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1. 发明申请

WO2016075204A1 METHODS AND ARRAYS FOR PRODUCING AND SEQUENCING MONOCLONAL CLUSTERS OF NUCLEIC ACID 审中-公开
标题翻译：用于生产和测序核酸单核苷酸的方法和阵列
公开(公告)号：WO2016075204A1
公开(公告)日：2016-05-19
申请号：PCT/EP2015/076353
申请日：2015-11-11
申请人： ILLUMINA, INC. , ILLUMINA CAMBRIDGE LTD.
发明人： GUNDERSON, Kevin L. , BAI, Jingwei , KELLINGER, Matthew William , BEIERLE, John M. , BOUTELL, Jonathan Mark , RIGATTI, Roberto , ROGERT BACIGALUPO, Maria Candelaria , BOYANOV, Boyan , MAISINGER, Klaus
IPC分类号： C12Q1/68 , B01J19/00 , C40B40/06 , C40B50/14
CPC分类号： C12Q1/6874 , B01J19/0046 , B01J2219/00317 , B01J2219/00585 , B01J2219/00596 , B01J2219/00608 , B01J2219/00637 , B01J2219/00722 , C12Q1/6806 , C12Q1/6837 , C12Q1/6853 , C40B40/06 , C40B50/14 , C12Q2565/513 , C12Q2565/543
摘要： Methods for capturing and amplifying target polynucleotides on a solid surface, in particular in a well in a microarray, wherein the microarray may comprise a) a substrate comprising at least one well, a surface surrounding the well and an inner well surface; b) a first layer covering the inner well surface and comprising at least one first capture primer pair; and c) a second layer covering the first layer and the surface surrounding the well. Alternatively, the microarray may comprise a) a substrate comprising at least one well, a surface surrounding the well and an inner well surface; and b) a layer covering the inner well surface and comprising at least one first capture primer pair and at least one second capture primer pair. In particular kinetic exclusion amplification is used in creating monoclonal populations of the nucleic acids in the wells. The application also discloses a method for modifying an immobilized capture primer comprising: a) contacting a substrate comprising a plurality of immobilized capture primers with a plurality of template nucleic acids to produce one or more immobilized template nucleic acids,wherein the plurality of immobilized capture primers comprises a first plurality of primers comprising a 3'-terminal universal capture region Y, e.g. primer P5, and a second plurality of primers comprising a 3'-terminal universal capture region Z, e.g. primer P7; and wherein each template nucleic acid is flanked by a 5'-terminal and a 3'-terminal universal capture region Y or Z and comprises one or more, e.g. SapI, restriction sites and a target-specific capture region between the one or more restriction sites and the 3'-terminal universal capture region; and b) extending one or more immobilized capture primer. Finally, the application discloses a method for modifying an immobilized capture primer comprising: a) contacting a substrate comprising a plurality of immobilized capture primers with a plurality of different seed nucleic acids to produce a plurality of different immobilized seed nucleic acids; b) extending two or more of the immobilized capture primers to produce a plurality of different immobilized extension products complementary to two or more of the plurality of different immobilized seed nucleic acids; and c) activating one immobilized extension product of the plurality of different immobilized extension products, to form an activated capture primer.
摘要翻译：用于在固体表面上特别是在微阵列中的阱中捕获和扩增靶多核苷酸的方法，其中所述微阵列可以包括a）包含至少一个阱的衬底，围绕所述阱的表面和内部阱表面; b）覆盖所述内部孔表面并包含至少一个第一捕获引物对的第一层; 以及c）覆盖所述第一层和围绕所述孔的表面的第二层。或者，微阵列可以包括：a）包含至少一个阱的衬底，围绕阱的表面和内部阱表面; 以及b）覆盖所述内部孔表面并包含至少一个第一捕获引物对和至少一个第二捕获引物对的层。特别地，动力学排除扩增用于产生孔中核酸的单克隆群体。本申请还公开了一种修饰固定化捕获引物的方法，其包括：a）使包含多个固定的捕获引物的底物与多个模板核酸接触以产生一种或多种固定的模板核酸，其中所述多个固定的捕获引物包括包含3'末端通用捕获区Y的第一多个引物，例如引物P5和包含3'末端通用捕获区Z的第二多个引物。引物P7; 并且其中每个模板核酸侧接有5'-末端和3'末端通用捕获区Y或Z，并且包含一个或多个，例如， SapI，限制性位点和一个或多个限制性位点与3'-末端通用捕获区之间的靶标特异性捕获区域; 和b）延伸一个或多个固定的捕获引物。最后，本申请公开了一种用于修饰固定化捕获引物的方法，其包括：a）使包含多个固定的捕获引物的底物与多种不同的种子核酸接触以产生多种不同的固定化种子核酸; b）延伸两个或更多个固定的捕获引物以产生与所述多个不同固定化种子核酸中的两种或更多种互补的多种不同的固定化延伸产物; 和c）激活所述多个不同的固定化延伸产物的一个固定化的延伸产物，以形成活化的捕获引物。

