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公开(公告)号：US20160040227A1
公开(公告)日：2016-02-11
申请号：US14829066
申请日：2015-08-18
申请人： Kalim U. Mir
发明人： Kalim U. Mir
CPC分类号： C12Q1/6874 , C12Q1/6818 , C12Q1/6869 , G01N21/6428 , G01N2021/6432 , G01N2021/6441 , C12Q2565/501 , C12Q2565/101 , C12Q2563/155 , C12Q2565/518 , C12Q2533/107 , C12Q2535/122 , C12Q2533/101 , C12Q2563/173 , C12Q2565/301 , C12Q2561/113
摘要： The present invention relates to a method of sequencing a target polynucleotide by enzymatic and/or chemical means. The sequencing method includes a method for characterizing multiple alleles in a sample, a method of calculating confidence levels in ascertained sequences, a method for comparing polynucleotide sequences and a method of resolving ambiguities in a polynucleotide sequence. It also provides methods for appropriately preparing samples, for immobilising template molecules, for organising the template molecules and to conduct the sequencing of many molecules in parallel. The method involves analysing molecules as members of an array. Many target polynucleotides or many segments of a single target polynucleotide can be sequenced simultaneously. In a preferred embodiment the method involves analysing individual molecules within an array and base calls are based on the signals from two or more molecules. A method to prevent non-specific signal in sequencing is also provided. The invention is readily automated, both for small-scale and large-scale operation and relevant algorithms and the composition of kits and systems are provided.
摘要翻译： 本发明涉及通过酶和/或化学方法测序靶多核苷酸的方法。 测序方法包括用于表征样品中多个等位基因的方法，计算确定序列中的置信水平的方法，用于比较多核苷酸序列的方法和解决多核苷酸序列中的模糊度的方法。 它还提供了适当制备样品，固定模板分子，组织模板分子和并行进行许多分子测序的方法。 该方法包括分析分子作为阵列的成员。 单个靶多核苷酸的许多靶多核苷酸或许多片段可以同时测序。 在优选实施方案中，该方法包括分析阵列内的各个分子，并且基于来自两个或更多个分子的信号进行碱基呼叫。 还提供了一种在排序中防止非特异性信号的方法。 本发明容易地自动化，用于小规模和大规模操作以及相关算法，并提供了套件和系统的组成。
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公开(公告)号：US09217177B2
公开(公告)日：2015-12-22
申请号：US13737534
申请日：2013-01-09
发明人： Kevin McKernan , Alan Blanchard , Lev Kotler , Gina Costa
CPC分类号： C12Q1/6874 , B82Y15/00 , B82Y30/00 , C12Q1/68 , C12Q1/6837 , C12Q1/6844 , C12Q1/6869 , C12Q2565/537 , C12Q2565/518 , C12Q2565/513 , C12Q2565/137 , C12Q2565/102 , C12Q2533/107 , C12Q2537/165
摘要： The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to beads. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages. In addition, the invention includes performing multiple sequencing reactions on a single template by removing initializing oligonucleotides and extended strands and performing subsequent reactions using different initializing oligonucleotides.
摘要翻译： 本发明提供了通过沿着单链模板进行连续循环的双链延伸来确定核酸序列的方法。 循环包括延伸，连接和优选切割的步骤。 在某些实施方案中，所述方法利用含有硫代磷酸酯键的延伸探针，并使用适合切割这种连接的试剂。 本发明提供使用至少两个可区分标记的探针家族确定关于序列的信息的方法。 在某些实施方案中，该方法在每个周期中从模板中的多个核苷酸中的每一个获取少于2位的信息。 在某些实施方案中，测序反应在附着于珠粒的模板上进行。 本发明还提供了含有硫代磷酸酯键的标记的延伸探针的集合。 此外，本发明包括通过除去初始化寡核苷酸和延伸的链并使用不同的初始化寡核苷酸进行后续反应，在单个模板上进行多个测序反应。
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公开(公告)号：US09200320B2
公开(公告)日：2015-12-01
申请号：US14571892
申请日：2014-12-16
发明人： Jonas Korlach , Stephen Turner , Eric Schadt
CPC分类号： C12Q1/6869 , C12Q1/702 , C12Q2565/518 , C12Q2547/101
摘要： The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to either enhance or inhibit such reactions. In certain preferred embodiments, RNA templates are used in single-molecule real-time sequencing reactions.
