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1. 发明申请

WO2016153999A1 MODIFIED NUCLEOTIDES AND USES THEREOF 审中-公开
标题翻译：改良的核苷酸及其用途
公开(公告)号：WO2016153999A1
公开(公告)日：2016-09-29
申请号：PCT/US2016/023139
申请日：2016-03-18
申请人： LIFE TECHNOLOGIES CORPORATION , LIFE TECHNOLOGIES GMBH
发明人： HINZ, Wolfgang , MENCHEN, Steven , GRAHAM, Ronald , VANDER HORN, Peter , HUBBELL, Earl , WOEHLER, Christian
IPC分类号： C12Q1/68 , G01N27/414
CPC分类号： C12Q1/6869 , G01N27/4145 , C12Q2525/117 , C12Q2565/30
摘要： In some embodiments, the disclosure relates generally to methods, as well as related, systems, compositions, kits and apparatuses, for nucleic acid analysis that involve the use of modified nucleotides, including terminator nucleotides and/or tagged nucleotides, in a template-dependent nucleotide incorporation reaction. In some embodiments, the nucleic acid analysis can be conducted at a single reaction site, or at a plurality of reaction sites in an array of reaction sites. Optionally, the array contains a plurality of reaction sites having about 1-100 million, or about 100-250 million, or about 200-500 million, or about 500-900 million, or more reaction sites. Optionally, each reaction site is in contact with, operatively coupled, or capacitively coupled to one or more sensors that are ion-sensitive FETs (isFETs) or chemically-sensitive FETs (chemFETs) sensors. Optionally, the reaction sites are in fluid communication with each other.
摘要翻译：在一些实施方案中，本公开一般涉及涉及在模板依赖性中使用经修饰的核苷酸（包括终止子核苷酸和/或标记的核苷酸）的核酸分析的方法以及相关的系统，组合物，试剂盒和装置核苷酸掺入反应。在一些实施方案中，核酸分析可以在单个反应位点或反应位点阵列中的多个反应位点进行。任选地，阵列包含多个具有约1-100百万，约100-250百万，或约200-500百万，或约500-900万个或更多个反应位点的反应位点。任选地，每个反应位点与作为离子敏感FET（isFET）或化学敏感FET（chemFET）传感器的一个或多个传感器接触，可操作地耦合或电容耦合。任选地，反应位点彼此流体连通。

2. 发明申请

WO2016100438A2 POLYMERASE COMPOSITIONS AND METHODS OF MAKING AND USING SAME 审中-公开
标题翻译：聚合酶组合物及其制备和使用方法
公开(公告)号：WO2016100438A2
公开(公告)日：2016-06-23
申请号：PCT/US2015/065977
申请日：2015-12-16
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： MAZUR, Daniel , TOZER, Eileen , CHEN, Sihong , VANDER HORN, Peter , LINCECUM, Tommie
IPC分类号： C12N9/12 , C12Q1/68
CPC分类号： C12Q1/686 , C12N9/1252 , C12Q1/6869 , C12Q2521/101 , C12Y207/07007
摘要： The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, modified polymerases and biologically active fragments thereof, such as modified Taq polymerases, are provided that allow for improved nucleic acid amplification. In some aspects, the disclosure provides modified polymerases having improved thermostability, accuracy, processivity and/or read length as compared to a referenceTaq polymerase. In some aspects, the disclosure relates to modified polymerases or biologically active fragments thereof, useful for amplification methods, and in practically illustrative embodiments, emulsion PCR.
摘要翻译：本公开提供了用于核酸聚合的组合物，方法，试剂盒，系统和装置。具体而言，提供了修饰的聚合酶及其生物活性片段，例如修饰的Taq聚合酶，其允许改善的核酸扩增。在一些方面，本公开内容提供了与参照Taq聚合酶相比具有改善的热稳定性，准确性，持续合成能力和/或阅读长度的修饰的聚合酶。在一些方面，本公开涉及可用于扩增方法的修饰聚合酶或其生物活性片段，并且在实际示例性实施方案中为乳液PCR。

