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1. 发明申请

WO2011021102A3 COMPOSITIONS AND METHODS FOR INTRAMOLECULAR NUCLEIC ACID REARRANGEMENT 审中-公开
标题翻译：分子内核酸重排的组合物和方法
公开(公告)号：WO2011021102A3
公开(公告)日：2011-04-28
申请号：PCT/IB2010002243
申请日：2010-08-13
申请人： POPULATION GENETICS TECH LTD , BRENNER SYDNEY , MIKAWA GI , OSBORNE ROBERT , SLATTER ANDREW
发明人： BRENNER SYDNEY , MIKAWA GI , OSBORNE ROBERT , SLATTER ANDREW
IPC分类号： C12N15/10 , C12N15/66 , C12Q1/68
CPC分类号： C12N15/1065 , C12Q1/6806 , C12Q1/6855 , C12Q1/686 , C12Q1/6874 , C12Q2563/179 , C12Q2537/143 , C12Q2535/122 , C12Q2525/161 , C12Q2525/155 , C12Q2525/143
摘要： Aspects of the present invention are drawn to processes for moving a region of interest in a polynucleotide from a first position to a second position with regard to a domain within the polynucleotide, also referred to as a "reflex method". In certain embodiments, the reflex method results in moving a region of interest into functional proximity to specific domain elements present in the polynucleotide (e.g., primer sites and/or MID). Compositions, kits and systems that find use in carrying out the reflex processes described herein are also provided.
摘要翻译：本发明的各方面涉及用于将多核苷酸中的感兴趣区域从第一位置移动到关于多核苷酸内的域的第二位置（也称为“反射方法”）的过程。在某些实施方案中，反射方法导致移动感兴趣区域到功能性接近多核苷酸中存在的特定结构域元件（例如，引物位点和/或MID）。还提供了用于执行本文所述的反射过程的组合物，试剂盒和系统。

2. 发明申请

WO2011055232A3 BASE-BY-BASE MUTATION SCREENING 审中-公开
标题翻译：基本的基本移植筛选
公开(公告)号：WO2011055232A3
公开(公告)日：2011-11-10
申请号：PCT/IB2010003306
申请日：2010-10-29
申请人： POPULATION GENETICS TECH LTD , BRENNER SYDNEY , MIKAWA GI
发明人： BRENNER SYDNEY , MIKAWA GI
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6827 , C12Q1/6858 , C12Q2537/1373 , C12Q2535/125 , C12Q2525/125
摘要： Aspects of the present invention are drawn to screening assays for isolating polynucleotides having a sequence variation or mutation. Embodiments of the screening assays include generating a population of polynucleotide duplexes having 5' overhang regions on one strand of the duplex (the "template" or "bottom strand") followed by isolating polynucleotide duplexes from the mixture that have one or more mismatched base at the 3' end of the other strand of the duplex (the "test" or "top" strand).
摘要翻译：本发明的方面涉及用于分离具有序列变异或突变的多核苷酸的筛选试验。筛选测定的实施方案包括产生在双链体（“模板”或“底部链”）的一条链上具有5'突出端区域的多核苷酸双链体群体，随后从具有一个或多个错配碱基的混合物中分离多核苷酸双链体双链的另一条链的3'末端（“测试”或“顶部”链）。

3. 发明申请

WO2012038839A2 INCREASING CONFIDENCE OF ALLELE CALLS WITH MOLECULAR COUNTING 审中-公开
标题翻译：利用分子计数提高ALLELE呼叫的信心
公开(公告)号：WO2012038839A2
公开(公告)日：2012-03-29
申请号：PCT/IB2011003160
申请日：2011-09-20
申请人： POPULATION GENETICS TECH LTD , CASBON JAMES , BRENNER SYDNEY , OSBORNE ROBERT , LICHTENSTEIN CONRAD
发明人： CASBON JAMES , BRENNER SYDNEY , OSBORNE ROBERT , LICHTENSTEIN CONRAD
IPC分类号： C12N15/09
CPC分类号： C12Q1/6855 , C12N15/1065 , C12Q1/6869 , C12Q1/6886 , C12Q1/70 , G06F19/18 , C12Q2525/179 , C12Q2525/191 , C12Q2545/101
摘要： Aspects of the present invention include methods and compositions for determining the number of individual polynucleotide molecules originating from the same genomic region of the same original sample that have been sequenced in a particular sequence analysis configuration or process. In these aspects of the invention, a degenerate base region (DBR) is attached to the starting polynucleotide molecules that are subsequently sequenced (e.g., after certain process steps are performed, e.g., amplification and/or enrichment). The number of different DBR sequences present in a sequencing run can be used to determine/estimate the number of different starting polynucleotides that have been sequenced. DBRs can be used to enhance numerous different nucleic acid sequence analysis applications, including allowing higher confidence allele call determinations in genotyping applications.
摘要翻译：本发明的方面包括用于确定源自相同原始样本的相同基因组区域的单个多核苷酸分子的数量的方法和组合物，所述原始样本已经在特定序列分析构造或过程中测序。在本发明的这些方面，将简并碱基区（DBR）连接到随后测序的起始多核苷酸分子上（例如在进行某些处理步骤后，例如扩增和/或富集）。测序运行中存在的不同DBR序列的数目可用于确定/估计已测序的不同起始多核苷酸的数目。 DBR可用于增强许多不同的核酸序列分析应用，包括允许在基因分型应用中进行更高可信度的等位基因呼叫测定。

