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1. 发明申请

WO0041122A3 NORMALIZATION, SCALING, AND DIFFERENCE FINDING AMONG DATA SETS 审中-公开
标题翻译：数据集中的正则化，缩放和差异发现
公开(公告)号：WO0041122A3
公开(公告)日：2000-09-28
申请号：PCT/US0000167
申请日：2000-01-05
申请人： CURAGEN CORP , BADER JOEL S , LIU YI , GOLD STEPHEN , DZIUDA DARIUS , GUSEV VLADIMIR , JUDSON RICHARD S , WENT GREGORY T
发明人： BADER JOEL S , LIU YI , GOLD STEPHEN , DZIUDA DARIUS , GUSEV VLADIMIR , JUDSON RICHARD S , WENT GREGORY T
IPC分类号： G06F17/10 , G06F19/00
CPC分类号： G06F17/10
摘要： This invention relates to a method of identifying a difference between at least two data sets made up of ordered elements utilizing internal features within the data sets for calculations relating to normalization, scaling, and difference finding.
摘要翻译：本发明涉及一种识别由有序元素组成的至少两个数据集之间的差异的方法，所述数据集利用数据集内的内部特征，用于与归一化，缩放和差异发现有关的计算。

2. 发明申请

WO0204661A3 METHODS FOR CLASSIFYING NUCLEIC ACIDS AND POLYPEPTIDES 审中-公开
标题翻译：分类核酸和多肽的方法
公开(公告)号：WO0204661A3
公开(公告)日：2003-09-25
申请号：PCT/US0141320
申请日：2001-07-09
申请人： CURAGEN CORP , BADER JOEL S , LIU YI , DZIUDA DARIUS M
发明人： BADER JOEL S , LIU YI , DZIUDA DARIUS M
IPC分类号： C12Q1/00 , C12Q1/68 , G01N33/48 , G01N33/50 , G06F19/20 , G06F19/24 , G06F19/00
CPC分类号： G06F19/20 , G06F19/24
摘要： The present invention provides novel methods to identify, classify, quantify and compare nucleic and polypeptides.
摘要翻译：本发明提供鉴定，分类，定量和比较核酸和多肽的新方法。

3. 发明申请

WO0149886A3 METHOD OF ANALYZING A NUCLEIC ACID 审中-公开
标题翻译：分析核酸的方法
公开(公告)号：WO0149886A3
公开(公告)日：2002-06-06
申请号：PCT/US0100300
申请日：2001-01-05
申请人： CURAGEN CORP , BADER JOEL S , GOLD STEVEN , GUSEV VLADIMIR , LI SHU XIA , SHENOY SURESH , CRASTA OSWALD R , BOUFFORD PASCAL
发明人： BADER JOEL S , GOLD STEVEN , GUSEV VLADIMIR , LI SHU XIA , SHENOY SURESH , CRASTA OSWALD R , BOUFFORD PASCAL
IPC分类号： C12N15/09 , C12Q1/68
CPC分类号： C12Q1/6851 , C12Q1/6809
摘要： Disclosed are methods of selectively analyzing a nucleic acid in a sample. The methods allow for selective identification of a target sequence in a population of nucleic acids. For example, the methods allow for confirmation of the identity of a nucleic acid tentatively identified in a quantitative expression analysis (QEA) assay.
摘要翻译：公开了选择性分析样品中的核酸的方法。所述方法允许选择性鉴定核酸群体中的靶序列。例如，所述方法允许确认在定量表达分析（QEA）测定中暂时鉴定的核酸的身份。