3. 发明申请

WO2015048763A1 POLYMERASE COMPOSITIONS, METHODS OF MAKING AND USING SAME 审中-公开
标题翻译：聚合物组合物，制备方法和使用方法
公开(公告)号：WO2015048763A1
公开(公告)日：2015-04-02
申请号：PCT/US2014/058361
申请日：2014-09-30
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： VANDER HORN, Peter , MAZUR, Daniel , NIKIFOROV, Theo , LANDES, Mindy , TOZER, Eileen
IPC分类号： C12Q1/68 , C12N9/12
CPC分类号： C12N9/1252 , C12Q1/686 , C12Q1/6869
摘要： The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, modified polymerases and biologically active fragments thereof are provided that allow for nucleic acid amplification. In some aspects, the disclosure provides modified polymerases having lower systematic error as compared to a reference polymerase. In one aspect, the disclosure relates to modified polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In some aspects, the disclosure relates to modified polymerases useful for the generation of nucleic acid libraries or nucleic acid templates. In some aspects, the disclosure relates to the identification of homologous amino acid mutations that can be transferred across classes or families of polymerases to provide novel polymerases with altered properties.
摘要翻译：本公开提供了可用于核酸聚合的组合物，方法，试剂盒，系统和装置。特别地，提供了允许核酸扩增的修饰的聚合酶及其生物活性片段。在一些方面，本公开提供与参考聚合酶相比具有较低系统误差的修饰聚合酶。一方面，本公开涉及可用于核酸测序，基因分型，拷贝数变异分析，配对末端测序和其他形式遗传分析的修饰聚合酶。在一些方面，本公开涉及可用于产生核酸文库或核酸模板的修饰聚合酶。在一些方面，本公开涉及可以跨越聚合酶类或家族转移的同源氨基酸突变的鉴定，以提供具有改变的性质的新型聚合酶。

4. 发明申请

WO2015051338A1 METHODS AND SYSTEMS FOR MODELING PHASING EFFECTS IN SEQUENCING USING TERMINATION CHEMISTRY 审中-公开
标题翻译：使用终止化学序列建模相关效应的方法和系统
公开(公告)号：WO2015051338A1
公开(公告)日：2015-04-09
申请号：PCT/US2014/059191
申请日：2014-10-03
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： KOLLER, Christian , SIKORA, Marcin , VANDER HORN, Peter
IPC分类号： G06F19/20
CPC分类号： G06F19/22 , G06F19/12 , G06F19/18 , G06F19/20
摘要： A method for nucleic acid sequencing includes receiving observed or measured nucleic acid sequencing data from a sequencing instrument that receives and processes a sample nucleic acid in a termination sequencing-by-synthesis process. The method also includes generating a set of candidate sequences of bases for the observed or measured nucleic acid sequencing data by determining a predicted signal for candidate sequences using a simulation framework. The simulation framework incorporates an estimated carry forward rate (CFR), an estimated incomplete extension rate (IER), an estimated droop rate (DR), an estimated reactivated molecules rate (RMR), and an estimated termination failure rate (TFR), the RMR being greater than or equal to zero and the TFR being lesser than one. The method also includes identifying, from the set of candidate sequences of bases, one candidate sequence leading to optimization of a solver function as corresponding to the sequence for the sample nucleic acid.
摘要翻译：用于核酸测序的方法包括接收来自测序仪器的观测或测量的核酸测序数据，所述测序仪器在终止测序合成过程中接收和处理样品核酸。该方法还包括通过使用模拟框架确定候选序列的预测信号来产生用于观察或测量的核酸测序数据的一组候选碱基序列。模拟框架包含估计结转率（CFR），估计不完全扩展率（IER），估计下降率（DR），估计的再活化分子率（RMR）和估计的终止失败率（TFR）， RMR大于或等于零，TFR小于1。该方法还包括从候选碱基序列的集合中鉴定出一个候选序列，导致解析函数的优化对应于样品核酸的序列。

