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81. 发明申请

WO03106642A2 COMPLEXITY MANAGEMENT OF GENOMIC DNA BY LOCUS SPECIFIC AMPLICATION 审中-公开
标题翻译：通过位置特异性扩增对基因组DNA进行复杂的管理
公开(公告)号：WO03106642A2
公开(公告)日：2003-12-24
申请号：PCT/US0318853
申请日：2003-06-16
申请人： AFFYMETRIX INC , JONES KEITH W , SHAPERO MICHAEL , LIU WEIWEI
发明人： JONES KEITH W , SHAPERO MICHAEL , LIU WEIWEI
IPC分类号： C12Q1/68 , C12N
CPC分类号： C12Q1/6876 , C12Q1/6809 , C12Q1/6837 , C12Q1/6858 , C12Q1/686 , C12Q2600/156 , C12Q2525/155 , C12Q2563/131 , C12Q2565/537 , C12Q2537/143 , C12Q2531/113 , C12Q2565/501 , C12Q2521/307
摘要： The present invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample to interrogate a collection of target sequences. In one embodiment complexity reduction can be accomplished by extension of a locus specific capture probe followed by amplification of the extended capture probe using common primers. The locus specific capture probes may be attached to a solid support. Multiple DNA sequences may be amplified simultaneously to produce a reduced complexity sample. The invention further provides for analysis of the above sample to interrogate sequences of interest such as polymorphisms. The amplified sample may be hybridized to an array, which may be specifically designed to interrogate the desired fragments for the presence or absence of a polymorphism.
摘要翻译：本发明提供了用于降低核酸样品的复杂性以询问靶序列集合的新方法和试剂盒。在一个实施方案中，可以通过扩增位点特异性捕获探针，然后使用常规引物扩增扩增的捕获探针来实现复杂性降低。轨迹特异性捕获探针可以连接到固体支持物上。可以同时扩增多个DNA序列以产生复杂度降低的样品。本发明还提供了上述样品的分析以询问目标序列，如多态性。扩增的样品可以与阵列杂交，其可以被特别设计用于询问所需片段的存在或不存在多态性。

82. 发明申请

WO2003087166A3 PHOTOACTIVATABLE SILANE COMPOUNDS AND METHODS FOR THEIR SYNTHESIS AND USE 审中-公开
公开(公告)号：WO2003087166A3
公开(公告)日：2003-10-23
申请号：PCT/US2003/010528
申请日：2003-04-07
申请人： AFFYMETRIX, INC. , LI, Handong , MCGALL, Glenn, H.
发明人： LI, Handong , MCGALL, Glenn, H.
IPC分类号： C07H21/00
摘要： In one aspect of the invention, photoactivatable silane compounds and methods for their synthesis and use are provided. In one embodiment, the photoactivatable silane compounds synthesized are represented by a formula: PG-LS-SN, wherein PG is a photoactivatable group, LS is a linkage and spacer group, and SN is a silane group. The silanes allow the photoactivatable silane compounds to be covalently bound to the surface of a substrate such as silica. The photoactivatable group forms a hydrophobic layer that can be photochemically cross-linked with a layer of hydrophilic functional polymers. In another embodiment, a method is disclosed to synthesize a substrate of hydrophobic layers and hydrophilic functional polymer layers thereafter onto glass surfaces. An array of biopolymers such as nucleic acids and peptides may then be covalently attached to the substrate using photolithography and biopolymer synthesis.

83. 发明申请

WO2003060526A3 HIGH THROUGHPUT RE-SEQUENCING AND VARIATION DETECTION USING HIGH DENSITY MICROARRAYS 审中-公开
公开(公告)号：WO2003060526A3
公开(公告)日：2003-07-24
申请号：PCT/US2002/041478
申请日：2002-12-23
申请人： AFFYMETRIX, INC. , WARRINGTON, Janet , SHAH, Nila
发明人： WARRINGTON, Janet , SHAH, Nila
IPC分类号： G01N35/00
摘要： In one embodiment of the invention, methods and systems are provided for high throughput genotyping. The system includes a sample preparation method, an automated sample preparation system comprising a robotic device for handling multiwell plates, a sample tracking system, automated array processing and a computer system for genotyping and for data analysis.

84. 发明申请

WO2003016484A3 GLEASON GRADE 4/5 PROSTATE CANCER GENES 审中-公开
公开(公告)号：WO2003016484A3
公开(公告)日：2003-02-27
申请号：PCT/US2002/026081
申请日：2002-08-16
申请人： AFFYMETRIX, INC.
发明人： WARRINGTON, Janet, A. , MAHADEVAPPA, Mamatha , ZHANG, Zhaomei , STAMEY, Thomas
IPC分类号： G01N33/53
摘要： Sixty-four down regulated and 22 up regulated genes have been indentified in Gleason grade 4/5 cancer, using the gene profile from benign prostatic hyperplasia as control tissue. Hepsin appears to be the most promising of the up regulated genes. PSMA is also highly overexpressed at the transcript level in grade 4/5 cancer, re-emphasizing its potential importance as a target for chemotherapy. The regulated genes can be used diagnostically, prognostically, and therapeutically. They can be used to form prostate specific expression monitoring tools.

