因型的抗病毒药具有抗性的方法和装置。一方面，本发明提供了如本文所公开的确定是否存在与NRTI抗性相关的突变或突变的组合的方法，从而评估FTC治疗在HIV感染的受试者中的有效性。提供了确定HIV-1抗性的计算机实施方法。

7. 发明申请

WO2005076892A2 METHOD FOR DETERMINING REDUCED SUSCEPTIBILITY OF HIV TO PROTEASE INHIBITOR TREATMENT 审中-公开
标题翻译：用于确定HIV对蛋白酶抑制剂治疗的降低可疑性的方法
公开(公告)号：WO2005076892A2
公开(公告)日：2005-08-25
申请号：PCT/US2005/003391
申请日：2005-02-04
申请人： VIROLOGIC, INC. , CHAPPEY, Colombe , PETROPOULOS, Christos, J. , PARKIN, Neil, T.
发明人： CHAPPEY, Colombe , PETROPOULOS, Christos, J. , PARKIN, Neil, T.
IPC分类号： C12Q1/68 , C12Q1/70 , G06F19/00
CPC分类号： C12Q1/703 , C12Q1/683 , G06F19/22
摘要： The present invention provides methods and devices for predicting whether a HIV variant will be resistant to an antiviral drug based on the variant's genotype. In one aspect, methods are provided comprising determining whether a combination of protease inhibitor resistance mutations meet certain conditions, as disclosed herein, thereby assessing the effectiveness of ritonavir-boosted indinavir therapy in the HIV-infected subject. Computer implemented methods comprising determining HIV resistance are provided.
摘要翻译：本发明提供了用于基于变体的基因型来预测HIV变体是否能够抗抗病毒药物的方法和装置。在一个方面，提供了方法，其包括确定蛋白酶抑制剂抗性突变的组合是否满足本文所公开的某些条件，从而评估利托那韦加强的茚地那韦治疗在HIV感染受试者中的有效性。提供了包括确定HIV抗性的计算机实施方法。

8. 发明申请

WO2009086197A1 HER-2 DIAGNOSTIC METHODS 审中-公开
标题翻译： HER-2诊断方法
公开(公告)号：WO2009086197A1
公开(公告)日：2009-07-09
申请号：PCT/US2008/087828
申请日：2008-12-19
申请人： MONOGRAM BIOSCIENCES, INC. , HUANG, Weidong , SPERINDE, Jeff , BATES, Michael , CHAPPEY, Colombe
发明人： HUANG, Weidong , SPERINDE, Jeff , BATES, Michael , CHAPPEY, Colombe
IPC分类号： G01N33/574
CPC分类号： G01N33/574 , G01N33/57415 , G01N2800/52
摘要： In certain aspects, the present invention provides methods for determining whether a Her-2 positive cancer is likely to respond to treatment with a Her2-acting agent and/or whether a patient with a Her-2 positive cancer is likely to have a slow disease progression. In other aspects, the present invention is drawn to methods for determining whether a subject with a Her-2 positive cancer is unlikely to respond to treatment with at least one chemotherapeutic agent in addition to a Her2-acting agent and/or whether a patient with a Her-2 positive cancer is likely to have a fast disease progression.
摘要翻译：在某些方面，本发明提供用于确定Her-2阳性癌症是否可能对Her2-作用剂的治疗有反应和/或是否具有Her-2阳性癌症的患者可能具有慢的疾病的方法进展。在其它方面，本发明涉及用于确定具有Her-2阳性癌症的受试者是否不太可能响应除了Her2作用剂之外的至少一种化学治疗剂的治疗和/或是否具有一个Her-2阳性的癌症很可能有一个快速的疾病进展。

9. 发明申请

WO2006130449A3 METHOD FOR DETERMINING RESISTANCE OF HIV TO NUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR TREATMENT 审中-公开
标题翻译：用于确定HIV对核苷酸逆转录酶抑制剂治疗的抗性的方法
公开(公告)号：WO2006130449A3
公开(公告)日：2009-05-14
申请号：PCT/US2006020364
申请日：2006-05-25
申请人： MONOGRAM BIOSCIENCES INC , PARKIN NEIL T , CHAPPEY COLOMBE , WHITCOMB JEANNETTE
发明人： PARKIN NEIL T , CHAPPEY COLOMBE , WHITCOMB JEANNETTE
IPC分类号： C12Q1/70
CPC分类号： C12Q1/6883 , C12Q2600/156
摘要： The present invention provides methods and devices for predicting whether an HIV-1 is resistant to an antiviral drug based on the HIV-1's genotype. In one aspect, the invention provides methods comprising determining whether a mutation or combination of mutations associated with NRTI resistance are present, as disclosed herein, thereby assessing the effectiveness of FTC therapy in the HIV-infected subject. Computer implemented methods comprising determining HIV-1 resistance are provided.
摘要翻译：本发明提供了用于预测HIV-1是否对基于HIV-1的基因型的抗病毒药具有抗性的方法和装置。一方面，本发明提供了如本文所公开的确定是否存在与NRTI抗性相关的突变或突变的组合的方法，从而评估FTC治疗在HIV感染的受试者中的有效性。提供了确定HIV-1抗性的计算机实施方法。

10. 发明申请

WO2008103490A2 METHODS AND COMPOSITIONS FOR DETERMINING ALTERED SUSCEPTIBILITY OF HIV-1 TO PROTEASE INHIBITOR TREATMENT 审中-公开
标题翻译：用于确定HIV-1对蛋白酶抑制剂治疗的改变的可疑性的方法和组合物
公开(公告)号：WO2008103490A2
公开(公告)日：2008-08-28
申请号：PCT/US2008/002439
申请日：2008-02-25
申请人： MONOGRAM BIOSCIENCES, INC. , PARKIN, Neil, T. , CHAPPEY, Colombe , STAWISKI, Eric
发明人： PARKIN, Neil, T. , CHAPPEY, Colombe , STAWISKI, Eric
IPC分类号： C12Q1/70
CPC分类号： C12Q1/18 , C12Q1/703 , G01N2333/16 , G01N2800/52
摘要： This invention relates to methods for determining altered susceptibility of HIV-I viruses to protease inhibitors (PIs) based on the viral genotypes. The methods generally comprise detecting, in a gene encoding protease and/or gag of the HIV-I, the presence of mutations correlated with altered susceptibility to amprenavir and/or darunavir.
摘要翻译：本发明涉及基于病毒基因型确定HIV-1病毒对蛋白酶抑制剂（PI）的易感性变化的方法。所述方法通常包括在编码HIV-1的蛋白酶和/或gag的基因中检测与对安普那加和/或地瑞那韦具有改变的易感性相关的突变的存在。

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