摘要翻译： 本发明一般涉及用于进行各种不同生物反应的单分子实时分析的组合物，方法和系统。 分析这些反应的能力提供了研究这些反应以及潜在鉴定影响这种反应的因素和/或方法的机会，例如增强或抑制这种反应。 在某些优选实施方案中，RNA模板用于单分子实时测序反应。
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24.发明申请LABEL-FREE METHODS FOR ISOLATION AND ANALYSIS OF NUCLEIC ACIDS ON SOLID PHASE DEVICE 有权用于固体相分离装置上核酸分离和分析的无标记方法公开(公告)号：US20150322486A1
公开(公告)日：2015-11-12
申请号：US14652099
申请日：2013-12-13
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6827 , C12N15/1006 , C12Q1/6806 , C12Q1/6825 , C12Q1/686 , C12Q2525/197 , C12Q2565/628 , C12Q2565/629 , C12Q2565/518 , C12Q2565/632
摘要： Methods and system for the isolation and/or analysis of nucleic acids on a solid phase device comprising (i) incubating a nucleic acid sample with Dimethyl adipimidate (DMA) on said solid phase under conditions that allow formation of a complex of the nucleic acid with the DMA; contacting the complex of (i) with said surface; and isolating and/or analyzing the nucleic acid of the complex.
摘要翻译： 用于在固相装置上分离和/或分析核酸的方法和系统，包括（i）在允许形成核酸复合物的条件下在所述固相上孵育核酸样品与二甲基己二亚胺（DMA） DMA; 使（i）的复合物与所述表面接触; 并分离和/或分析复合物的核酸。
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公开(公告)号：US09045798B1
公开(公告)日：2015-06-02
申请号：US11377136
申请日：2006-03-15
CPC分类号： C12Q1/6869 , B01J2219/00497 , B01J2219/005 , B01J2219/00576 , B01J2219/00648 , B01J2219/00722 , C07H21/04 , C12Q1/6818 , C12Q1/6825 , C12Q2525/113 , C12Q2525/117 , C12Q2563/107 , C12Q2563/149 , C12Q2565/518 , C12Q2523/307
摘要： The present invention provides novel compositions, methods and apparatus for DNA sequencing that can be performed, e.g., in a two-electrode chamber. The present invention also provides a method for sequencing a nucleic acid comprising immobilizing a plurality of complexes comprising a target nucleic acid, a primer nucleic acid, and a polymerase onto a surface, contacting the surface with a plurality of charged particles comprising a nucleotide phosphate by applying an electric field, reversing the electric field to transport unbound charged particles away from the surface, and detecting the incorporation of a nucleotide phosphate into a single molecule of the primer nucleic acid.
摘要翻译： 本发明提供了可以例如在双电极室中进行的用于DNA测序的新型组合物，方法和装置。 本发明还提供了一种对核酸进行测序的方法，包括将包含靶核酸，引物核酸和聚合酶的多种复合物固定在表面上，使表面与包含磷酸核苷酸的多个带电粒子接触， 施加电场，反转电场以将未结合的带电粒子输送离开表面，以及检测将核苷酸磷酸酯掺入引物核酸的单个分子中。
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公开(公告)号：US20150111774A1
公开(公告)日：2015-04-23
申请号：US14477550
申请日：2014-09-04
申请人： NGK INSULATORS, LTD.
发明人： Kousuke Niwa , Toshikazu Hirota
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6837 , C12Q1/689 , C12Q2600/16 , C12Q2525/161 , C12Q2537/162 , C12Q2565/518
摘要： The disclosure of this Description includes: a step of preparing a solid-phase body provided with a detection probe having a predetermined nucleotide sequence; a step of preparing a signaling target nucleic acid having a signal generating part for detecting the target nucleic acid; a step of bringing the signaling target nucleic acid, the detection probe, and an oligonucleotide being a mediator having a first site that hybridizes specifically with the target nucleic acid and a second site (preferably 20 to 50 nucleotides or more preferably 20 to 25 nucleotides in length) that hybridizes specifically with a part having the predetermined nucleotide sequence of the detection probe into contact with one another so that a hybridization product of these components can be formed; and a step of obtaining data based on the signal generating part of the signaling target nucleic acid on the solid-phase body.
摘要翻译： 本说明书的公开内容包括：制备具有预定核苷酸序列的检测探针的固相体的步骤; 制备具有用于检测靶核酸的信号产生部分的信号传导靶核酸的步骤; 使信号靶核酸，检测探针和寡核苷酸作为具有与靶核酸特异性区别的第一位点的介质和第二位点（优选为20〜50个核苷酸，更优选为20〜25个核苷酸的第 长度），其与具有检测探针的预定核苷酸序列的部分特异性地彼此接触，从而可以形成这些成分的杂交产物; 以及基于固相体上的信号传导靶核酸的信号产生部分获得数据的步骤。
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公开(公告)号：US20150111204A1
公开(公告)日：2015-04-23
申请号：US14318104
申请日：2014-06-27
申请人： Fluidigm Corporation
发明人： Stanley Lapidus
IPC分类号： C12Q1/68
CPC分类号： C12Q1/68 , C12Q1/6869 , C12Q1/6874 , C12Q2565/518 , C12Q2563/107 , C12Q2533/101
摘要： The invention provides methods and devices for detecting, enumerating or identifying target nucleic acid molecules using immobilized capture probes and single molecule sequencing techniques.
