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1. 发明申请

WO2013188582A1 KINETIC EXCLUSION AMPLIFICATION OF NUCLEIC ACID LIBRARIES 审中-公开
标题翻译：核酸排放图的动力学排除放大图
公开(公告)号：WO2013188582A1
公开(公告)日：2013-12-19
申请号：PCT/US2013/045491
申请日：2013-06-12
申请人： ILLUMINA, INC.
发明人： SHEN, Min-Jui Richard , BOUTELL, Jonathan Mark , STEPHENS, Kathryn M. , RONAGHI, Mostafa , GUNDERSON, Kevin L. , VENKATESAN, Bala Murali , BOWEN, M. Shane , VIJAYAN, Kandaswamy
IPC分类号： C12Q1/68 , G01N27/447
CPC分类号： C12Q1/6848 , B01J19/0046 , B01J2219/00585 , B01J2219/00587 , B01J2219/00608 , B01J2219/00621 , B01J2219/00637 , B01J2219/00653 , B01J2219/00675 , B01J2219/00722 , C12Q1/6844 , C12Q1/6874 , C12Q2521/507 , C12Q2527/101 , C12Q2527/113 , C12Q2535/122 , C12Q2565/513 , C12Q2565/537
摘要： A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
摘要翻译：一种方法，包括（a）提供包含位点阵列的扩增试剂和具有不同靶核酸的溶液; 和（b）使扩增试剂反应以产生每个具有来自溶液的靶核酸的扩增子的克隆群的扩增位点。反应可以包括以平均传输速率同时将核酸输送到位点，以及以平均扩增速率扩增转运到位点的核酸，其中平均扩增速率超过平均传输速率。该反应可以包括从转运到每个位点的核酸产生第一扩增子，并产生来自核酸或第一扩增子的后续扩增子，其中后续扩增子产生的平均速率超过在其中生成第一个扩增子。

2. 发明申请

WO2012106081A2 METHODS FOR REDUCING NUCLEIC ACID DAMAGE 审中-公开
标题翻译：降低核酸损伤的方法
公开(公告)号：WO2012106081A2
公开(公告)日：2012-08-09
申请号：PCT/US2012/021040
申请日：2012-01-12
申请人： ILLUMINA, INC. , ILLUMINA CAMBRIDGE LTD. , KLAUSING, Kay , SHEN, Min-Jui Richard , MOORE, John , SMITH, Vincent , HALL, Kevin , GORMLEY, Niall Anthony , IOANNOU, Avgousta , FRITZILAS, Epameinondas , RIGATTI, Roberto
发明人： KLAUSING, Kay , SHEN, Min-Jui Richard , MOORE, John , SMITH, Vincent , HALL, Kevin , GORMLEY, Niall Anthony , IOANNOU, Avgousta , FRITZILAS, Epameinondas , RIGATTI, Roberto
IPC分类号： C12Q1/68 , C12Q1/48 , G01N33/53
CPC分类号： C12P19/34 , C12N15/1003 , C12Q1/6806 , C12Q2521/531 , C12Q2527/125 , C12Q2563/131
摘要： Provided herein is a method of inhibiting degradation of nucleic acids during a nucleic acid processing step selected from fragmentation and detection comprising contacting the nucleic acids with a solution comprising gallic acid, analogues, derivatives thereof or mixtures thereof, during the processing step, wherein the contacting inhibits degradation of the nucleic acids. Also provided herein is a method of inhibiting light-induced degradation of nucleic acids. Additionally, provided herein is a method of reducing or inhibiting nucleic acid damage during preparation of a nucleic acid sample comprising fragmenting the nucleic acid sequences in the sample in a solution comprising one of more compounds, the compounds inhibiting degradation of the nucleic acid sequences in the sample.
摘要翻译：本文提供了一种在选择片段化和检测的核酸加工步骤期间抑制核酸降解的方法，包括在加工步骤期间使核酸与包含没食子酸，其类似物，衍生物或其混合物的溶液接触，其中所述接触抑制核酸的降解。本文还提供抑制光诱导的核酸降解的方法。此外，本文提供的是在制备核酸样品期间减少或抑制核酸损伤的方法，包括在包含一种或多种化合物的溶液中碎片样品中的核酸序列，所述化合物抑制核酸序列的降解样品。

3. 发明申请

WO2017019456A2 SPATIAL MAPPING OF NUCLEIC ACID SEQUENCE INFORMATION 审中-公开
标题翻译：核酸序列信息的空间映射
公开(公告)号：WO2017019456A2
公开(公告)日：2017-02-02
申请号：PCT/US2016/043385
申请日：2016-07-21
申请人： ILLUMINA, INC.
发明人： SO, Alex , LIU, Li , SHEN, Min-Jui Richard , SALATHIA, Neeraj , STEPHENS, Kathryn M. , JAGER, Anne , WILSON, Timothy , FULLERTON, Justin , RAMIREZ, Sean M. , KAPLAN, Shannon , PANTOJA, Rigo , VENKATESAN, Bala Murali , MODIANO, Steven
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6837 , C12Q2565/514 , C12Q2565/543 , C12Q2565/125 , C12Q2563/143 , C12Q2563/155 , C12Q2543/10
摘要： Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.
摘要翻译：提出了用于组织样品中核酸的空间检测和分析的方法和组合物。所述方法可以使得能够表征组织中的转录组和/或基因组变异，同时保留关于组织的空间信息。