2. 发明申请

WO2014144569A1 SUPER RESOLUTION IMAGING 审中-公开
标题翻译：超分辨率成像
公开(公告)号：WO2014144569A1
公开(公告)日：2014-09-18
申请号：PCT/US2014/029037
申请日：2014-03-14
申请人： ILLUMINA, INC.
发明人： KHURANA, Tarun , GUNDERSON, Kevin L. , WU, Yir-Shyuan , KAIN, Robert C.
IPC分类号： C12Q1/68 , G01N27/02 , G01N21/64 , G01N33/543
CPC分类号： C12Q1/6874 , G01N27/27 , G01N27/3275 , C12Q2565/101 , C12Q2565/607 , C12Q2565/629
摘要： A detection apparatus that includes (a) an array of responsive pads on a substrate surface; (b) an array of pixels, wherein each pixel in the array has a detection zone on the surface that includes a subset of at least two of the pads; and (c) an activation circuit to apply a force at a first and second pad in the subset, wherein the activation circuit is configured to apply a different force at the first pad compared to the second pad, and wherein the activation circuit has a switch to selectively alter the force at the first pad and the second pad.
摘要翻译：一种检测装置，其包括：（a）衬底表面上的响应垫阵列; （b）像素阵列，其中所述阵列中的每个像素具有在所述表面上的包括所述至少两个所述焊盘的子集的检测区域; 以及（c）激活电路，用于在所述子集中的第一和第二焊盘处施加力，其中所述激活电路被配置为在第一焊盘处施加与第二焊盘相比不同的力，并且其中所述激活电路具有开关以选择性地改变在第一焊盘和第二焊盘处的力。

3. 发明申请

WO2019055867A1 SEQUENCE-DETECTION SYSTEM 审中-公开
公开(公告)号：WO2019055867A1
公开(公告)日：2019-03-21
申请号：PCT/US2018/051212
申请日：2018-09-14
申请人： ILLUMINA, INC.
发明人： MANDELL, Jeffrey G. , GUNDERSON, Kevin L. , KEEHAN, Michael Gregory , GARCIA, Erin Christine , GUNDLACH, Jens H.
IPC分类号： C12Q1/48 , C12Q1/68 , G01N27/00 , G01N30/02 , B05D5/12
摘要： The current document discusses a detection system comprising a mechanical-change sensor that exhibits one or more mechanical changes when specifically interacting with entities within a target, each entity having a type, a mechanical-change-to-signal transducer that transduces the one or more mechanical changes into a signal, and an analysis subsystem that determines the types of entities within the target using the signal.

