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1. 发明申请

US20060292611A1 Paired end sequencing 失效
公开(公告)号：US20060292611A1
公开(公告)日：2006-12-28
申请号：US11448462
申请日：2006-06-06
申请人： Jan Berka , Zhoutao Chen , Michael Egholm , Brian Godwin , Stephen Hutchison , John Leamon , Gary Sarkis , Jan Simons
发明人： Jan Berka , Zhoutao Chen , Michael Egholm , Brian Godwin , Stephen Hutchison , John Leamon , Gary Sarkis , Jan Simons
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6806 , C12N15/10 , C12N15/1093 , C12Q1/6809 , C12Q1/6869 , C12Q2537/155 , C12Q2525/191 , C12Q2521/301 , C12Q2533/107 , C12Q2531/125 , C12Q2521/319 , C12Q2521/125 , C12Q2565/518 , C12Q2563/131
摘要： The present invention provides for a method of preparing a target nucleic acid fragments to produce a smaller nucleic acid which comprises the two ends of the target nucleic acid. Specifically, the invention provides cloning and DNA manipulation strategies to isolate the two ends of a large target nucleic acid into a single small DNA construct for rapid cloning, sequencing, or amplification.

2. 发明授权

US07601499B2 Paired end sequencing 失效
标题翻译：配对测序
公开(公告)号：US07601499B2
公开(公告)日：2009-10-13
申请号：US11448462
申请日：2006-06-06
申请人： Jan Berka , Zhoutao Chen , Michael Egholm , Brian C. Godwin , Stephen Kyle Hutchison , John Harris Leamon , Gary James Sarkis , Jan Fredrik Simons
发明人： Jan Berka , Zhoutao Chen , Michael Egholm , Brian C. Godwin , Stephen Kyle Hutchison , John Harris Leamon , Gary James Sarkis , Jan Fredrik Simons
IPC分类号： C12Q1/68 , C12P19/34 , C07H21/04
CPC分类号： C12Q1/6806 , C12N15/10 , C12N15/1093 , C12Q1/6809 , C12Q1/6869 , C12Q2537/155 , C12Q2525/191 , C12Q2521/301 , C12Q2533/107 , C12Q2531/125 , C12Q2521/319 , C12Q2521/125 , C12Q2565/518 , C12Q2563/131
摘要： The present invention provides for a method of preparing a target nucleic acid fragments to produce a smaller nucleic acid which comprises the two ends of the target nucleic acid. Specifically, the invention provides cloning and DNA manipulation strategies to isolate the two ends of a large target nucleic acid into a single small DNA construct for rapid cloning, sequencing, or amplification.
摘要翻译：本发明提供了制备靶核酸片段以产生包含靶核酸两端的较小核酸的方法。具体地，本发明提供克隆和DNA操作策略，以将大靶核酸的两端分离成单个小型DNA构建体用于快速克隆，测序或扩增。