4. 发明申请

WO2011107887A2 METHODS FOR REPLICATING POLYNUCLEOTIDES WITH SECONDARY STRUCTURE 审中-公开
标题翻译：用二级结构代替多核苷酸的方法
公开(公告)号：WO2011107887A2
公开(公告)日：2011-09-09
申请号：PCT/IB2011000830
申请日：2011-02-28
申请人： POPULATION GENETIC TECHNOLOGIES LTD , BRENNER SYDNEY , OSBORNE ROBERT , SLATTER ANDREW
发明人： BRENNER SYDNEY , OSBORNE ROBERT , SLATTER ANDREW
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6848 , C12Q1/6853 , C12Q2537/143 , C12Q2525/161 , C12Q2525/143
摘要： Aspects of the present invention are drawn to processes for replicating polynucleotide sequences having secondary structure(s) that reduce or inhibit the replication process. Compositions, kits and systems that find use in carrying out the replication processes described herein are also provided.
摘要翻译：本发明的方面涉及用于复制具有减少或抑制复制过程的二级结构的多核苷酸序列的方法。还提供了用于实施本文所述的复制过程的组合物，试剂盒和系统。

5. 发明申请

WO2006081222A2 ISOTHERMAL DNA AMPLIFICATION 审中-公开
标题翻译：同位素DNA扩增
公开(公告)号：WO2006081222A2
公开(公告)日：2006-08-03
申请号：PCT/US2006002391
申请日：2006-01-23
申请人： COMPASS GENETICS LLC , BRENNER SYDNEY , MIKAWA GI
发明人： BRENNER SYDNEY , MIKAWA GI
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12P19/34 , C12Q1/6865 , C12Q2565/537 , C12Q2525/301
摘要： The present invention provides for amplification of one or more polynucleotides by multi-staged linear amplifications using one or more RNA polymerases. At each stage RNA transcripts are accumulated at a linear rate, so that multiple stages provide for faster than linear transcript accumulation. In one aspect, the invention provides for polynucleotide amplification by ligating hairpin adaptors to an end of polynucleotides wherein the hairpin adaptors each contain a promoter sequence oriented so that transcription proceeds in the direction of the loop of the hairpin adaptor. Upon transcription through such loop region and to the complementary strand a replicate is made of the promoter sequence as well as the polynucleotide, thereby permitting exponential amplification upon reverse transcription, second strand synthesis, and repetition of the above cycle. Preferably such amplification is carried out under isothermal reaction conditions.
摘要翻译：本发明通过使用一种或多种RNA聚合酶的多级线性扩增来提供一种或多种多核苷酸的扩增。在每个阶段，RNA转录物以线性速率累积，使得多个阶段提供比线性转录物积累更快的阶段。在一个方面，本发明通过将发夹衔接子连接到多核苷酸的末端来提供多核苷酸扩增，其中发夹衔接子各自含有取向的启动子序列，使得转录沿发夹衔接子的环的方向进行。在通过这种环区转录和互补链时，由启动子序列以及多核苷酸重复，从而允许逆转录，第二链合成和上述循环的重复进行指数扩增。优选地，这种扩增在等温反应条件下进行。