4. 发明申请

WO2019028166A1 HYDROGEL BEADS FOR NUCLEOTIDE SEQUENCING 审中-公开
公开(公告)号：WO2019028166A1
公开(公告)日：2019-02-07
申请号：PCT/US2018/044855
申请日：2018-08-01
申请人： ILLUMINA, INC.
发明人： WU, Yir-Shyuan , CHEN, Xi-Jun , GORPE-YASAR, Filiz , NOÉ, Falko , LIN, Charles , KHURANA, Tarun Kumar , MASHAYEKHI, Foad , DAGGUMATI, Pallavi , STEEMERS, Frank J. , GUNDERSON, Kevin L. , FISHER, Jeffrey S.
IPC分类号： C12Q1/6806
摘要： Systems, methods, and compositions provided herein relate to preparation of beads encapsulating genetic material. Some embodiments include preparation of nucleic acid libraries within the bead, wherein the bead includes pores that allow diffusion of reagents while retaining genetic material.

5. 发明申请

WO2016183218A1 FIELD-EFFECT APPARATUS AND METHODS FOR SEQUENCING NUCELIC ACIDS 审中-公开
标题翻译：场效应装置以及用于测序核酸的方法
公开(公告)号：WO2016183218A1
公开(公告)日：2016-11-17
申请号：PCT/US2016/031891
申请日：2016-05-11
申请人： ILLUMINA, INC. , THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
发明人： GUNDERSON, Kevin L. , BAI, Jingwei , CHEN, Cheng-Yao , MANDELL, Jeffrey G. , PEISAJOVICH, Sergio , BOYANOV, Boyan , COLLINS, Philip G. , WEISS, Gregory A.
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , C12Q2521/543 , C12Q2565/607
摘要： The present disclosure provides a method for sequencing nucleic acids. The method can include polymerase catalyzed incorporation of nucleotides into a nascent nucleic acid strand against a nucleic acid template, wherein the polymerase is attached to a charge sensor that detects nucleotide incorporation events. One or more non-natural nucleotide types that each produce a unique signatures at the charge sensor can be used to uniquely identify different nucleotides in the template nucleic acid.
摘要翻译：本公开提供了用于测序核酸的方法。该方法可以包括将核苷酸聚合酶催化结合到针对核酸模板的新生核酸链中，其中聚合酶连接到检测核苷酸掺入事件的电荷传感器。每个在电荷传感器上产生独特标记的一种或多种非天然核苷酸类型可用于唯一地鉴定模板核酸中的不同核苷酸。

6. 发明申请

WO2019055856A1 TUNING AND CALIBRATION FEATURES OF A SEQUENCE-DETECTION SYSTEM 审中-公开
公开(公告)号：WO2019055856A1
公开(公告)日：2019-03-21
申请号：PCT/US2018/051191
申请日：2018-09-14
申请人： ILLUMINA, INC.
发明人： MANDELL, Jeffrey G. , GUNDERSON, Kevin L. , KEEHAN, Michael Gregory , GARCIA, Erin Christine
IPC分类号： C12Q1/68
摘要： The current document discusses electromechanical sequence detectors that transduce changes in the shape of a shape-change sensor component into an electrical signal from which one or more derived values are generated. In a disclosed implementation, the sequence-detection system comprises a mechanical-change sensor that changes shape when specifically interacting with entities within a target, a shape-to-signal-transduction component that transduces changes in the shape of the mechanical-change sensor into an electrical signal, an analysis subsystem that determines the types of entities within the target using the electrical signal, and a control subsystem that continuously monitors operational characteristics of the sequence-detection system and adjusts sequence-detection system operational parameters.

