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21. 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。

22. 发明申请

WO2014108810A3 SAMPLE PREPARATION ON A SOLID SUPPORT 审中-公开
标题翻译：固体支持样品制备
公开(公告)号：WO2014108810A3
公开(公告)日：2014-12-04
申请号：PCT/IB2014000610
申请日：2014-01-08
申请人： ILLUMINA CAMBRIDGE LTD
发明人： GORMLEY NIALL ANTHONY , SMITH GEOFFREY PAUL
IPC分类号： C12Q1/68
CPC分类号： C12N15/1065 , B01J19/0046 , B01J2219/00286 , B01J2219/00608 , B01J2219/00722 , C12N15/1093 , C12Q1/6834 , C12Q1/6869 , C12Q1/6874 , C40B40/08 , C40B50/14 , C40B50/18 , C12Q2521/543 , C12Q2525/191 , C12Q2535/122 , C12Q2565/518
摘要： Presented are methods and compositions for using immobilized transposase and a transposon end for generating an immobilized library of 5 '-tagged double-stranded target DNA on a surface. The methods are useful for generating 5'- and 3 '-tagged DNA fragments for use in a variety of processes, including massively parallel DNA sequencing.
摘要翻译：提出了使用固定化转座酶和转座子末端来产生表面上5'标记的双链靶DNA的固定化文库的方法和组合物。该方法可用于产生5'和3'标记的DNA片段，用于多种方法，包括大规模并行DNA测序。

23. 发明申请

WO2014108810A8 SAMPLE PREPARATION ON A SOLID SUPPORT 审中-公开
标题翻译：样品准备在一个固体支持
公开(公告)号：WO2014108810A8
公开(公告)日：2014-09-25
申请号：PCT/IB2014000610
申请日：2014-01-08
申请人： ILLUMINA CAMBRIDGE LTD
发明人： GORMLEY NIALL ANTHONY , SMITH GEOFFREY PAUL
IPC分类号： C12Q1/68
CPC分类号： C12N15/1065 , B01J19/0046 , B01J2219/00286 , B01J2219/00608 , B01J2219/00722 , C12N15/1093 , C12Q1/6834 , C12Q1/6869 , C12Q1/6874 , C40B40/08 , C40B50/14 , C40B50/18 , C12Q2521/543 , C12Q2525/191 , C12Q2535/122 , C12Q2565/518
摘要： Presented are methods and compositions for using immobilized transposase and a transposon end for generating an immobilized library of 5 '-tagged double-stranded target DNA on a surface. The methods are useful for generating 5'- and 3 '-tagged DNA fragments for use in a variety of processes, including massively parallel DNA sequencing.
摘要翻译：提供了使用固定化转座酶和转座子末端用于在表面上产生5'-标记的双链靶DNA的固定文库的方法和组合物。该方法可用于产生5'和3'标记的DNA片段，用于各种过程，包括大规模平行DNA测序。

24. 发明申请

WO2011034690A2 CENTROID MARKERS FOR IMAGE ANALYSIS OF HIGH DENSITY CLUSTERS IN COMPLEX POLYNUCLEOTIDE SEQUENCING 审中-公开
标题翻译：中心标记用于复杂多核苷酸序列中高密度簇的图像分析
公开(公告)号：WO2011034690A2
公开(公告)日：2011-03-24
申请号：PCT/US2010/046380
申请日：2010-08-23
申请人： ILLUMINA CAMBRIDGE, LTD. , KERSEY, Alan, D. , BOUTELL, Jonathan, Mark
发明人： KERSEY, Alan, D. , BOUTELL, Jonathan, Mark
IPC分类号： C12Q1/68 , C12N15/11
CPC分类号： C12Q1/6874 , C12Q1/6806 , C12Q2565/543 , C12Q2563/107 , C12Q2535/122
摘要： Improved compositions, methods, apparatus, and kits for high-throughput nucleic acid amplification, detection and sequencing are disclosed. A nucleic acid cluster having an identifiable center is produced by generating on a solid support an immobilized nucleic acid complement from a template, one of which comprises a detectable label; and amplifying the complement and the template to obtain a nucleic acid cluster on the support, the cluster having a substantially central location marked by the detectable label and a surrounding region comprising immobilized copies. Also disclosed are nucleotide sequence determination in nucleic acid clusters so produced, center position annotation in the clusters, assignment of sequence information to overlapping clusters, and related compositions and methods
摘要翻译：公开了用于高通量核酸扩增，检测和测序的改进的组合物，方法，装置和试剂盒。具有可识别中心的核酸簇通过在固体支持物上产生来自模板的固定化核酸互补物而产生，所述模板中的一个包含可检测标记; 以及扩增补体和模板以获得载体上的核酸簇，所述簇具有由可检测标记标记的基本中心位置和包含固定拷贝的周围区域。还公开了如此产生的核酸簇中的核苷酸序列测定，簇中的中心位置注释，序列信息与重叠簇的分配以及相关的组合物和方法