摘要翻译： 本发明提供了使用固定的捕获探针和单分子测序技术来检测，列举或鉴定靶核酸分子的方法和装置。
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公开(公告)号：US20150105273A1
公开(公告)日：2015-04-16
申请号：US14571892
申请日：2014-12-16
发明人： Jonas KORLACH , Stephen Turner , Eric Schadt
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , C12Q1/702 , C12Q2565/518 , C12Q2547/101
摘要： The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to either enhance or inhibit such reactions. In certain preferred embodiments, RNA templates are used in single-molecule real-time sequencing reactions.
摘要翻译： 本发明一般涉及用于进行各种不同生物反应的单分子实时分析的组合物，方法和系统。 分析这些反应的能力提供了研究这些反应以及潜在鉴定影响这种反应的因素和/或方法的机会，例如增强或抑制这种反应。 在某些优选实施方案中，RNA模板用于单分子实时测序反应。
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公开(公告)号：US20150086994A1
公开(公告)日：2015-03-26
申请号：US14509006
申请日：2014-10-07
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , B01J2219/00497 , B01J2219/005 , B01J2219/00576 , B01J2219/00648 , B01J2219/00722 , C07H21/04 , C12Q1/6818 , C12Q1/6825 , C12Q2525/113 , C12Q2525/117 , C12Q2563/107 , C12Q2563/149 , C12Q2565/518 , C12Q2523/307
摘要： The present invention provides novel compositions, methods and apparatus for DNA sequencing that can be performed, e.g., in a two-electrode chamber. The present invention also provides a method for sequencing a nucleic acid comprising immobilizing a plurality of complexes comprising a target nucleic acid, a primer nucleic acid, and a polymerase onto a surface, contacting the surface with a plurality of charged particles comprising a nucleotide phosphate by applying an electric field, reversing the electric field to transport unbound charged particles away from the surface, and detecting the incorporation of a nucleotide phosphate into a single molecule of the primer nucleic acid.
摘要翻译： 本发明提供了可以例如在双电极室中进行的用于DNA测序的新型组合物，方法和装置。 本发明还提供了一种对核酸进行测序的方法，包括将包含靶核酸，引物核酸和聚合酶的多种复合物固定在表面上，使表面与包含磷酸核苷酸的多个带电粒子接触， 施加电场，反转电场以将未结合的带电粒子输送离开表面，以及检测将核苷酸磷酸酯掺入引物核酸的单个分子中。
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公开(公告)号：US20150050657A1
公开(公告)日：2015-02-19
申请号：US14377104
申请日：2013-05-28
发明人： Roberto Rigatti , Jonathan Boutell
IPC分类号： C12P19/34
CPC分类号： C12P19/34 , C12Q1/6853 , C12Q2563/155 , C12Q2565/518 , C12Q2565/629
摘要： Provided herein is a method of selecting target nucleic acids on a support. The method includes providing a plurality of beads each bead comprising one or more oligonucleotides, providing a support with a plurality of primers with a sequence complementary to at least a portion of the oligonucleotides on the beads, contacting the beads with the support wherein the oligonucleotides on the beads bind to the primers on the support, performing an extension reaction by extending the primers on the support to produce capture oligonucleotides, contacting the support comprising the capture oligonucleotides with the target nucleic acids, and extending the capture oligonucleotides bound to target nucleic acids to produce target extension products comprising a sequence complementary to at least a portion of the target nucleic acids. Optionally, the method further includes amplifying the target extension products.
摘要翻译： 本文提供了选择载体上靶核酸的方法。 该方法包括提供多个珠粒，每个珠粒包含一个或多个寡核苷酸，为多个引物提供载体，所述多个引物具有与珠粒上至少一部分寡核苷酸互补的序列，使珠粒与载体接触， 珠子与载体上的引物结合，通过将载体上的引物延伸以产生捕获寡核苷酸，使包含捕获寡核苷酸的载体与靶核酸接触并将与靶核酸结合的捕获寡核苷酸延伸到靶核酸上，从而进行延伸反应 产生包含与靶核酸的至少一部分互补的序列的靶延伸产物。 可选地，该方法还包括放大目标扩展产品。
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