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31. 发明申请

WO2006069346A2 METHYLATION-SENSITIVE RESTRICTION ENZYME ENDONUCLEASE METHOD OF WHOLE GENOME METHYLATION ANALYSIS 审中-公开
标题翻译：甲基化敏感限酶法核酸内切酶全基因组甲基化分析
公开(公告)号：WO2006069346A2
公开(公告)日：2006-06-29
申请号：PCT/US2005/046896
申请日：2005-12-20
申请人： ILLUMINA, INC. , GUNDERSON, Kevin
发明人： GUNDERSON, Kevin
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6827 , C12Q2521/331 , C12Q2521/101 , C12Q2539/103
摘要： The invention provides methods of identifying a plurality of reactive recognition sites for a restriction endonuclease in genomic DNA. In particular embodiments, the methods can be used to identify methylation state of a plurality of CpG target sites in genomic DNA. The method can include steps of treating genomic DNA with a restriction endonuclease, thereby producing genomic DNA fragments; ligating the fragments, thereby forming a concatenated DNA; and identifying sequence portions of the concatenated DNA that are re-ordered compared to the genomic DNA.
摘要翻译：本发明提供了鉴定基因组DNA中限制性内切核酸酶的多个反应性识别位点的方法。在特定的实施方案中，该方法可用于鉴定基因组DNA中多个CpG靶位点的甲基化状态。该方法可以包括用限制性内切核酸酶处理基因组DNA的步骤，由此产生基因组DNA片段; 连接片段，从而形成连接的DNA; 并鉴定与基因组DNA相比重新排序的级联DNA的序列部分。

32. 发明申请

WO2004007755A3 MULTIPLEX NUCLEIC ACID REACTIONS 审中-公开
公开(公告)号：WO2004007755A3
公开(公告)日：2004-01-22
申请号：PCT/US2003/022171
申请日：2003-07-15
申请人： ILLUMINA, INC. , CHEE, Mark , FAN, Jian-Bing , GUNDERSON, Kevin
发明人： CHEE, Mark , FAN, Jian-Bing , GUNDERSON, Kevin
IPC分类号： C12Q1/68
摘要： The invention is directed to a variety of multiplexing methods used to amplify and/or genotype a variety of samples simultaneously. The invention provides a method of detecting a target sequence. The method consists of: (a) contacting a first and second probe with a target sequence under conditions where complementary probes form a hybridization complex with the target sequence, the first probe comprising an upstream universal priming site and a target specific sequence, the second probe comprising a downstream universal priming site and a target-specific sequence, wherein one of the first or second probes comprise an adapter sequence; (b) extending the first or second probe of the hybridization complex to form a modified probe; (c) amplifying the modified probe to form an amplicon, and (d) detecting the amplicon. A method of detecting the relative amounts of two or more target sequences is also provided. The method consists of (a) contacting a first and a second probe with first and second target sequences in an initial population under conditions where complementary probes form a hybridization complex with the target sequences, the first and second probes comprising a universal priming site, an adapter sequence and a target-specific sequence; (b) linearly amplifying the first and second probes forming the hybridization complex to produce first and second amplicons having distinctive adapter sequences, and (c) determining a relative amount of the first and second amplicons distinguishable by the adapter sequence, wherein the relative amount of the amplicons is indicative of the relative amounts of the first and second target sequences in the initial population. Further provided is a method of amplifying a target sequence to produce a signal within a dynamic range of a detection assay. The method consists of: (a) hybridizing a target-specific probe having an upstream universal priming site (UUP), a downstream universal priming site (DUP) and an adapter sequence with a set of differential primers, the set of differential primers comprising an upstream primer and first and second downstream primers, the second downstream primer having a lower Tm compared to the upstream primer and the first downstream primer; (b) amplifying the probe with the set of differential primers for two or more cycles of enzymatic polymerization; (c) increasing hybridization stringency to suppress hybridization of the second downstream primer, and (d) amplifying the probe from the upstream and the first downstream primers of the set for at least one cycle of enzymatic polymerization, wherein differential signals of amplicons produced from amplification of the first or the second downstream primers fall within a dynamic range of a detection assay.

33. 发明申请

WO2016061517A2 CONTIGUITY PRESERVING TRANSPOSITION 审中-公开
标题翻译：对等保存转换
公开(公告)号：WO2016061517A2
公开(公告)日：2016-04-21
申请号：PCT/US2015/056040
申请日：2015-10-16
申请人： ILLUMINA CAMBRIDGE LIMITED , STEEMERS, Frank J. , GUNDERSON, Kevin L. , ZHANG, Fan , BETLEY, Jason Richard , GORMLEY, Niall Anthony , MEULEMAN, Wouter , WEIR, Jacqueline , IOANNOU, Avgousta , JENKINS, Gareth , JACKSON, Rosamond , MORRELL, Natalie , POKHOLOK, Dmitry K. , NORBERG, Steven J. , HE, Molly , KIA, Amirali , GORYSHIN, Igor , PANTOJA, Rigo
发明人： STEEMERS, Frank J. , GUNDERSON, Kevin L. , ZHANG, Fan , BETLEY, Jason Richard , GORMLEY, Niall Anthony , MEULEMAN, Wouter , WEIR, Jacqueline , IOANNOU, Avgousta , JENKINS, Gareth , JACKSON, Rosamond , MORRELL, Natalie , POKHOLOK, Dmitry K. , NORBERG, Steven J. , HE, Molly , KIA, Amirali , GORYSHIN, Igor , PANTOJA, Rigo
IPC分类号： C12N15/10
CPC分类号： C12N15/1093 , C12N15/1065 , C12Q2525/191 , C12Q2563/179 , C12Q2565/514
摘要： Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.
摘要翻译：本文提供的实施方案涉及用于制备靶核酸的条形码化DNA片段的固定文库，鉴定基因组变体，确定靶核酸的邻接信息，定相信息和甲基化状态的方法和组合物酸