7. 发明申请

WO2016019030A1 HYBRID NANOPORE SENSORS 审中-公开
标题翻译： HYBRID NANOPORE传感器
公开(公告)号：WO2016019030A1
公开(公告)日：2016-02-04
申请号：PCT/US2015/042680
申请日：2015-07-29
申请人： ILLUMINA, INC.
发明人： BOYANOV, Boyan , MANDELL, Jeffrey G. , GUNDERSON, Kevin L. , BAI, Jingwei , QIANG, Liangliang , BAAS, Bradley
IPC分类号： G01N33/487
CPC分类号： C12Q1/6874 , G01N27/44782 , G01N27/44791 , G01N33/48721
摘要： In one aspect, a detection apparatus comprises a solid support with an array of solid-state nanopores and a plurality of lipid nanodiscs with protein nanopores, wherein the lipid nanodiscs are disposed on the solid support such that they form seals at the solid-state nanopores. In another aspect, a detection apparatus comprises one or more nanopores that are surrounded by a membrane, wherein each nanopore is tethered to an electrode.
摘要翻译：在一个方面，检测装置包括具有固体纳米孔阵列的固体支持物和具有蛋白质纳米孔的多个脂质纳米圆盘，其中脂质纳米圆盘设置在固体支持物上，使得它们在固态纳米孔隙下形成密封。另一方面，检测装置包括被膜包围的一个或多个纳米孔，其中每个纳米孔束缚于电极。

8. 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。

9. 发明申请

WO2016130704A2 METHODS AND COMPOSITIONS FOR ANALYZING CELLULAR COMPONENTS 审中-公开
标题翻译：分析细胞成分的方法和组合物
公开(公告)号：WO2016130704A2
公开(公告)日：2016-08-18
申请号：PCT/US2016/017391
申请日：2016-02-10
申请人： ILLUMINA, INC.
发明人： GUNDERSON, Kevin L. , STEEMERS, Frank J. , FISHER, Jeffrey S. , RIGATTI, Roberto
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6806 , C12Q2537/143 , C12Q2563/149 , C12Q2563/159 , C12Q2563/185
摘要： Embodiments of the present invention relate to analyzing components of a cell. In some embodiments, the present invention relate to analyzing components of a single cell. In some embodiments, the methods and compositions relate to sequencing nucleic acids. In some embodiments, the methods and compositions relate to identifying and/or quantitating nucleic acid, proteins, organelles, and/or cellular metabolites.
摘要翻译：本发明的实施例涉及分析小区的组件。在一些实施例中，本发明涉及分析单个小区的组件。在一些实施方案中，所述方法和组合物涉及测序核酸。在一些实施方案中，所述方法和组合物涉及鉴定和/或定量核酸，蛋白质，细胞器和/或细胞代谢物。

10. 发明申请

WO2015095226A2 PRESERVING GENOMIC CONNECTIVITY INFORMATION IN FRAGMENTED GENOMIC DNA SAMPLES 审中-公开
标题翻译：保留遗传基因组DNA样品中的基因连通性信息
公开(公告)号：WO2015095226A2
公开(公告)日：2015-06-25
申请号：PCT/US2014/070658
申请日：2014-12-16
申请人： ILLUMINA, INC.
发明人： FISHER, Jeffrey S. , STEEMERS, Frank J. , AMINI, Sasan , GUNDERSON, Kevin L.
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q2535/119 , C12Q2535/122 , C12Q2565/513 , C12Q2565/543
摘要： A method of sequencing a target nucleic acid polymer by (a) modifying a target nucleic acid polymer to produce a modified nucleic acid polymer; (b) producing fragments of the modified nucleic acid polymer, wherein the fragments are attached to locations on a solid support surface (c) determining nucleotide sequences from the fragments at the locations; and (d) producing a representation of the nucleotide sequence for the target nucleic acid polymer based on the nucleotide sequences from the fragments and the relative distances between the locations on the solid support surface.
摘要翻译：一种通过（a）修饰靶核酸聚合物以产生修饰的核酸聚合物来测序靶核酸聚合物的方法; （b）产生经修饰的核酸聚合物的片段，其中所述片段连接到固体支持物表面上的位置（c），从所述位置的片段确定核苷酸序列; 和（d）基于来自片段的核苷酸序列和固体支持物表面上的位置之间的相对距离，产生靶核酸聚合物的核苷酸序列的表示。

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