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1. 发明申请

WO2018064311A2 METHODS AND SYSTEMS FOR REDUCING PHASING ERRORS WHEN SEQUENCING NUCLEIC ACIDS USING TERMINATION CHEMISTRY 审中-公开
标题翻译：用于终止使用终止化学法测序核酸时减少相差错的方法和系统
公开(公告)号：WO2018064311A2
公开(公告)日：2018-04-05
申请号：PCT/US2017/053973
申请日：2017-09-28
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： HUBBELL, Earl
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6825 , C12Q1/6869 , C12Q1/6874 , C12Q2533/101 , C12Q2565/301 , C12Q2565/607
摘要： A method for nucleic acid sequencing may include disposing a plurality of template nucleic acid molecules in a plurality of defined spaces disposed on a sensor array, at least some of the plurality of template nucleic acid molecules having a sequencing primer and a polymerase operably bound therewith; advancing one or more nucleotide species over the plurality of template nucleic acid molecules with the sequencing primer and the polymerase operably bound therewith; measuring a signal generated by nucleotide incorporations resulting from advancing the one or more nucleotide species; and exposing the plurality of template nucleic acid molecules to a cleaving reagent subsequent to the advancing and measuring. The cleaving reagent can remove labeling reagents attached to the one or more nucleotide species. The advancing and measuring steps can be performed for different orders of the one or more nucleotide species prior to a subsequent exposing of the plurality of template nucleic acid molecules to the cleaving reagent.
摘要翻译：用于核酸测序的方法可以包括将多个模板核酸分子置于设置在传感器阵列上的多个限定空间中，所述多个模板核酸分子中的至少一些具有测序引物和与之可操作结合的聚合酶; 使所述测序引物和聚合酶与所述多个模板核酸分子可操作地结合在所述多个模板核酸分子上前进一个或多个核苷酸物种; 测量由推进所述一种或多种核苷酸物种产生的核苷酸掺入产生的信号; 以及在推进和测量之后将多个模板核酸分子暴露于裂解试剂。切割试剂可去除附着于一种或多种核苷酸物种的标记试剂。在随后将多个模板核酸分子暴露于裂解试剂之前，可以针对一个或多个核苷酸物种的不同顺序进行推进和测量步骤。