3. 发明申请

US20130261027A1 NUCLEIC ACID ADAPTORS AND USES THEREOF 有权
标题翻译：核酸适配器及其用途
公开(公告)号：US20130261027A1
公开(公告)日：2013-10-03
申请号：US13877203
申请日：2011-09-29
申请人： Bin Li , Zhoutao Chen , Tanya Biorac , Melvin Wei
发明人： Bin Li , Zhoutao Chen , Tanya Biorac , Melvin Wei
IPC分类号： C12N15/10
CPC分类号： C12Q1/6876 , C12N9/1252 , C12N9/20 , C12N15/1093 , C12N15/64 , C12Q1/6806 , C12Q1/6832 , C12Y207/07007 , C12Y301/01003 , C12Q2521/131 , C12Q2525/191 , C12Q2527/107 , C12Q2537/163 , C12Q2563/179
摘要： Provided herein are compositions, systems, methods, and kits for joining together the ends of one or more polynucleotides using at least one pair of blocking oligonucleotide adaptors. Blocking oligonucleotide adaptors can be used to reduce the formation of adaptor dimers or trimers (or higher-order concatemers) which can improve the yield of desirable polynucleotide-adaptor products in any recombinant nucleic acid workflow. Blocking oligonucleotide adaptors can comprise a double-stranded oligonucleotide adaptor (duplex) having an overhang cohesive portion that anneals with a blocking oligonucleotide which can be a separate single-stranded oligonucleotide. A blocking oligonucleotide, when annealed to an overhang portion, can prevent undesirable hybridization of the overhang portion to another nucleic acid, such as the overhang portion from another blocking oligonucleotide adaptor or a polynucleotide of interest.
摘要翻译：本文提供了使用至少一对封闭寡核苷酸衔接子将一个或多个多核苷酸的末端连接在一起的组合物，系统，方法和试剂盒。阻断寡核苷酸衔接子可用于减少适配器二聚体或三聚体（或更高级并行物）的形成，其可以改善任何重组核酸工作流程中期望的多核苷酸 - 衔接子产物的产量。阻断寡核苷酸衔接子可以包含具有悬伸粘性部分的双链寡核苷酸衔接子（双链体），其与可以是单独的单链寡核苷酸的封闭寡核苷酸退火。当与突出部分退火时，封闭寡核苷酸可以防止突出部分与另一种核酸（例如来自另一种封闭寡核苷酸衔接子或感兴趣的多核苷酸的突出部分）的不期望的杂交。

4. 发明申请

US20090053724A1 System and method for adaptive reagent control in nucleic acid sequencing 审中-公开
标题翻译：核酸测序中适应性试剂控制的系统和方法
公开(公告)号：US20090053724A1
公开(公告)日：2009-02-26
申请号：US12215455
申请日：2008-06-27
申请人： George Thomas Roth , John Richard Nobile , Maithreyan Srinivasan , Zhoutao Chen , James Matthew Nealis , Xavier Victor Gomes
发明人： George Thomas Roth , John Richard Nobile , Maithreyan Srinivasan , Zhoutao Chen , James Matthew Nealis , Xavier Victor Gomes
IPC分类号： C12Q1/68 , C12Q1/00 , C12M1/36 , C12M1/34 , C12Q1/34
CPC分类号： C12Q1/6869 , C12Q2565/301
摘要： An embodiment of a method for adaptive reagent control is described that comprising a) introducing a first concentration of an enzyme reagent into a reaction environment with a reaction substrate, where the enzyme reagent and reaction substrate are constituent parts of a sequencing process; b) measuring a level of activity of the first concentration of the enzyme reagent in the reaction environment, where the level of activity comprises a measurable product of a reaction between the enzyme reagent and the reaction substrate; c) identifying an optimal concentration using the measured level of activity of the first concentration; and d) performing the sequencing process in the reaction environment using the optimal concentration of the enzyme reagent, where the sequencing process comprises an iterative series of sequencing reactions.
摘要翻译：描述了一种用于自适应试剂控制的方法的实施方案，其包括：a）将酶试剂的第一浓度与反应底物引入反应环境，其中酶试剂和反应底物是测序过程的组成部分; b）测量反应环境中酶试剂的第一浓度的活性水平，其中活性水平包括酶试剂和反应底物之间的反应的可测量的产物; c）使用所测量的第一浓度的活性水平鉴定最佳浓度; 和d）使用酶试剂的最佳浓度在反应环境中进行测序过程，其中测序过程包括迭代的一系列测序反应。