34. 发明申请

WO2013137922A3 FUNCTIONALIZATION AND PURIFICATION OF MOLECULES BY REVERSIBLE GROUP EXCHANGE 审中-公开
标题翻译：通过可逆组交换功能和纯化分子
公开(公告)号：WO2013137922A3
公开(公告)日：2013-11-14
申请号：PCT/US2012049339
申请日：2012-08-02
申请人： ILLUMINA INC , STEEMERS FRANK J , GUNDERSON KEVIN , YORK KERRI
发明人： STEEMERS FRANK J , GUNDERSON KEVIN , YORK KERRI
IPC分类号： C12N15/10
CPC分类号： C07H1/06 , C07D495/04 , C07H1/00 , C07H21/00 , C12N15/1003 , C12Q1/6811
摘要： Embodiments of the present disclosure include methods and compositions for functionalizing molecules, such as oligonucleotides, with functional groups, including polyhistidine tags useful in affinity methods. Some embodiments include methods for modifying and purifying complex mixtures of molecules by exchange of functional tags.
摘要翻译：本公开的实施方案包括用于官能化分子（例如具有官能团的寡核苷酸）的方法和组合物，包括用于亲和方法的多组氨酸标签。一些实施方案包括通过交换功能性标签来修饰和纯化分子的复杂混合物的方法。

35. 发明申请

WO2005003304A2 METHODS AND COMPOSITIONS FOR WHOLE GENOME AMPLIFICATION AND GENOTYPING 审中-公开
标题翻译：全基因组扩增和基因组的方法和组合
公开(公告)号：WO2005003304A2
公开(公告)日：2005-01-13
申请号：PCT/US2004/019545
申请日：2004-06-17
申请人： ILLUMINA, INC. , GUNDERSON, Kevin , STEEMERS, Frank
发明人： GUNDERSON, Kevin , STEEMERS, Frank
IPC分类号： C12N
CPC分类号： C12Q1/6827 , C12Q1/6816 , C12Q1/682 , C12Q1/6837 , C12Q1/6848 , C12Q2565/537 , C12Q2565/549 , C12Q2565/513 , C12Q2537/143 , C12Q2535/125 , C12Q2537/163 , C12Q2525/301 , C12Q2522/101
摘要： This invention provides methods of amplifying genomic DNA to obtain an amplified representative population of genome fragments. Methods are further provided for obtaining amplified genomic DNA representations of a desired complexity. The invention further provides methods for simultaneously detecting large numbers of typable loci for an amplified representative population of genome fragments. Accordingly the methods can be used to genotype individuals on a genome-wide scale.
摘要翻译：本发明提供扩增基因组DNA以获得扩增的代表性基因组片段的方法。进一步提供了获得所需复杂度的扩增基因组DNA表达的方法。本发明还提供了用于同时检测扩增的代表性基因组片段群体的大量类型基因座的方法。因此，该方法可用于在全基因组范围内对个体进行基因型分型。

36. 发明申请

WO1997027317A1 NUCLEIC ACID ANALYSIS TECHNIQUES 审中-公开
标题翻译：核酸分析技术
公开(公告)号：WO1997027317A1
公开(公告)日：1997-07-31
申请号：PCT/US1997001603
申请日：1997-01-22
申请人： AFFYMETRIX, INC. , LOCKHART, David, J. , CHEE, Mark , GUNDERSON, Kevin , LAI, Chaoqiang , WODICKA, Lisa , CRONIN, Maureen, T. , LEE, Danny , TRAN, Huu, M. , MATSUZAKI, Hajime , McGALL, Glenn, H. , BARONE, Anthony, D.
发明人： AFFYMETRIX, INC.
IPC分类号： C12Q01/00
CPC分类号： C12Q1/6809 , C07H19/052 , C07H19/12 , C07H21/00 , C12Q1/6816 , C12Q1/6837 , C12Q2600/156 , C40B40/00 , C12Q2565/501 , C12Q2521/501
摘要： The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater then 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase. In another embodiment, the end labeling can be accomplished by providing a nucleic acid, providing labeled nucleoside triphosphates, and attaching the nucleoside triphosphates to the nucleic acid using a terminal transferase.
摘要翻译：本发明提供用于鉴定两个或多个样品之间的核酸丰度差异（例如，表达水平）的简化方法。该方法包括提供包含大量（例如大于1,000个）任意选择的不同寡核苷酸探针的阵列，其中每个不同探针的序列和位置是已知的。来自两个或更多个样品的核酸样品（例如mRNA）与探针阵列杂交，并检测杂交模式。样本之间的杂交模式的差异表明这些样品之间各种基因的表达差异。本发明还提供了一种终止标记核酸的方法。在一个实施方案中，该方法包括提供核酸，提供标记的寡核苷酸，然后将寡核苷酸酶连接到核酸上。因此，例如，当核酸是RNA时，可以使用RNA连接酶连接标记的寡核糖核苷酸。在另一个实施方案中，末端标记可以通过提供核酸，提供标记的核苷三磷酸和使用末端转移酶将核苷三磷酸与核酸连接来实现。

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