4. 发明申请

WO0149886A8 METHOD OF ANALYZING A NUCLEIC ACID 审中-公开
标题翻译：分析核酸的方法
公开(公告)号：WO0149886A8
公开(公告)日：2001-11-08
申请号：PCT/US0100300
申请日：2001-01-05
申请人： CURAGEN CORP , BADER JOEL S , GOLD STEVEN , GUSEV VLADIMIR , LI SHU XIA , SHENOY SURESH , CRASTA OSWALD R , BOUFFORD PASCAL
发明人： BADER JOEL S , GOLD STEVEN , GUSEV VLADIMIR , LI SHU XIA , SHENOY SURESH , CRASTA OSWALD R , BOUFFORD PASCAL
IPC分类号： C12N15/09 , C12Q1/68
CPC分类号： C12Q1/6851 , C12Q1/6809
摘要： Disclosed are methods of selectively analyzing a nucleic acid in a sample. The methods allow for selective identification of a target sequence in a population of nucleic acids. For example, the methods allow for confirmation of the identity of a nucleic acid tentatively identified in a quantitative expression analysis (QEA) assay.
摘要翻译：公开了选择性分析样品中的核酸的方法。该方法允许选择性鉴定核酸群体中的靶序列。例如，所述方法允许确认在定量表达分析（QEA）测定中初步鉴定的核酸的身份。

5. 发明申请

WO03014703A2 NUCLEIC ACIDS, POLYPEPTIDES, SINGLE NUCLEOTIDE POLYMORPHISMS AND METHODS OF USE THEREOF 审中-公开
标题翻译：核酸，多肽，单核苷酸多态性及其使用方法
公开(公告)号：WO03014703A2
公开(公告)日：2003-02-20
申请号：PCT/US0225480
申请日：2002-08-09
申请人： CURAGEN CORP , GROSSE WILLIAM M , ALSOBROOK JOHN P II , BURGESS CATHERINE E , BADER JOEL S
发明人： GROSSE WILLIAM M , ALSOBROOK JOHN P II , BURGESS CATHERINE E , BADER JOEL S
IPC分类号： G01N33/50 , A61K38/00 , A61K38/17 , A61K48/00 , A61P1/14 , A61P3/00 , A61P3/04 , A61P3/06 , A61P3/10 , A61P7/00 , A61P9/10 , A61P25/00 , A61P25/16 , A61P25/28 , A61P31/00 , A61P35/00 , A61P37/00 , C07H21/04 , C07K14/47 , C07K16/18 , C12N1/15 , C12N1/19 , C12N1/21 , C12N5/06 , C12N5/10 , C12N15/09 , C12P21/02 , C12Q1/68 , G01N33/68 , G01N
CPC分类号： C12Q1/6876 , C12Q2600/156
摘要： Disclosed herein is a nucleic acid sequence that encodes a novel polypeptide. Also disclosed is a polypeptide encoded by the nucleic acid sequence , and antibodies, which immunospecifically-bind to the polypeptide, as well as derivatives, variants, mutants, or fragments of the aforementioned polypeptide, polynucleotide, or antibody. The invention further discloses therapeutic, diagnostic and research methods for diagnosis, treatment, and prevention of disorders involving this novel human nucleic acid and protein. The invention also provides nucleic acids containing single-nucleotide polymorphisms identified for transcribed human sequences, as well as methods of using the nucleic acids.
摘要翻译：本文公开了编码新型多肽的核酸序列。还公开了由核酸序列编码的多肽和免疫特异性结合多肽的抗体以及前述多肽，多核苷酸或抗体的衍生物，变体，突变体或片段。本发明还公开了用于诊断，治疗和预防涉及该新型人核酸和蛋白质的病症的治疗，诊断和研究方法。本发明还提供含有针对转录的人序列鉴定的单核苷酸多态性的核酸，以及使用该核酸的方法。