5. 发明申请

US20090233291A1 Paired end sequencing 审中-公开
标题翻译：配对测序
公开(公告)号：US20090233291A1
公开(公告)日：2009-09-17
申请号：US12322119
申请日：2009-01-28
申请人： Zhoutao Chen , Brian Christopher Godwin , Gianni Calogero Ferreri , David Roderick Riches
发明人： Zhoutao Chen , Brian Christopher Godwin , Gianni Calogero Ferreri , David Roderick Riches
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6809 , C12Q1/6869 , C12Q2531/125 , C12Q2521/125 , C12Q2565/518 , C12Q2563/131 , C12Q2521/301 , C12Q2521/319 , C12Q2521/507 , C12Q2521/313 , C12Q2525/307 , C12Q2525/191 , C12Q2539/103 , C12Q2525/155
摘要： An embodiment of a method for obtaining a DNA construct comprising two end regions of a target nucleic acid in an in vitro reaction is described that comprises the steps of: fragmenting a large nucleic acid molecule to produce a target nucleic acid molecule; ligating a recombination adaptor element to each end of the target nucleic acid molecule to produce an adapted target nucleic acid molecule; exposing the adapted target nucleic acid to a site specific recombinase to produce a circular nucleic acid product and a linear nucleic acid product from the adapted target nucleic acid, wherein the circular nucleic acid product comprises the target nucleic acid molecule; and fragmenting the circular nucleic acid product to produce a template nucleic acid molecule comprising a sequence region from each end of the target nucleic acid molecule.
摘要翻译：描述了在体外反应中获得包含靶核酸的两个末端区域的DNA构建体的方法的实施方案，其包括以下步骤：将大核酸分子片段化以产生靶核酸分子; 将重组衔接子元件连接到靶核酸分子的每个末端以产生适应的靶核酸分子; 将适配的靶核酸暴露于位点特异性重组酶以产生来自适应的靶核酸的环状核酸产物和线性核酸产物，其中所述环状核酸产物包含靶核酸分子; 并将环状核酸产物片段化以产生包含靶核酸分子每端的序列区的模板核酸分子。

6. 发明申请

US20090203086A1 System and method for improved signal detection in nucleic acid sequencing 审中-公开
标题翻译：在核酸测序中改进信号检测的系统和方法
公开(公告)号：US20090203086A1
公开(公告)日：2009-08-13
申请号：US12322284
申请日：2009-01-29
申请人： Yi-Ju Chen , Jong-Bum Kim , Andrew Daniel Kebbel , James Matthew Nealis , Zhoutao Chen
发明人： Yi-Ju Chen , Jong-Bum Kim , Andrew Daniel Kebbel , James Matthew Nealis , Zhoutao Chen
IPC分类号： C12P19/34 , B01J8/00 , C12M1/00 , C07H1/00
CPC分类号： B01L3/5027 , B01J2219/00286 , B01J2219/00391 , B01J2219/00529 , B01J2219/00585 , B01J2219/0059 , B01J2219/00704 , B01J2219/0072 , B01J2219/00722 , B01L3/502715 , B01L3/5085 , B01L7/52 , B01L2200/0647 , B01L2300/0636 , B01L2300/0654 , B01L2300/0877 , B01L2400/0622 , G01N21/03 , G01N2021/0325
摘要： An embodiment of a system for reducing crosstalk in a parallel sequencing platform is described that comprises a substrate with a plurality of individual reaction environments that include a species of nucleic acid template, and a plurality of spatially localized reactants, wherein the localized reactants minimize the transmission of reaction products to a neighboring reaction environment due to a relative position of the localized reactants in the reaction environment.
摘要翻译：描述了用于减少并行测序平台中的串扰的系统的实施例，其包括具有多个单独的反应环境的衬底，所述多个单独的反应环境包括一些核酸模板和多个空间定位的反应物，其中所述局部反应物使传输最小化由于局部反应物在反应环境中的相对位置，反应产物与相邻的反应环境有关。