2. 发明申请

WO2017144653A1 SINGLE NUCLEOTIDE DETECTION METHOD 审中-公开
标题翻译：单核苷酸检测方法
公开(公告)号：WO2017144653A1
公开(公告)日：2017-08-31
申请号：PCT/EP2017/054306
申请日：2017-02-24
申请人： BASE4 INNOVATION LIMITED
发明人： BALMFORTH, Barnaby
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , C12Q1/6827 , C12Q2521/319 , C12Q2521/331 , C12Q2521/501 , C12Q2525/125 , C12Q2525/131 , C12Q2563/159 , C12Q2565/107 , C12Q2565/301 , C12Q2565/629 , C12Q2525/307 , C12Q2525/301
摘要： A method of sequencing a nucleic acid characterised by the steps of (1) generating a stream of single nucleotides by progressive pyrophosphorolysis of the nucleic acid; (2) producing at least one substantially double-stranded oligonucleotide used probe by reacting, in the presence of a polymerase and a ligase, one of the single nucleotides with a corresponding probe system comprising (a) a first single-stranded oligonucleotide labelled with first and second regions of characteristic detectable element types in an undetectable state located respectively on the X' and Y' end sides of a third region comprising a restriction enzyme recognition site element including the capture site and an exonuclease-blocking site on the X' side thereof (wherein either X' is 3' and Y' is 5' or X' is 5' and Y' is 3') and (b) second and third single-stranded oligonucleotides capable of hybridising to complementary regions on the first oligonucleotide flanking the capture site; (2a) either (i) treating the used probe with a conventional or nicking substitution-dependent restriction endonuclease to cut the first oligonucleotide strand at the recognition site if and only if the single nucleotide captured comprises a nucleobase which is substituted or (ii) treating the used probe with a conventional or nicking substitution-sensitive restriction endonuclease to cut the first oligonucleotide strand at the recognition site if and only if the single nucleotide captured comprises a nucleobase which is unsubstituted; (3) digesting the first oligonucleotide strand of the used probe with an enzyme having double-stranded exonucleolytic activity in the X'-Y' direction corresponding to the first oligonucleotide to yield detectable elements derived from either the first region, the second region, or the first and second regions in a detectable state and a single-stranded fourth oligonucleotide which is at least in part the sequence complement of the first oligonucleotide; (4) reacting the fourth oligonucleotide with another first oligonucleotide to produce a substantially double-stranded oligonucleotide product corresponding to the used probe; (5) repeating steps (2a), (3) and (4) in a cycle and (6) detecting the detectable elements released in each iteration of step (3) wherein if the endonuclease employed is of the conventional type the second or third oligonucleotide includes an endonucleolysis directing linkage at or close to its X' or Y' end respectively. Corresponding biological probe systems are also disclosed.
摘要翻译：对核酸进行测序的方法，其特征在于以下步骤：（1）通过核酸的进行性焦磷酸分解产生单核苷酸流; （2）通过在聚合酶和连接酶存在下，使单核苷酸中的一个与相应的探针系统反应，产生至少一个基本上双链寡核苷酸的探针，所述探针系统包含（a）用第一标记的第一单链寡核苷酸以及分别位于包含限制酶识别位点元件的第三区域的X'和Y'端侧的处于不可检测状态的特征可检测元件类型的第二区域，所述限制酶识别位点元件在其X'侧包含捕获位点和外切核酸酶阻断位点（其中X'为3'且Y'为5'或X'为5'且Y'为3'）和（b）第二和第三单链寡核苷酸，所述第二和第三单链寡核苷酸能够与第一寡核苷酸上的互补区杂交捕获地点; （2a）（i）当且仅当所捕获的单个核苷酸包含被取代的核碱基或（ii）处理（i）用常规或切口取代依赖性限制性内切核酸酶处理用过的探针以在识别位点切割第一寡核苷酸链时当且仅当捕获的单个核苷酸包含未被取代的核碱基时，所用的具有常规或切口取代敏感性限制性内切核酸酶的探针在识别位点切割第一寡核苷酸链; （3）用与第一寡核苷酸对应的X'-Y'方向的具有双链核酸外切酶活性的酶消化所用探针的第一寡核苷酸链，以产生源自第一区域，第二区域或第二区域的可检测元件处于可检测状态的第一和第二区域以及至少部分为第一寡核苷酸的序列互补序列的单链第四寡核苷酸; （4）使第四寡核苷酸与另一个第一寡核苷酸反应以产生对应于所用探针的基本上双链的寡核苷酸产物; （5）在一个循环中重复步骤（2a），（3）和（4），和（6）检测在步骤（3）的每次重复中释放的可检测元素，其中如果使用的核酸内切酶是常规类型，则第二或第三寡核苷酸包括分别在其X'或Y'端或其附近的核苷酸内切引导连接。相应的生物探针系统也被公开。

3. 发明申请

WO2016116757A1 IMPROVED DROPLET SEQUENCING APPARATUS AND METHOD 审中-公开
标题翻译：改进的滴液测序装置和方法
公开(公告)号：WO2016116757A1
公开(公告)日：2016-07-28
申请号：PCT/GB2016/050130
申请日：2016-01-21
申请人： BASE4 INNOVATION LIMITED
发明人： BALMFORTH, Barnaby , FRAYLING, Cameron Alexander , ISAAC, Thomas Henry
IPC分类号： B01L3/00 , B01L3/02
CPC分类号： B01L3/502784 , B01F3/0807 , B01F13/0062 , B01L3/0268 , B01L3/502761 , B01L3/5088 , B01L2300/0819 , C12Q1/6869 , C12Q2563/159 , C12Q2565/629 , C12Q2563/149 , C12Q2565/301 , C12Q2565/518
摘要： An apparatus for sequencing a polynucleotide analyte is provided and comprises; • a first zone in which a stream of single nucleotides is generated by progressive digestion of a molecule of the analyte attached to a particle located therein and exposed to a flowing aqueous medium; • a second zone in which a corresponding stream of aqueous droplets is generated from the aqueous medium and the nucleotide stream and wherein at least some of the droplets contain a single nucleotide and • a third zone in which each droplet is stored and/or interrogated to reveal a property characteristic of the single nucleotide it may contain; characterised in that the first zone comprises a microfluidic channel through which the aqueous medium flows and the location comprises a hollow seating in a wall thereof to which suction can be applied and into which the particle can be close-fitted.
摘要翻译：提供了一种用于测序多核苷酸分析物的装置，包括： •第一区，其中通过逐渐消化附着于位于其中并暴露于流动水性介质的颗粒的分析物的分子产生单个核苷酸流; •第二区，其中从水性介质和核苷酸流产生相应的水滴流，并且其中至少一些液滴含有单个核苷酸和第三区，其中每个液滴被储存和/或询问到揭示其可能含有的单核苷酸的特性; 其特征在于，所述第一区域包括微流体通道，所述水性介质流过所述微流体通道，并且所述位置包括位于其壁中的中空座部，所述空腔可以被施加到所述空腔，所述颗粒可以紧密配合到所述壁中。