85. 发明申请

WO2002091110A2 METHOD, SYSTEM AND COMPUTER SOFTWARE FOR PROVIDING A GENOMIC WEB PORTAL 审中-公开
标题翻译：用于提供基因网络门户的方法，系统和计算机软件
公开(公告)号：WO2002091110A2
公开(公告)日：2002-11-14
申请号：PCT/US2002/013902
申请日：2002-05-02
申请人： AFFYMETRIX, INC. , KULP, David, C. , SIANI-ROSE, Michael, A. , SUN, Shaw , SHIGETA, Ron, T. , LIU, Gouying , TRUTANE, Stephen, Chervitz
发明人： KULP, David, C. , SIANI-ROSE, Michael, A. , SUN, Shaw , SHIGETA, Ron, T. , LIU, Gouying , TRUTANE, Stephen, Chervitz
IPC分类号： G06F
CPC分类号： G06F19/28 , G06F19/20
摘要： A genomic portal system (400) receives from a user a selection of one or more probe-set identifiers (222) associated with one or more probe sets. The probe-set identifiers may be submitted in a batch file and may include one or more annotation terms. The system also correlates the user-selected probe-set identifiers with one or more biological sequences, and correlates the one or more biological sequences with a first set of probe sets. A network server (520, 530) identifies the first set of probe sets to the user. The genomic portal system may also receive from a user a selection of one or more probe-set identifiers associated with one or more probe sets, wherein the probe-set identifiers include one or more biological sequences. The system periodically update one or more local genomic databases (518), clusters the one or more biological sequences based on the local genomic databases, and provide the clustered data to a user.
摘要翻译：基因组入口系统（400）从用户接收与一个或多个探针组相关联的一个或多个探针组标识符（222）的选择。探针集标识符可以以批处理文件提交，并且可以包括一个或多个注释术语。该系统还将用户选择的探针组标识符与一个或多个生物序列相关联，并且将一个或多个生物序列与第一组探针组相关联。网络服务器（520,530）向用户识别第一组探测集。基因组门户系统还可以从用户接收与一个或多个探针组相关联的一个或多个探针组标识符的选择，其中所述探针组标识符包括一个或多个生物序列。系统周期性地更新一个或多个局部基因组数据库（518），基于局部基因组数据库对一个或多个生物序列进行聚类，并将群集数据提供给用户。

86. 发明申请

WO2002077283A1 METHODS FOR DETECTING TRANSCRIPTS 审中-公开
标题翻译：检测转录物的方法
公开(公告)号：WO2002077283A1
公开(公告)日：2002-10-03
申请号：PCT/US2001/049227
申请日：2001-12-21
申请人： AFFYMETRIX, INC. , WANG, Hui , SMEEKENS, Steven , MCGALL, Glen , CAO, Yanxiang
发明人： WANG, Hui , SMEEKENS, Steven , MCGALL, Glen , CAO, Yanxiang
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6837 , C12Q2533/101 , C12Q2521/107
摘要： Methods are provided for analyzing a large number of RNAs. In one embodiment of the invention, RNAs are hybridized with a nucleic acid probe (primer) array. The primers are extended using reverse transcriptase with the RNAs as templated. The resulting primer extension products are detected. The methods are useful for gene expression monitoring, sequence variation detection and transcriptional mapping/annotation.
摘要翻译：提供了分析大量RNA的方法。在本发明的一个实施方案中，RNA与核酸探针（引物）阵列杂交。使用逆转录酶扩增引物，其中RNA被模板化。检测所得到的引物延伸产物。该方法可用于基因表达监测，序列变异检测和转录映射/注释。

87. 发明申请

WO2002073502A1 METHOD AND COMPUTER SOFTWARE PRODUCT FOR DETERMINING ORIENTATION OF SEQUENCE CLUSTERS 审中-公开
标题翻译：方法和计算机软件产品用于确定序列簇的方向
公开(公告)号：WO2002073502A1
公开(公告)日：2002-09-19
申请号：PCT/US2002/007437
申请日：2002-03-11
申请人： AFFYMETRIX, INC. , CAWLEY, Simon , WHEELER, Raymond , WONG, Brant , WILLIAMS, Alan , KULP, David
发明人： CAWLEY, Simon , WHEELER, Raymond , WONG, Brant , WILLIAMS, Alan , KULP, David
IPC分类号： G06F19/00
CPC分类号： G06F19/18 , G06F19/20
摘要： In one embodiment of the invention, computerized methods are provided for determining the orientation of EST sequence Clusters. The method employs Bayesian analysis of evidence.
摘要翻译：在本发明的一个实施方案中，提供了用于确定EST序列簇的取向的计算机化方法。该方法采用贝叶斯分析证据。

