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1. 发明申请

WO2022040176A1 SEQUENCE-SPECIFIC TARGETED TRANSPOSITION AND SELECTION AND SORTING OF NUCLEIC ACIDS 审中-公开
公开(公告)号：WO2022040176A1
公开(公告)日：2022-02-24
申请号：PCT/US2021/046292
申请日：2021-08-17
申请人： ILLUMINA, INC. , ILLUMINA CAMBRIDGE LIMITED
发明人： STEEMERS, Frank J. , BOUTELL, Jonathan Mark , GATTI LAFRANCONI, Pietro , MILLER, Oliver Jon , BELL, Emma , RICOULT, Sebastien Georg Gabriel , GORMLEY, Niall Anthony , SCHNEIDER, Kim
IPC分类号： C12N15/10 , C12Q1/6806
摘要： A variety of different types of targeted transposome complexes are described herein that may be used to mediate sequence-specific targeted transposition of nucleic acids. Also described herein is a method of characterizing desired samples in a mixed pool of samples comprising both desired samples and unwanted samples comprising, to produce sequencing data from double-stranded nucleic acid, initially sequencing a library comprising a plurality of nucleic acid samples from a mixed pool, wherein each nucleic acid library comprises nucleic acids from a single sample and a unique sample barcode to distinguish the nucleic acids from the single sample from the nucleic acids from other samples in the library; analyzing the sequencing data and identifying unique sample barcodes associated with sequencing data from desired samples; performing a selection step on the library comprising enriching nucleic acid samples from desired samples and/or depleting nucleic acid samples from unwanted samples; and resequencing the nucleic acid library.

2. 发明申请

WO2021133768A1 NANOPARTICLE WITH SINGLE SITE FOR TEMPLATE POLYNUCLEOTIDE ATTACHMENT 审中-公开
公开(公告)号：WO2021133768A1
公开(公告)日：2021-07-01
申请号：PCT/US2020/066547
申请日：2020-12-22
申请人： ILLUMINA, INC. , ILLUMINA CAMBRIDGE LIMITED , ILLUMINA SINGAPORE PTE. LTD.
发明人： GEORGE, Wayne N. , BOUTELL, Jonathan Mark , LESSARD-VIGER, Mathieu , NIRANTAR, Saurabh , GATTI LAFRANCONI, Pietro , MCDONALD, Seth , TEO, Yin Nah , BACIGALUPO, Maria Rogert , PEISAJOVICH, Sergio , BRUSTAD, Eric , HOWARD, Michael , YANG, Xiangyuan , BOWEN, M. Shane , NEMIROSKI, Alex , BRODIN, Jeffrey , VINCENT, Ludovic , BERTI, Lorenzo , BROWN, Andrew A. , SHEN, Fei , STORMS, Lena , BENICE, Olivia
IPC分类号： C12Q1/6869 , B01J19/0046 , B01J2219/00317 , B01J2219/00608 , B01J2219/00722 , B82Y30/00 , C12Q1/6806 , C12Q1/6874 , C12Q2565/513
摘要： Provided is a nanoparticle including a scaffold, a single template site for bonding a template polynucleotide to the scaffold, and a plurality of accessory sites for bonding accessory oligonucleotides to the scaffold, wherein the scaffold is selected from one or more scaffold DNA molecules and one or more scaffold polypeptides, the single template site for bonding a template polynucleotide to the scaffold is selected from a covalent template bonding site and a noncovalent template bonding site and the plurality of accessory sites for bonding accessory oligonucleotides to the scaffold are selected from covalent accessory oligonucleotide bonding sites and noncovalent accessory oligonucleotide bonding sites. Also provided are methods of using the nanoparticle, in particular in sequencing by synthesis.

3. 发明申请

WO2023278739A1 FLOW CELLS 审中-公开
公开(公告)号：WO2023278739A1
公开(公告)日：2023-01-05
申请号：PCT/US2022/035781
申请日：2022-06-30
申请人： ILLUMINA, INC. , ILLUMINA CAMBRIDGE LIMITED
发明人： BOUTELL, Jonathan Mark , GEORGE, Wayne N. , MA, Xiaoyu , WU, Xiaolin , XI, Weixian
IPC分类号： C12Q1/6874 , C12Q1/689
摘要： An example of a kit includes a flow cell, a primer fluid, and a cleaving fluid. The flow cell includes at least one surface functionalized with a polymeric hydrogel including azide functional groups or amine functional groups. The primer fluid includes a plurality of alkyne-containing primers, each alkyne-containing primer having an amino cleavable group attaching a primer sequence of the alkyne-containing primer to an alkyne-containing moiety of the alkyne-containing primer. The cleaving fluid includes a substance that is reactive with the amino cleavable group.