6. 发明申请

WO2007087262A3 SELECTIVE GENOME AMPLIFICATION 审中-公开
标题翻译：选择性基因组扩增
公开(公告)号：WO2007087262A3
公开(公告)日：2007-12-21
申请号：PCT/US2007001679
申请日：2007-01-22
申请人： COMPASS GENETICS LLC , BRENNER SYDNEY , MIKAWA GI , MACEVICZ STEPHEN C
发明人： BRENNER SYDNEY , MIKAWA GI , MACEVICZ STEPHEN C
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6855 , C12P19/34 , C12Q1/6865 , C12Q2525/301 , C12Q2525/143 , C12Q2531/143
摘要： The invention provides methods and compositions for amplifying selected polynucleotides, especially selected subsets of restriction fragments. Generally, methods of the invention are implemented by ligating adaptors containing at least one promoter sequence to such fragments under conditions that promote the formation of closed single stranded or double stranded structures, which are capable of serving as cyclical templates for transcription.
摘要翻译：本发明提供了用于扩增选择的多核苷酸，特别是选定的限制性片段子集的方法和组合物。一般而言，本发明的方法通过在促进形成闭合的单链或双链结构的条件下将含有至少一个启动子序列的衔接子连接到此类片段上来实施，所述闭合的单链或双链结构能够充当用于转录的循环模板。

7. 发明申请

WO2009031054A3 METHODS AND COMPOSITIONS FOR ISOLATING NUCLEIC ACID SEQUENCE VARIANTS 审中-公开
标题翻译：分离核酸序列变异体的方法和组合物
公开(公告)号：WO2009031054A3
公开(公告)日：2009-12-17
申请号：PCT/IB2008003320
申请日：2008-06-27
申请人： POPULATION GENETICS TECHNOLOGI , BRENNER SYDNEY
发明人： BRENNER SYDNEY
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6827 , C12Q1/6869 , C12Q2565/537 , C12Q2533/101 , C12Q2525/186 , C12Q2531/119 , C12Q2565/514 , C12Q2535/101
摘要： The invention is drawn to isolating sequence variants of a genetic locus of interest using a modified iterative primer extension method. The nucleic acids analyzed are generally single stranded and have a reference sequence which is used as a basis for performing iterative single nucleotide extension reactions from a hybridized polymerization primer. The iterative polymerization reactions are configured such that polymerization of the strand will continue if the sequence of the nucleic acid being analyzed matches the reference sequence, whereas polymerization will be terminated if the nucleic acid being analyzed does not match the reference sequence. Nucleic acid strands that have mutations can be isolated using a variety of methods and sequenced to determine the precise identity of the mutation/polymorphism. By performing the method on both strands of the nucleic acid being analyzed, virtually all possible mutations can be identified.
摘要翻译：本发明是使用改进的迭代引物延伸方法来分离遗传基因座的序列变体。分析的核酸通常是单链的，并且具有参考序列，其用作从杂交聚合引物进行迭代单核苷酸延伸反应的基础。配置迭代聚合反应，使得如果被分析的核酸序列与参考序列匹配，则链的聚合将持续，而如果所分析的核酸与参考序列不一致则聚合将终止。可以使用多种方法分离具有突变的核酸链，并测序以确定突变/多态性的精确同一性。通过对正在分析的核酸的两条链进行该方法，实际上可以鉴定所有可能的突变。

8. 发明申请

WO2006099604A3 METHODS AND COMPOSITIONS FOR ASSAY READOUTS ON MULTIPLE ANALYTICAL PLATFORMS 审中-公开
标题翻译：用于多个分析平台测量准备的方法和组合
公开(公告)号：WO2006099604A3
公开(公告)日：2009-04-23
申请号：PCT/US2006009898
申请日：2006-03-16
申请人： COMPASS GENETICS LLC , BRENNER SYDNEY
发明人： BRENNER SYDNEY
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6816 , C12Q1/68 , C12Q2537/143 , C12Q2525/185 , C12Q2525/151 , C12Q2565/125 , C12Q2565/501
摘要： The invention provides methods and compositions for reading out the results of multiplex assays on various analytical platforms, such as microarrays, bead arrays, electrophoresis devices, and the like. An important feature of the invention includes methods for converting different sets of oligonucleotide tags used for labeling into oligonucleotide tags specific for a particular analytical platform. The invention further includes compositions comprising oligonucleotide tags having convenient properties for labeling and conversion, particularly ligation tags that employ ligation reaction specificity as well as sequence specificity in order to discriminate between tags.
摘要翻译：本发明提供用于读出多种分析平台如微阵列，珠阵列，电泳装置等的多重测定结果的方法和组合物。本发明的一个重要特征包括用于将用于标记的不同组的寡核苷酸标签转换成特定于特定分析平台的寡核苷酸标签的方法。本发明还包括包含具有方便的标记和转化性质的寡核苷酸标签的组合物，特别是使用连接反应特异性的连接标签以及序列特异性以区分标签。