4. 发明申请

WO2011106368A2 AMPLIFICATION METHODS TO MINIMISE SEQUENCE SPECIFIC BIAS 审中-公开
标题翻译：最小化序列特异性偏差的放大方法
公开(公告)号：WO2011106368A2
公开(公告)日：2011-09-01
申请号：PCT/US2011/025851
申请日：2011-02-23
申请人： ILLUMINA, INC. , RIGATTI, Roberto , BOUTELL, Jonathan Mark , SHEN, Min-Jui Richard
发明人： RIGATTI, Roberto , BOUTELL, Jonathan Mark , SHEN, Min-Jui Richard
IPC分类号： C12Q1/68 , C12N15/10
CPC分类号： C12P19/34 , C09K3/00 , C12Q1/686 , C12Q2565/518 , C12Q2527/137
摘要： Methods for amplifying nucleic acids are provided. The methods can be used to minimise sequence specific bias caused by the preferential amplification of certain nucleic acid sequences. Methods are described which can lower the efficiency of AT rich templates relative to GC rich templates, thereby minimising GC bias during amplification reactions with multiple templates of different sequence. The methods are suited to solid phase amplification, for example, utilising flow cells
摘要翻译：提供了扩增核酸的方法。这些方法可以用于最小化由某些核酸序列的优先扩增引起的序列特异性偏差。描述了可以降低AT富含模板相对于GC富集模板的效率的方法，由此使具有不同序列的多个模板的扩增反应期间的GC偏差最小化。该方法适用于固相扩增，例如利用流动池

5. 发明申请

WO2014116851A2 METHODS AND SYSTEMS FOR USING A CLOUD COMPUTING ENVIRONMENT TO SHARE BIOLOGICAL RELATED DATA 审中-公开
标题翻译：使用云计算环境分享生物相关数据的方法和系统
公开(公告)号：WO2014116851A2
公开(公告)日：2014-07-31
申请号：PCT/US2014/012782
申请日：2014-01-23
申请人： ILLUMINA, INC.
发明人： SHEN, Min-Jui Richard , LIN, Charles
IPC分类号： G06F19/28
CPC分类号： G06Q30/0627 , G06F19/22 , G06F19/28 , G06Q30/0601 , G06Q30/0609 , G06Q30/0635
摘要： The present disclosure provides a novel approach for shifting or distributing various information (e.g., protocols, analysis methods, sample preparation data, sequencing data, etc.) to a cloud-based network. For example, the techniques relate to a cloud computing environment (12) configured to receive this information from one or more individual sample preparation devices (38), sequencing devices (18), and/or computing systems. In turn, the cloud computing environment (12) may generate information for use in the cloud computing environment (12) and/or to provide the generated information to the devices to guide a genomic analysis workflow. Further, the cloud computing environment (12) may be used to facilitate the sharing of sample preparation protocols for use with generic sample preparation cartridges and/or monitoring the popularity of the sample preparation protocols.
摘要翻译：本公开提供了一种用于将各种信息（例如协议，分析方法，样本准备数据，排序数据等）转移或分发到基于云的网络的新颖方法。例如，这些技术涉及被配置为从一个或多个单独的样本准备设备（38），排序设备（18）和/或计算系统接收该信息的云计算环境（12）。反过来，云计算环境（12）可以生成用于云计算环境（12）的信息和/或将生成的信息提供给设备以指导基因组分析工作流程。此外，云计算环境（12）可以用于促进与通用样品制备盒一起使用的样品制备协议的共享和/或监测样品制备方案的普及。

6. 发明申请

WO2013044018A1 METHODS AND COMPOSITIONS FOR NUCLEIC ACID SEQUENCING 审中-公开
标题翻译：核酸序列的方法和组合
公开(公告)号：WO2013044018A1
公开(公告)日：2013-03-28
申请号：PCT/US2012/056556
申请日：2012-09-21
申请人： ILLUMINA, INC. , KAIN, Robert C. , LIU, Xiaohai , FENG, Wenyi , HIRSCHBEIN, Bernard , ELTOUKHY, Helmy A. , WU, Xiaolin , SMITH, Geoffrey Paul , BOUTELL, Jonathan Mark , JOSEPH, Thomas , SMITH, Randall , SHEN, Min-Jui Richard , TREGIDGO, Carolyn , KLAUSING, Kay
发明人： KAIN, Robert C. , LIU, Xiaohai , FENG, Wenyi , HIRSCHBEIN, Bernard , ELTOUKHY, Helmy A. , WU, Xiaolin , SMITH, Geoffrey Paul , BOUTELL, Jonathan Mark , JOSEPH, Thomas , SMITH, Randall , SHEN, Min-Jui Richard , TREGIDGO, Carolyn , KLAUSING, Kay
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6869 , C12Q2525/113 , C12Q2535/122 , C12Q2563/107
摘要： The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected.
摘要翻译：本公开提供了用于检测样品中多个不同核苷酸的方法和系统。具体地，本公开提供了使用比检测到的核苷酸数目少于检测到的核苷酸数目和/或比检测到的核苷酸数目更少的成像事件来检测样品中的多个不同核苷酸。