5. 发明申请

WO2013023176A2 POLYMERASE COMPOSITIONS, METHODS OF MAKING AND USING SAME 审中-公开
标题翻译：聚合酶组合物，其制备和使用方法
公开(公告)号：WO2013023176A2
公开(公告)日：2013-02-14
申请号：PCT/US2012/050423
申请日：2012-08-10
申请人： LIFE TECHNOLOGIES CORPORATION , VANDER HORN, Peter , NIKIFOROV, Theo , LUO, Guobin , LANDES, Mindy , MAZUR, Daniel , TOZER, Eileen , LINCECUM, Tommie
发明人： VANDER HORN, Peter , NIKIFOROV, Theo , LUO, Guobin , LANDES, Mindy , MAZUR, Daniel , TOZER, Eileen , LINCECUM, Tommie
IPC分类号： C12Q1/68
CPC分类号： C12N9/1252 , C12Q1/6846 , C12Q1/686 , C12Y207/07007
摘要： The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, modified polymerases and biologically active fragment thereof are provided that allow for nucleic acid amplification. In one aspect, the disclosure relates to modified polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In some aspects, the disclosure relates to modified polymerases useful for the generation of nucleic acid libraries or nucleic acid templates for use in various downstream processes. In some aspects, the disclosure relates to the identification of homologous amino acid mutations that can be transferred across classes or families of polymerases to provide novel polymerases with altered catalytic properties. In some aspects, the disclosure provides modified polymerases having enhanced catalytic properties as compared to a reference polymerase.
摘要翻译：本公开提供了用于核酸聚合的组合物，方法，试剂盒，系统和装置。具体而言，提供了允许核酸扩增的修饰聚合酶及其生物活性片段。在一个方面，本公开涉及用于核酸测序，基因分型，拷贝数变异分析，配对末端测序和其他形式的遗传分析的修饰的聚合酶。在一些方面，本公开涉及用于产生供各种下游过程使用的核酸文库或核酸模板的修饰聚合酶。在一些方面，本公开涉及鉴定可以跨聚合酶的类或家族转移以提供具有改变的催化性质的新聚合酶的同源氨基酸突变。在一些方面，本公开内容提供了与参考聚合酶相比具有增强的催化性质的修饰聚合酶。

6. 发明申请

WO2017058810A2 POLYMERASE COMPOSITIONS AND KITS, AND METHODS OF USING AND MAKING THE SAME 审中-公开
标题翻译：聚合物组合物和组合物，以及使用和制备它们的方法
公开(公告)号：WO2017058810A2
公开(公告)日：2017-04-06
申请号：PCT/US2016/053994
申请日：2016-09-27
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： MAZUR, Daniel , VANDER HORN, Peter , TOZER, Eileen , CHEN, Sihong , LUO, Guobin , SHIRLEY, Joshua , HEINEMANN, Kevin
IPC分类号： C12Q1/68 , C12N9/12
CPC分类号： C12N9/1252 , C12Q1/686 , C12Y207/07007 , C12Q2521/101
摘要： The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, recombinant polymerases and biologically active fragments thereof are provided that allow for nucleic acid amplification. In some aspects, the disclosure provides recombinant polymerases that yield lower systematic error rates and/or improved accuracy, when used in sequencing by synthesis reactions as compared to a control polymerase. In one aspect, the disclosure relates to recombinant polymerases useful for nucleic acid sequencing, genotyping, copy number variation analysis, paired-end sequencing and other forms of genetic analysis. In another aspect, the recombinant polymerases are useful for the amplification of nucleic acid templates during PCR, emPCR, isothermal amplification, recombinase polymerase amplification, rolling circle amplification, strand displacement amplification and proximity ligation amplification. In some aspects, the disclosure relates to recombinant polymerases useful for the generation of nucleic acid libraries and/or nucleic acid templates.
摘要翻译：本公开提供了可用于核酸聚合的组合物，方法，试剂盒，系统和装置。特别地，提供允许核酸扩增的重组聚合酶及其生物活性片段。在一些方面，当与对照聚合酶相比时，通过合成反应进行测序时，本公开提供了产生较低系统误差率和/或改善的准确度的重组聚合酶。一方面，本公开涉及可用于核酸测序，基因分型，拷贝数变异分析，配对末端测序和其他形式遗传分析的重组聚合酶。另一方面，重组聚合酶可用于在PCR，emPCR，等温扩增，重组酶聚合酶扩增，滚环扩增，链置换扩增和接近连接扩增期间扩增核酸模板。在一些方面，本公开涉及可用于产生核酸文库和/或核酸模板的重组聚合酶。

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