4. 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。

5. 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。

6. 发明申请

WO2022165188A1 METHODS, COMPOSITIONS AND KITS TO IMPROVE SEEDING EFFICIENCY OF FLOW CELLS WITH POLYNUCLEOTIDES 审中-公开
公开(公告)号：WO2022165188A1
公开(公告)日：2022-08-04
申请号：PCT/US2022/014329
申请日：2022-01-28
申请人： ILLUMINA, INC. , ILLUMINA CAMBRIDGE LIMITED
发明人： WU, Yir-Shyuan , GORPE-YASAR, Filiz , KHURANA, Tarun Kuman , BOUTELL, Jonathan Mark
IPC分类号： C12Q1/6806 , C12Q1/6834 , C12Q1/6844
摘要： The disclosure relates to methods, compositions, and kits for improving seeding efficiency of flow cells with polynucleotides, and applications thereof, including for sequencing.

7. 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

8. 发明申请

WO2023081654A1 PRIMER SETS AND METHODS AND KITS INCORPORATING THE PRIMER SETS 审中-公开
公开(公告)号：WO2023081654A1
公开(公告)日：2023-05-11
申请号：PCT/US2022/079075
申请日：2022-11-01
申请人： ILLUMINA, INC. , ILLUMINA CAMBRIDGE LIMITED
发明人： ARMIJO, Esteban , BOUTELL, Jonathan Mark , BRODIN, Jeffrey , CARRAMI, Eli M. , ROGERT BACIGALUPO, Maria Candelaria , SMITH, Randall , LESSARD-VIGER, Mathieu , VINCENT, Ludovic
IPC分类号： C12Q1/6869
摘要： An example primer set includes first and second nuclease resistant primers. The first nuclease resistant primer includes a first sequence; a first cleavage site attached at a 3' end of the first sequence; and a first nuclease resistant modification incorporated between the first sequence and the first cleavage site. The second nuclease resistant primer includes a second sequence that is different from the first sequence; a second nuclease resistant modification incorporated at a 3' end of the second sequence; and a second cleavage site attached between the second sequence and the second nuclease resistant modification. The second cleavage site is different from the first cleavage site.

9. 发明申请

WO2022087150A2 SEQUENCING TEMPLATES COMPRISING MULTIPLE INSERTS AND COMPOSITIONS AND METHODS FOR IMPROVING SEQUENCING THROUGHPUT 审中-公开
公开(公告)号：WO2022087150A2
公开(公告)日：2022-04-28
申请号：PCT/US2021/055878
申请日：2021-10-20
申请人： ILLUMINA, INC. , ILLUMINA CAMBRIDGE LIMITED
发明人： KHURANA, Tarun , WU, Yir-Shyuan , GORMLEY, Niall Anthony , BOUTELL, Jonathan Mark
IPC分类号： C12Q1/6834 , C12Q1/6874
摘要： Described herein is a polynucleotide for use as a sequencing template comprising multiple inserts. Also described herein are method of generating and using these polynucleotides and methods of use of such templates, including analysis of contiguity information. Further, sequencing templates comprising an insert sequence and a copy of the insert sequence can be used to correct for random errors generated during sequencing or amplification or to identify nucleobase damage or other mutation that leads to non-canonical base pairing in a double-stranded nucleic acid. Methods of performing methylation analysis are also described herein.

10. 发明申请

WO2019126040A1 FLOW CELLS WITH HYDROGEL COATING 审中-公开
公开(公告)号：WO2019126040A1
公开(公告)日：2019-06-27
申请号：PCT/US2018/066011
申请日：2018-12-17
申请人： ILLUMINA, INC. , ILLUMINA CAMBRIDGE LIMITED
发明人： REN, Hongji , BOUTELL, Jonathan Mark , MOON, John A. , BOWEN, M. Shane , NEMIROSKI, Alex , SKINNER, Gary Mark , CHEN, Kenny
IPC分类号： B01J19/00 , C12Q1/6874 , C08F220/58 , C09D105/12 , C09D133/26 , C09D171/02
摘要： In an example of the method, a functionalized coating layer is applied in depressions of a patterned flow cell substrate. The depressions are separated by interstitial regions. A primer is grafted to the functionalized coating layer to form a grafted functionalized coating layer in the depressions. A hydrogel is applied on at least the grafted functionalized coating layer.

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