7. 发明授权

EP2768972B1 METHODS AND COMPOSITIONS FOR NUCLEIC ACID SEQUENCING 有权
标题翻译：核酸测序的方法和组合物
公开(公告)号：EP2768972B1
公开(公告)日：2017-07-12
申请号：EP12766838.2
申请日：2012-09-21
申请人： Illumina, Inc.
发明人： KAIN, Robert C. , LIU, Xiaohai , FENG, Wenyi , HIRSCHBEIN, Bernard , ELTOUKHY, Helmy A. , WU, Xiaolin , SMITH, Geoffrey Paul , BOUTELL, Jonathan Mark , JOSEPH, Thomas , SMITH, Randall , SHEN, Min-Jui Richard , TREGIDGO, Carolyn , KLAUSING, Kay
IPC分类号： C12Q1/68
摘要： The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected.
摘要翻译：本公开提供了用于检测样品中的多个不同核苷酸的方法和系统。特别地，本公开内容提供了利用比被检测的核苷酸的数量少的检测部分和/或比被检测的核苷酸的数量少的成像事件来检测样品中的多个不同核苷酸。

8. 发明公开

EP3981886A1 COMPOSITIONS FOR NUCLEIC ACID SEQUENCING 审中-公开
公开(公告)号：EP3981886A1
公开(公告)日：2022-04-13
申请号：EP21189843.2
申请日：2012-09-21
申请人： Illumina, Inc.
发明人： BOUTELL, Jonathan Mark , ELTOUKHY, Helmy A. , FENG, Wenyi , HIRSCHBEIN, Bernard , JOSEPH, Thomas , KAIN, Robert C. , KLAUSING, Kay , LIU, Xiaohai , SHEN, Min-Jui Richard , SMITH, Geoffrey Paul , TREGIDGO, Carolyn , WU, Xiaolin , SMITH, Randall
IPC分类号： C12Q1/6869 , C12Q1/6874
摘要： The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected. Disclosed is also a reversibly blocked nucleotide conjugate, which is indirectly labelled with a hapten attached via a linker to the nucleobase, wherein the hapten is detectable by a binding partner-fluorescent moiety conjugate.

9. 发明公开

EP2776165A2 INTEGRATED SEQUENCING APPARATUSES AND METHODS OF USE 无效
标题翻译： INTEGRIERTE SEQUENZIERUNGSVORRICHTUNGEN UND VERWENDUNGSVERFAHREN
公开(公告)号：EP2776165A2
公开(公告)日：2014-09-17
申请号：EP12795930.2
申请日：2012-11-06
申请人： Illumina, Inc.
发明人： SHEN, Min-Jui Richard , KAIN, Robert C. , KUHN, Kenneth M. , TALASAZ, AmirAli Hajhossein , JAMSHIDI, Arash , SAKALDASIS, George , VERMAAS, Eric , BOHM, Sebastian , KHURANA, Tarun , ELTOUKHY, Helmy A. , GONG, Jian
IPC分类号： B01L3/00
CPC分类号： C12Q1/6874 , B01L3/502792 , B01L2200/0673 , B01L2300/0636 , B01L2300/069 , B01L2300/0816 , B01L2300/0851 , B01L2300/165 , B01L2400/0427
摘要： Provided are methods and apparatuses for performing sequencing using droplet manipulation, for example, via electrowetting-based techniques. Also provided are integrated methods and apparatuses for performing sample preparation and sequencing on the same apparatus. In addition, provided are methods of reducing reagent waste and preloaded consumable cartridges comprising reagents for sample preparation and/or sequencing.
摘要翻译：提供了用于使用液滴操纵进行排序的方法和装置，例如通过基于电润湿的技术。还提供了用于在相同装置上进行样品制备和测序的综合方法和装置。此外，提供了减少试剂废物的方法和包含用于样品制备和/或测序的试剂的预装消耗筒。

10. 发明公开

EP3957747A1 SPATIAL MAPPING OF NUCLEIC ACID SEQUENCE INFORMATION 审中-公开
公开(公告)号：EP3957747A1
公开(公告)日：2022-02-23
申请号：EP21186417.8
申请日：2016-07-21
申请人： Illumina, Inc.
发明人： SO, Alex , Liu, Li , SHEN, Min-Jui Richard , SALATHIA, Neeraj , STEPHENS, Kathryn M. , JAGER, Anne , WILSON, Timothy , FULLERTON, Justin , RAMIREZ, Sean M. , KAPLAN, Shannon , PANTOJA, Rigo , VENKATESAN, Bala Murali , MODIANO, Steven
IPC分类号： C12Q1/6837 , C12Q1/6874
摘要： Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.

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