6. 发明申请

WO0229110A2 EFFICIENT TESTS OF ASSOCIATION FOR QUANTITATIVE TRAITS AND AFFECTED-UNAFFECTED STUDIES USING POOLED DNA 审中-公开
标题翻译：使用碘化DNA进行定量检测和有针对性的研究的有效测试
公开(公告)号：WO0229110A2
公开(公告)日：2002-04-11
申请号：PCT/US0131373
申请日：2001-10-09
申请人： CURAGEN CORP , GEMINI GENOMICS LTD , BADER JOEL S , BANSAL ARUNA , SHAM PAK
发明人： BADER JOEL S , BANSAL ARUNA , SHAM PAK
IPC分类号： A01H1/00 , C12Q1/68 , G06F19/18 , G06F19/22 , G06F19/00
CPC分类号： G06F19/18 , G06F19/22
摘要： Risk assessment and diagnosis of a complex disorder often requires measuring an underlying quantitative phenotype. Association studies in unrelated populations can implicate genetic factors contributing to disease risk, and experiments using pooled DNA provide a less costly but necessarily less powerful alternative to methods based on individual genotyping. Although the sample sites required for pooling and individual genotyping studies have been compared in certain instances, general results have not been reported in the context of association studies, nor have there been clear comparisons of pooling based on quantitative and qualitative (affected/unaffected) phenotypes. Here we use exact numerical calculations and analytical approximations to examine the sample size requirements of association tests for quantitative traits and affected-unaffected studies using pooled DNA. We show, in analogy with selection experiments, that the optimal design for virtually any quantitative phenotype is to pool the top and bottom 27 % of individuals, regardless of marker frequency or inheritance mode; this design requires a population only 24 % larger than that required for individual genotyping. Furthermore, this design is approximately four times more efficient than typical affected-unaffected studies of DNA pooled from individuals classified as affected or unaffected.
摘要翻译：复杂疾病的风险评估和诊断通常需要测量潜在的定量表型。不相关人群的关联研究可能涉及导致疾病风险的遗传因素，使用合并DNA的实验提供了基于个体基因分型的方法成本较低但必然较不强大的替代方法。虽然在某些情况下比较了汇集和个体基因分型研究所需的样本地点，但在关联研究的背景下还没有报告一般结果，也没有基于定量和定性（受影响/未受影响）表型的汇总的明确比较。在这里，我们使用精确的数值计算和分析近似来检查使用合并的DNA的数量性状和受影响的未受影响的研究的关联检验的样本量要求。我们类似于选择实验显示，几乎任何定量表型的最佳设计都是汇集个人的顶部和底部27％，而不管标记频率或遗传模式如何; 这种设计需要的人口比单个基因分型所需的人口大24％。此外，这种设计比从属于受影响或未受影响的个体的DNA的典型受影响的未受影响的研究中大大提高了四倍。

7. 发明申请

WO0120039A3 METHOD OF SEQUENCING A NUCLEIC ACID 审中-公开
标题翻译：测序核酸的方法
公开(公告)号：WO0120039A3
公开(公告)日：2002-03-21
申请号：PCT/US0025290
申请日：2000-09-15
申请人： CURAGEN CORP , ROTHBERG JONATHAN M , BADER JOEL S , DEWELL SCOTT B , MCDADE KEITH , SIMPSON JOHN W , BERKA JAN , COLANGELO CHRISTOPHER M
发明人： ROTHBERG JONATHAN M , BADER JOEL S , DEWELL SCOTT B , MCDADE KEITH , SIMPSON JOHN W , BERKA JAN , COLANGELO CHRISTOPHER M
IPC分类号： G01N33/50 , C12M1/00 , C12N15/09 , C12Q1/68 , G01N21/05 , G01N21/17 , G01N33/15 , G01N33/53 , G01N33/566 , H04N5/225 , B01J19/00
CPC分类号： C12Q1/6837 , C12Q1/6827 , C12Q1/6869 , C12Q1/6874 , C12Q2531/125 , C12Q2535/101 , C12Q2565/301
摘要： Disclosed herein are methods and apparatuses for sequencing a nucleic acid. In one aspect, the method includes annealing a population of circular nucleic acid molecules to a plurality of anchor primers linked to a solid support, and amplifying those members of the population of circular nucleic acid molecules which anneal to the target nucleic acid, and then sequencing the amplified molecules by detecting the presence of a sequence by-product such as pyrophosphate.
摘要翻译：本文公开了用于测序核酸的方法和装置。一方面，该方法包括将多个环状核酸分子退火至与固体支持物连接的多个锚定引物，并扩增与靶核酸退火的环状核酸分子群体的那些成员，然后测序通过检测序列副产物如焦磷酸盐的存在来扩增分子。