25. 发明申请

WO2016061517A3 CONTIGUITY PRESERVING TRANSPOSITION 审中-公开
标题翻译：保持运输的连续性
公开(公告)号：WO2016061517A3
公开(公告)日：2016-06-23
申请号：PCT/US2015056040
申请日：2015-10-16
申请人： ILLUMINA CAMBRIDGE LTD , STEEMERS FRANK J , GUNDERSON KEVIN L , ZHANG FAN , BETLEY JASON RICHARD , GORMLEY NIALL ANTHONY , MEULEMAN WOUTER , WEIR JACQUELINE , IOANNOU AVGOUSTA , JENKINS GARETH , JACKSON ROSAMOND , MORRELL NATALIE , POKHOLOK DMITRY K , NORBERG STEVEN J , HE MOLLY , KIA AMIRALI , GORYSHIN IGOR , PANTOJA RIGO
发明人： STEEMERS FRANK J , GUNDERSON KEVIN L , ZHANG FAN , BETLEY JASON RICHARD , GORMLEY NIALL ANTHONY , MEULEMAN WOUTER , WEIR JACQUELINE , IOANNOU AVGOUSTA , JENKINS GARETH , JACKSON ROSAMOND , MORRELL NATALIE , POKHOLOK DMITRY K , NORBERG STEVEN J , HE MOLLY , KIA AMIRALI , GORYSHIN IGOR , PANTOJA RIGO
IPC分类号： C12N15/10
CPC分类号： C12N15/1093 , C12N15/1065 , C12Q2525/191 , C12Q2563/179 , C12Q2565/514
摘要： Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.
摘要翻译：本文提供的实施方案涉及用于制备靶核酸的条形码DNA片段的固定化文库，鉴定基因组变体，确定目标核酸的邻接信息，定相信息和甲基化状态的方法和组合物。

26. 发明申请

WO2012106081A3 METHODS FOR REDUCING NUCLEIC ACID DAMAGE 审中-公开
标题翻译：减少核酸损伤的方法
公开(公告)号：WO2012106081A3
公开(公告)日：2012-11-01
申请号：PCT/US2012021040
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：本文提供了在选自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，其中接触抑制核酸的降解。本文还提供了抑制核酸的光诱导降解的方法。另外，本文提供了在制备核酸样品期间减少或抑制核酸损伤的方法，其包括在包含一种或多种化合物的溶液中使样品中的核酸序列片段化，所述化合物抑制核酸样品中核酸序列降解样品。

27. 发明申请

WO2010038042A1 NUCLEIC ACID SAMPLE ENRICHMENT FOR SEQUENCING APPLICATIONS 审中-公开
标题翻译：用于测序应用的核酸样品
公开(公告)号：WO2010038042A1
公开(公告)日：2010-04-08
申请号：PCT/GB2009/002366
申请日：2009-10-02
申请人： ILLUMINA CAMBRIDGE LTD. , BOUTELL, Jonathan, Mark
发明人： BOUTELL, Jonathan, Mark
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6806 , C12Q1/686 , C12Q2531/113 , C12Q2565/501 , C12Q2525/161
摘要： The present invention relates to the field of molecular biology, and more specifically to methods for reducing the complexity of a nucleic acid sample.
摘要翻译：本发明涉及分子生物学领域，更具体地涉及降低核酸样品复杂性的方法。

28. 发明授权

US12091712B2 Systems and methods for measurement and sequencing of bio-molecules 有权
公开(公告)号：US12091712B2
公开(公告)日：2024-09-17
申请号：US16169756
申请日：2018-10-24
申请人： Illumina Cambridge, Ltd.
发明人： Mark F. Oldham , Eric S. Nordman , Timothy M. Woudenberg , Gaurav Goyal , Masoud Vakili , Toshihiko Honkura , Sam Woo , Hisao Kawasaki , Kazusuke Mihara
IPC分类号： C12Q1/6869 , C12Q1/68 , G01N27/327 , G01N33/00 , G01N33/487
CPC分类号： C12Q1/6869 , C12Q1/68 , G01N27/3275 , G01N27/3276 , G01N27/3278 , G01N33/00 , G01N33/48721 , C12Q2565/631 , C12Q1/6869 , C12Q2563/116 , C12Q2563/185 , C12Q2565/631
摘要： The present disclosure provides systems and methods for sequencing nucleic acid molecules using tunneling labels. A sequence of a nucleic acid molecule may be identified with high accuracy using a chip comprising sensors, wherein each individual sensor may comprise at least two electrodes separated by a gap. The electrodes may be configured to generate at least one electrical signal upon binding of a tunneling label associated with a nucleotide. Epigenetic information can also be determined at the same time as a nucleic acid sequence.

29. 发明申请

US20200335178A1 DETECTING REPEAT EXPANSIONS WITH SHORT READ SEQUENCING DATA 审中-公开
公开(公告)号：US20200335178A1
公开(公告)日：2020-10-22
申请号：US16869455
申请日：2020-05-07
申请人： Illumina Cambridge Ltd.
发明人： Michael A. Eberle , Richard Shaw
IPC分类号： G16B30/00 , G16B20/00 , C12Q1/6883
摘要： The disclosed embodiments concern methods, apparatus, systems and computer program products for determining the presence or absence of repeat expansions of interest, including repeat expansions of repeat sequences that are medically significant. Some embodiments provide methods for identifying and calling medically relevant repeat expansions using anchored reads. An anchored read is a paired end read that is unaligned to a repeat sequence under consideration, but it is paired with an anchor read that is aligned to or near the repeat sequence. Some embodiments use both anchor and anchored reads to determine the presence or absence of the repeat expansions. System, apparatus, and computer program products are also provided for determining repeat expansion implementing the methods disclosed.

30. 发明申请

US20220412872A1 LINEAR FOURIER FIDUCIAL 有权
公开(公告)号：US20220412872A1
公开(公告)日：2022-12-29
申请号：US17592895
申请日：2022-02-04
申请人： ILLUMINA CAMBRIDGE LTD.
发明人： Helge Nareid
IPC分类号： G01N15/14 , G06T7/73
摘要： The present approach relates generally to image-based approaches for detecting deviations from a linear movement when scanning a surface. More particularly, the approach relates to the use of linear fiducials to detect, in real-time, deviations from a linear scan path during operation of a scanning imaging system. Such linear fiducials may include both sample sites and blank regions or sites or, in certain embodiments, may utilize elongated sample sites (e.g., linear features) within the linear fiducial.

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