9. 发明申请

WO9935293A3 SOLID PHASE SELECTION OF DIFFERENTIALLY EXPRESSED GENES 审中-公开
标题翻译：固定相选择差异表达基因
公开(公告)号：WO9935293A3
公开(公告)日：1999-09-30
申请号：PCT/US9900666
申请日：1999-01-08
申请人： LYNX THERAPEUTICS INC , ALBRECHT GLEN , BRENNER SYDNEY , DUBRIDGE ROBERT
发明人： ALBRECHT GLEN , BRENNER SYDNEY , DUBRIDGE ROBERT
IPC分类号： C12N15/10 , C12Q1/68
CPC分类号： C12Q1/6834 , C12N15/1096 , C12Q1/6809 , C12Q2565/518 , C12Q2521/313 , C12Q2525/191
摘要： The invention provides a method and materials for monitoring and isolating differentially expressed genes. In accordance with the method of the invention, differently labeled populations of DNAs from sources to be compared are competitively hybridized with reference DNA cloned on solid phase supports, e.g. microparticles, to provide a differential expression library which, in the preferred embodiment, may be manipulated by fluorescence-activated cell sorting (FACS). Monitoring the relative signal intensity of the different fluorescent labels on the microparticles permits quantitative analysis of expression levels relative to the reference DNA. The invention also provides a method for identifying and isolating rare genes. Populations of microparticles having relative signal intensities of interest can be isolated by FACS and the attached DNAs identified by sequencing, such as with massively parallel signature sequencing (MPSS), or with conventional DNA sequencing protocols.
摘要翻译：本发明提供了用于监测和分离差异表达基因的方法和材料。根据本发明的方法，来自待比较来源的不同标记的DNA群体与克隆在固相载体上的参考DNA竞争性杂交，例如，微粒，以提供在优选实施方案中可以通过荧光激活细胞分选（FACS）操纵的差异表达文库。监测微粒上不同荧光标记的相对信号强度允许相对于参照DNA的表达水平进行定量分析。本发明还提供了鉴定和分离稀有基因的方法。具有感兴趣的相对信号强度的微粒的群体可以通过FACS和通过测序鉴定的所连接的DNA进行分离，例如通过大规模并行签名测序（MPSS）或常规DNA测序方案。

10. 发明申请

WO0113958A3 DRUG CONJUGATES AND METHODS OF DESIGNING THE SAME 审中-公开
标题翻译：药物结合物及其设计方法
公开(公告)号：WO0113958A3
公开(公告)日：2002-01-31
申请号：PCT/US0023593
申请日：2000-08-28
申请人： BRENNER SYDNEY , GOELET PHILIP , STACKHOUSE JOSEPH , MILLWARD STEVEN W
发明人： BRENNER SYDNEY , GOELET PHILIP , STACKHOUSE JOSEPH , MILLWARD STEVEN W
IPC分类号： C12N15/09 , A61K47/34 , A61K47/48 , C40B40/02 , C40B50/06
CPC分类号： A61K47/54
摘要： The invention relates to drug conjugates and methods of their design. One embodiment of the invention is directed to a method of designing vector-linker-pharmacophore ("VLP") conjugates that is generally applicable to a wide variety of vectors, linkers, and pharmacophores. The invention also encompasses a method of improving the delivery of a pharmacophore to a patient, as well as a method of improving the therapeutic efficacy of a pharmacophore and a method of decreasing the toxicity of a pharmacophore. A method of increasing the concentration of a pharmacophore in a cell is further encompassed by the invention.
摘要翻译：本发明涉及药物缀合物及其设计方法。本发明的一个实施方案涉及通常适用于多种载体，接头和药效团的载体 - 接头 - 药效团（“VLP”）缀合物的设计方法。本发明还包括改善药效团向患者的递送的方法，以及改善药效团的治疗功效的方法和降低药效团的毒性的方法。增加细胞中药效团浓度的方法进一步包括在本发明中。

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