8. 发明申请

WO0216643A8 DNA POOLING METHODS FOR QUANTITATIVE TRAITS USING UNRELATED POPULATIONS OR SIB PAIRS 审中-公开
标题翻译：使用不相关的人口或SIB对的定量旅行的DNA填充方法
公开(公告)号：WO0216643A8
公开(公告)日：2003-04-10
申请号：PCT/US0125924
申请日：2001-08-20
申请人： CURAGEN CORP , BADER JOEL S , BANSAL ARUNA , SHAM PAK
发明人： BADER JOEL S , BANSAL ARUNA , SHAM PAK
IPC分类号： C12Q1/68 , G01N33/48 , G01N33/50 , G06F19/18 , G06F19/24
CPC分类号： C12Q1/6883 , C12Q2600/156 , G06F19/18 , G06F19/24
摘要： Identifying the genetic determinants for disease and disease prediposition remains one of the outstanding goals of the human genome project. When large patient populations are available, genetic approaches using single nucleotide polymorphism markers have the potential to identify relevant genes directly. While indivieual genotyping is the most powerful method for establishing association, determining allele frequencies in DNA pooled on the basis of phenotypic value can also reveal association at much-reduced cost. Here we analyze pooling methods to establish association between a genetic polymorphism and a quantitative phenotype. Exact results are provided for the statistical power for a number of pooling designs where the phenotype is described by a variance components model and the fraction of the population pooled is optimized to minimize the population requirements. For low to moderate sibling phenotypic correlation, unrelated population requirements. For low to moderate sibling phenotypic correlation, unrelated populations are more powerful than sib pair populations with an equal number of individuals, for sibling phenotypic correlations above 75 %, however, designs selecting the sib pairs with the greatest phenotype difference become more powerful. For sibling phenotype correlations below 75 %, pooling extreme unrelated individuals is the most powerful design for sib pair populations. The optimal pooling fractions for each design are constant over a wide range of parameters. These results for quantitative phenotypes differ from those reported for qualitative phenotypes, for which unrelated populations are more powerful than sib pairs and concordant designs are more powerful than discordant, and have immediate relevance to ongoing association studies and anticipated whole-genome scans.
摘要翻译：识别疾病和疾病倾向的遗传决定因素仍然是人类基因组计划的突出目标之一。当大量患者群体可用时，使用单核苷酸多态性标记的遗传方法有可能直接鉴定相关基因。虽然独立的基因分型是建立关联的最强大的方法，但确定基于表型价值的DNA中等位基因频率的确定也可以显着降低成本。在这里我们分析汇集方法建立遗传多态性与定量表型之间的关联。提供了许多汇总设计的统计功能的精确结果，其中表型由方差分量模型描述，并且汇总的人口的分数被优化以最小化人口需求。对于低至中等同胞表型相关性，无关人口要求。对于低至中等同胞表型相关性，不相关群体比具有相等数量个体的同胞对群体更强大，对于同位素表型相关性高于75％，然而，选择具有最大表型差异的同胞对的设计变得更加强大。对于低于75％的同胞表型相关性，汇集极端不相关的个体是同胞对群体最强大的设计。每个设计的最佳合并分数在广泛的参数范围内是恒定的。定量表型的这些结果与针对定性表型报道的结果不同，对于这些结果，不相关的人群比同胞对更强大，一致的设计比不一致更强大，并且与正在进行的关联研究和预期的全基因组扫描具有直接关联。