7. 发明授权

US09540637B2 Nucleic acid adaptors and uses thereof 有权
标题翻译：核酸适配器及其用途
公开(公告)号：US09540637B2
公开(公告)日：2017-01-10
申请号：US13877203
申请日：2011-09-29
申请人： Bin Li , Zhoutao Chen , Tanya Biorac , Melvin Shiwade Wei
发明人： Bin Li , Zhoutao Chen , Tanya Biorac , Melvin Shiwade Wei
IPC分类号： C12Q1/68 , C12P19/34 , C12N15/10
CPC分类号： C12Q1/6876 , C12N9/1252 , C12N9/20 , C12N15/1093 , C12N15/64 , C12Q1/6806 , C12Q1/6832 , C12Y207/07007 , C12Y301/01003 , C12Q2521/131 , C12Q2525/191 , C12Q2527/107 , C12Q2537/163 , C12Q2563/179
摘要： Provided herein are compositions, systems, methods, and kits for joining together the ends of one or more polynucleotides using at least one pair of blocking oligonucleotide adaptors. Blocking oligonucleotide adaptors can be used to reduce the formation of adaptor dimers or trimers (or higher-order concatemers) which can improve the yield of desirable polynucleotide-adaptor products in any recombinant nucleic acid workflow. Blocking oligonucleotide adaptors can comprise a double-stranded oligonucleotide adaptor (duplex) having an overhang cohesive portion that anneals with a blocking oligonucleotide which can be a separate single-stranded oligonucleotide. A blocking oligonucleotide, when annealed to an overhang portion, can prevent undesirable hybridization of the overhang portion to another nucleic acid, such as the overhang portion from another blocking oligonucleotide adaptor or a polynucleotide of interest.
摘要翻译：本文提供了使用至少一对封闭寡核苷酸衔接子将一个或多个多核苷酸的末端连接在一起的组合物，系统，方法和试剂盒。阻断寡核苷酸衔接子可用于减少适配器二聚体或三聚体（或更高级并行物）的形成，其可以改善任何重组核酸工作流程中期望的多核苷酸 - 衔接子产物的产量。阻断寡核苷酸衔接子可以包含具有悬伸粘性部分的双链寡核苷酸衔接子（双链体），其与可以是单独的单链寡核苷酸的封闭寡核苷酸退火。当与突出部分退火时，封闭寡核苷酸可以防止突出部分与另一种核酸（例如来自另一种封闭寡核苷酸衔接子或感兴趣的多核苷酸的突出部分）的不期望的杂交。

8. 发明授权

US09139874B2 Bi-directional sequencing compositions and methods 有权
标题翻译：双向测序组合物和方法
公开(公告)号：US09139874B2
公开(公告)日：2015-09-22
申请号：US13543521
申请日：2012-07-06
申请人： Jason Myers , Zhoutao Chen , Devin Dressman , Theo Nikiforov
发明人： Jason Myers , Zhoutao Chen , Devin Dressman , Theo Nikiforov
IPC分类号： C12P19/34 , C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6806 , C12Q1/6869 , C12Q2521/307 , C12Q2521/325 , C12Q2525/125 , C12Q2535/119 , C12Q2565/518
摘要： In some embodiments, methods for obtaining sequence information from a nucleic acid template linked to a support include hybridizing a first primer to a template strand linked to a support, sequencing a portion of the nucleic acid template, thereby forming an extended first primer product that is complementary to a portion of the nucleic acid template. In some embodiments, the method further includes introducing a nick into a portion of the template strand that is hybridized to the extended first primer product, degrading a portion of the template strand from the nick using a degrading agent, where a portion of the extended first primer remains hybridized to an undegraded portion of the template strand, and sequencing at least some of the single-stranded portion of the extended first primer by synthesis.
摘要翻译：在一些实施方案中，从与支持物连接的核酸模板获得序列信息的方法包括将第一引物与连接于载体的模板链杂交，对核酸模板的一部分进行测序，从而形成延伸的第一引物产物，与核酸模板的一部分互补。在一些实施方案中，所述方法还包括将切口引入与延伸的第一引物产物杂交的模板链的一部分中，使用降解剂将模板链的一部分从切口中降解，其中延伸的第一底物引物保留与模板链的未降解部分杂交，并通过合成测序延伸的第一引物的至少一些单链部分。

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