88. 发明申请

WO0011218A9 EXPRESSION MONITORING FOR HUMAN CYTOMEGALOVIRUS (HCMV) INFECTION 审中-公开
标题翻译：人类细胞病毒（HCMV）感染的表达监测
公开(公告)号：WO0011218A9
公开(公告)日：2002-08-29
申请号：PCT/US9918772
申请日：1999-08-20
申请人： AFFYMETRIX INC , PRINCETON UNIVERSITY OFFICE OF , GINGERAS THOMAS , SHENK THOMAS , ZHU HUA
发明人： GINGERAS THOMAS , SHENK THOMAS , ZHU HUA
IPC分类号： C12Q1/68 , C12Q1/70 , A61B5/00 , G01N35/00
CPC分类号： C12Q1/6883 , C12Q1/6837 , C12Q1/705 , C12Q2600/158 , G01N2333/045
摘要： Certain human genes have been found to be induced or repressed in host cells infected with HCMV. A large set of such genes has been identified. These have diagnostic use in determining the extent of tissue damage caused by the infection as well as in determining the stage of disease progression of the HCMV infection. Such genes are likely those involved in mediating the pathology of the infected tissues. Thus by identifying agents which are able to reverse the induction or repression of such genes, one can find candidate therapeutic agents for use in treating and or preventing HCMV-caused disease pathologies.
摘要翻译：已经发现某些人类基因在用HCMV感染的宿主细胞中被诱导或抑制。已经鉴定了大量这样的基因。这些具有诊断用途来确定由感染引起的组织损伤的程度以及确定HCMV感染的疾病进展阶段。这些基因很可能涉及介导感染组织的病理学。因此，通过鉴定能够逆转这些基因的诱导或抑制的试剂，可以找到用于治疗和/或预防HCMV引起的疾病病理学的候选治疗剂。

89. 发明申请

WO0113281A9 METHOD AND SYSTEM FOR PROVIDING AN ENTERPRISE DATABASE 审中-公开
标题翻译：提供企业数据库的方法和系统
公开(公告)号：WO0113281A9
公开(公告)日：2002-08-01
申请号：PCT/US0040664
申请日：2000-08-17
申请人： AFFYMETRIX INC
发明人： BALABAN DAVID J , SNYDER JAMES
IPC分类号： G06F17/30 , G06Q10/10
CPC分类号： G06F17/30595 , G06Q10/10 , Y10S707/99936 , Y10S707/99943 , Y10S707/99945 , Y10S707/99948
摘要： Described is a novel relational database architecture that is adapted to storing information regarding the terms of one or more contracts, and the actions required to be performed under it. The database resides on a computer-readable storage medium as part of a multi-user computer network. By using simple subroutines readily apparent to one skilled in the computer arts, one can automatically generate alerts whenever an action needs to be performed. These alerts are then transmitted to users along the multi-computer network, appearing in an e-mail message that specifies the action, the individuals performing it, and the duties of each of these individuals. In this manner, one can ensure timely execution of the actions required under a contract.
摘要翻译：描述了一种新颖的关系数据库架构，其适于存储关于一个或多个合同的条款的信息，以及需要在其下执行的动作。作为多用户计算机网络的一部分，数据库驻留在计算机可读存储介质上。通过使用对于计算机领域的技术人员来说显而易见的简单子程序，每当需要执行动作时，可以自动地生成警报。然后，这些警报被传送到多计算机网络上的用户，出现在指定行动的电子邮件消息中，执行该操作的个人以及每个人的职责。以这种方式，可以确保及时执行合同要求的行动。

90. 发明申请

WO0242485A2 METHODS AND COMPUTER SOFTWARE PRODUCTS FOR SELECTING NUCLEIC ACID PROBES 审中-公开
标题翻译：用于选择核酸探针的方法和计算机软件产品
公开(公告)号：WO0242485A2
公开(公告)日：2002-05-30
申请号：PCT/US0143742
申请日：2001-11-21
申请人： AFFYMETRIX INC , MEI RUI , WEBSTER TERESA
发明人： MEI RUI , WEBSTER TERESA
IPC分类号： C12Q1/68 , G06F19/20 , C12Q
CPC分类号： G06F19/20 , C12Q1/6813 , C12Q2527/107
摘要： Methods and computer software products are provided for selecting nucleic acid probes. In one embodiment, perfect match intensity, mismatch intensity and the slope of quantitative response of a probe are predicted. A unified quality score is calculated. Probes are selected based on the unified quality score.
摘要翻译：提供了用于选择核酸探针的方法和计算机软件产品。在一个实施例中，预测了探针的完美匹配强度，不匹配强度和定量响应的斜率。计算统一的质量得分。根据统一的质量得分选择探针。

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