9. 发明申请

WO0216643A3 DNA POOLING METHODS FOR QUANTITATIVE TRAITS USING UNRELATED POPULATIONS OR SIB PAIRS 审中-公开
标题翻译：使用不相关的人口或SIB对的定量旅行的DNA填充方法
公开(公告)号：WO0216643A3
公开(公告)日：2004-02-26
申请号：PCT/US0125924
申请日：2001-08-20
申请人： CURAGEN CORP , BADER JOEL S , BANSAL ARUNA , SHAM PAK
发明人： BADER JOEL S , BANSAL ARUNA , SHAM PAK
IPC分类号： C12Q1/68 , G01N33/48 , G01N33/50 , G06F19/18 , G06F19/24 , G06F19/00
CPC分类号： C12Q1/6883 , C12Q2600/156 , G06F19/18 , G06F19/24
摘要： Identifying the genetic determinants for disease and disease prediposition remains one of the outstanding goals of the human genome project. When large patient populations are available, genetic approaches using single nucleotide polymorphism markers have the potential to identify relevant genes directly. While indivieual genotyping is the most powerful method for establishing association, determining allele frequencies in DNA pooled on the basis of phenotypic value can also reveal association at much-reduced cost. Here we analyze pooling methods to establish association between a genetic polymorphism and a quantitative phenotype. Exact results are provided for the statistical power for a number of pooling designs where the phenotype is described by a variance components model and the fraction of the population pooled is optimized to minimize the population requirements. For low to moderate sibling phenotypic correlation, unrelated population requirements. For low to moderate sibling phenotypic correlation, unrelated populations are more powerful than sib pair populations with an equal number of individuals, for sibling phenotypic correlations above 75 %, however, designs selecting the sib pairs with the greatest phenotype difference become more powerful. For sibling phenotype correlations below 75 %, pooling extreme unrelated individuals is the most powerful design for sib pair populations. The optimal pooling fractions for each design are constant over a wide range of parameters. These results for quantitative phenotypes differ from those reported for qualitative phenotypes, for which unrelated populations are more powerful than sib pairs and concordant designs are more powerful than discordant, and have immediate relevance to ongoing association studies and anticipated whole-genome scans.
摘要翻译：识别疾病和疾病倾向的遗传决定因素仍然是人类基因组计划的突出目标之一。当大量患者群体可用时，使用单核苷酸多态性标记的遗传方法有可能直接鉴定相关基因。虽然独立的基因分型是建立关联的最强大的方法，但确定基于表型价值的DNA中等位基因频率的确定也可以显着降低成本。在这里我们分析汇集方法建立遗传多态性与定量表型之间的关联。提供了许多汇总设计的统计功能的精确结果，其中表型由方差分量模型描述，并且汇总的人口的分数被优化以最小化人口需求。对于低至中等同胞表型相关性，无关人口要求。对于低至中等同胞表型相关性，不相关群体比具有相等数量个体的同胞对群体更强大，对于同位素表型相关性高于75％，然而，选择具有最大表型差异的同胞对的设计变得更加强大。对于低于75％的同胞表型相关性，汇集极端不相关的个体是同胞对群体最强大的设计。每个设计的最佳合并分数在广泛的参数范围内是恒定的。定量表型的这些结果与针对定性表型报道的结果不同，对于这些结果，不相关的人群比同胞对更强大，一致的设计比不一致更强大，并且与正在进行的关联研究和预期的全基因组扫描具有直接关联。

10. 发明申请

WO0227034A3 METHOD OF IDENTIFYING GENETIC REGIONS ASSOCIATED WITH DISEASE AND PREDICTING RESPONSIVENESS TO THERAPEUTIC AGENTS 审中-公开
标题翻译：鉴定与疾病相关的遗传性地区的方法和对治疗药物的预测反应
公开(公告)号：WO0227034A3
公开(公告)日：2003-08-14
申请号：PCT/US0130672
申请日：2001-10-01
申请人： CURAGEN CORP , BADER JOEL S
发明人： BADER JOEL S
IPC分类号： C12Q1/68 , G01N33/48 , G01N33/50 , G06F19/18 , G06F19/24
CPC分类号： G06F19/18 , G06F19/24
摘要： The invention relates to a method of identifying genetic regions related to disease and to predicting the response to therapeutic agents. The invention provides a method of identifying a genetic region associated with a disease and/or associated with responsiveness to a therapeutic agent.
摘要翻译：本发明涉及鉴定与疾病相关的遗传区域并预测对治疗剂的反应的方法。本发明提供了鉴定与疾病相关和/或与对治疗剂的反应性有关的遗传区域的方法。

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