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1. 发明申请

US20200277580A1 POLYMERASE COMPOSITIONS, METHODS OF MAKING AND USING SAME 审中-公开
公开(公告)号：US20200277580A1
公开(公告)日：2020-09-03
申请号：US16850629
申请日：2020-04-16
申请人： Life Technologies Corporation
发明人： Peter VANDER HORN , Theo NIKIFOROV , Guobin LUO , Mindy LANDES , Daniel MAZUR , Eileen TOZER , Tommie LINCECUM
IPC分类号： C12N9/12 , C12Q1/6844 , C12Q1/686
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.

2. 发明申请

US20170369857A1 NUCLEOTIDE TRANSIENT BINDING FOR SEQUENCING METHODS 审中-公开
公开(公告)号：US20170369857A1
公开(公告)日：2017-12-28
申请号：US15690945
申请日：2017-08-30
申请人： Life Technologies Corporation
发明人： Peter VANDER HORN , Cheng-Yao CHEN , Guobin LUO , Michael PREVITE , Jamshid TEMIROV , Theo NIKIFOROV , Zhaohui ZHOU , Hongye SUN , Yufang WANG , Stefanie Yukiko NISHIMURA , Hongyi WANG , Marian PERIS , Barnett ROSENBLUM , Michael PHELAN
IPC分类号： C12N9/12 , C12Q1/68
CPC分类号： C12N9/1252 , C12Q1/68 , C12Q1/6804 , C12Q1/6818 , C12Q1/6827 , C12Q1/6869 , C12Q1/6872 , C12Y207/07007 , G01N2500/00 , C12Q2565/632 , C12Q2563/137 , C12Q2563/107 , C12Q2565/30 , C12Q2537/157
摘要： Provided herein are compositions and systems for use in polymerase-dependent, nucleotide transient-binding methods. The methods are useful for deducing the sequence of a template nucleic acid molecule and single nucleotide polymorphism (SNP) analyses. The methods rely on the fact that the polymerase transient-binding time for a complementary nucleotide is longer compared to that of a non-complementary nucleotide. The labeled nucleotides transiently-binds the polymerase in a template-dependent manner, but does not incorporate. The methods are conducted under any reaction condition that permits transient binding of a complementary or non-complementary nucleotide to a polymerase, and inhibits nucleotide incorporation.

3. 发明申请

US20180119217A1 MODIFIED NUCLEOTIDES AND USES THEREOF 审中-公开
公开(公告)号：US20180119217A1
公开(公告)日：2018-05-03
申请号：US15561445
申请日：2016-03-18
申请人： LIFE TECHNOLOGIES CORPORATION , LIFE TECHNOLOGIES GMBH
发明人： Wolfgang HINZ , Steven MENCHEN , Ronald GRAHAM , Peter VANDER HORN , Earl HUBBELL , Christian WOEHLER , Roman ROZHKOV , Barnett ROSENBLUM
IPC分类号： C12Q1/6874
CPC分类号： C12Q1/6874 , C12Q2565/607
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.

4. 发明申请

US20170260512A1 POLYMERASE COMPOSITIONS, METHODS OF MAKING AND USING SAME 审中-公开
公开(公告)号：US20170260512A1
公开(公告)日：2017-09-14
申请号：US15481858
申请日：2017-04-07
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： Peter VANDER HORN , Daniel MAZUR , Theo NIKIFOROV , Mindy LANDES , Eileen TOZER
IPC分类号： C12N9/12 , C12Q1/68
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.

5. 发明申请

US20200299655A1 POLYMERASE COMPOSITIONS, METHODS OF MAKING AND USING SAME 审中-公开
公开(公告)号：US20200299655A1
公开(公告)日：2020-09-24
申请号：US16894469
申请日：2020-06-05
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： Peter VANDER HORN , Daniel MAZUR , Theo NIKIFOROV , Mindy LANDES , Eileen TOZER
IPC分类号： C12N9/12 , 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.

6. 发明申请

US20200043571A1 METHODS AND SYSTEMS FOR MODELING PHASING EFFECTS IN SEQUENCING USING TERMINATION CHEMISTRY 审中-公开
公开(公告)号：US20200043571A1
公开(公告)日：2020-02-06
申请号：US16550374
申请日：2019-08-26
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： Christian KOLLER , Marcin SIKORA , Peter VANDER HORN
IPC分类号： G16B40/10 , G16B5/00 , G16B20/00 , G16B25/00 , G16B30/00 , C12Q1/6869
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.

7. 发明申请

US20190270974A1 POLYMERASE COMPOSITIONS AND KITS, AND METHODS OF USING AND MAKING THE SAME 审中-公开
公开(公告)号：US20190270974A1
公开(公告)日：2019-09-05
申请号：US16415063
申请日：2019-05-17
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： Daniel MAZUR , Peter VANDER HORN , Eileen TOZER , Sihong CHEN , Guobin LUO , Joshua SHIRLEY , Kevin HEINEMANN
IPC分类号： C12N9/12 , C12Q1/686
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.

8. 发明申请

US20170096648A1 POLYMERASE COMPOSITIONS AND KITS, AND METHODS OF USING AND MAKING THE SAME 审中-公开
公开(公告)号：US20170096648A1
公开(公告)日：2017-04-06
申请号：US15277834
申请日：2016-09-27
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： DANIEL MAZUR , Peter VANDER HORN , Eileen TOZER , Sihong CHEN , Guobin LUO , Joshua SHIRLEY , Kevin HEINEMANN
IPC分类号： 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.

9. 发明申请

US20200231948A1 NUCLEOTIDE TRANSIENT BINDING FOR SEQUENCING METHODS 审中-公开
公开(公告)号：US20200231948A1
公开(公告)日：2020-07-23
申请号：US16825788
申请日：2020-03-20
申请人： Life Technologies Corporation
发明人： Peter VANDER HORN , Cheng-Yao CHEN , Guobin LUO , Michael PREVITE , Jamshid TEMIROV , Theo NIKIFOROV , Zhaohui ZHOU , Hongye SUN , Yufang WANG , Stefanie Yukiko NISHIMURA , Hongyi WANG , Marian PERIS , Barnett ROSENBLUM , Michael PHELAN
IPC分类号： C12N9/12 , C12Q1/6827 , C12Q1/6869 , C12Q1/6872 , C12Q1/6804 , C12Q1/6818 , C12Q1/68
摘要： Provided herein are compositions and systems for use in polymerase-dependent, nucleotide transient-binding methods. The methods are useful for deducing the sequence of a template nucleic acid molecule and single nucleotide polymorphism (SNP) analyses. The methods rely on the fact that the polymerase transient-binding time for a complementary nucleotide is longer compared to that of a non-complementary nucleotide. The labeled nucleotides transiently-binds the polymerase in a template-dependent manner, but does not incorporate. The methods are conducted under any reaction condition that permits transient binding of a complementary or non-complementary nucleotide to a polymerase, and inhibits nucleotide incorporation.

10. 发明申请

US20150100247A1 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：US20150100247A1
公开(公告)日：2015-04-09
申请号：US14506520
申请日：2014-10-03
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： Christian KOLLER , Marcin SIKORA , Peter VANDER HORN
IPC分类号： G06F19/22 , G06F19/12 , G06F19/18
CPC分类号： G16B40/10 , C12Q1/6869 , G16B5/00 , G16B20/00 , G16B25/00 , G16B30/00
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。

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