4. 发明申请

WO2014047646A1 MULTIPLEX PYROSEQUENCING USING NON-INTERFERING NOISE CANCELLING POLYNUCLEOTIDE IDENTIFICATION TAGS 审中-公开
标题翻译：使用非干扰噪声消除多核苷酸鉴定标签进行多重选择
公开(公告)号：WO2014047646A1
公开(公告)日：2014-03-27
申请号：PCT/US2013/061460
申请日：2013-09-24
申请人： CB BIOTECHNOLOGIES, INC.
发明人： HAN, Jian , WANG, Chunlin
IPC分类号： C12P19/34 , C07H21/04
CPC分类号： C12Q1/6881 , C12Q1/6869 , C12Q2531/113 , C12Q2537/143 , C12Q2565/301
摘要： The present disclosure generally pertains to a multiplex method for analyzing samples comprising using polynucleotide amplification to produce amplified products wherein one or more target sequences are tagged with a non-interfering, non- canceling target-specific polynucleotide identification tag, pyrosequencing the amplified products through the non-canceling target-specific polynucleotide identification tag sequence to detect the presence of one or more specific polynucleotide identification tags. The presence of a specific polynucleotide identification tag being correlated with the presence of a specific target sequence.
摘要翻译：本公开通常涉及用于分析样品的多重方法，其包括使用多核苷酸扩增产生扩增产物，其中一个或多个靶序列用非干扰的，非抵消的靶特异性多核苷酸鉴定标签进行标记，通过所述扩增产物非取消靶特异性多核苷酸鉴定标签序列，以检测一个或多个特异性多核苷酸鉴定标签的存在。特定多核苷酸识别标签的存在与特定靶序列的存在相关。

5. 发明申请

WO2013084917A1 ボロン酸基固定化支持体を用いたピロリン酸検出法审中-公开
标题翻译：使用固定化硼酸支持体的磷酸检测方法
公开(公告)号：WO2013084917A1
公开(公告)日：2013-06-13
申请号：PCT/JP2012/081466
申请日：2012-12-05
申请人：株式会社日立製作所
发明人：西田　洋一 , 神原　秀記
IPC分类号： G01N27/414 , C12Q1/48 , C12Q1/68 , G01N27/416 , G01N33/53 , C12N15/09
CPC分类号： C12Q1/6811 , C12N15/09 , C12Q1/68 , C12Q1/6869 , G01N27/4145 , C12Q2527/125 , C12Q2565/301
摘要：　本発明は、酵素反応、とりわけDNAポリメラーゼやDNAリガーゼにより放出されるピロリン酸を直接検出することにより、簡便かつ直接的にDNA配列決定を行うことができる方法を提供することを課題とする。本発明は、導電性支持体に固定化したボロン酸基が可逆的にピロリン酸と結合し、そのとき誘導される電気的変化を測定することにより、ピロリン酸を検出するための方法及びデバイスを提供する。
摘要翻译：本发明的目的在于提供一种能够简单且直接地进行使用酶反应的DNA序列测定的方法的问题，特别是通过直接检测通过DNA聚合酶和/或DNA连接酶释放的焦磷酸。本发明提供一种通过测量固定在导电性支撑体上的硼酸与焦磷酸可逆地结合而引入的电变化来检测焦磷酸的方法和装置。

6. 发明申请

WO2012082145A1 LIGAND IDENTIFICATION 审中-公开
标题翻译：配对标识
公开(公告)号：WO2012082145A1
公开(公告)日：2012-06-21
申请号：PCT/US2010/061129
申请日：2010-12-17
申请人： THE BOARD OF REGENTS OF THE UNIVERSITY OF TEXAS SYSTEM , PASQUALINI, Renata , ARAP, Wadih , GIORDANO, Ricardo J , DIAS-NETO, Emmanuel , NUNES, Diana N.
发明人： PASQUALINI, Renata , ARAP, Wadih , GIORDANO, Ricardo J , DIAS-NETO, Emmanuel , NUNES, Diana N.
IPC分类号： G01N33/53
CPC分类号： C12N15/1037 , C12Q1/6869 , C12Q2600/158 , G01N33/6845 , C12Q2527/119 , C12Q2535/122 , C12Q2565/30 , C12Q2565/607 , C12Q2565/301
摘要： The present disclosure provides new and improved phage display methodologies. Among other things, the present invention provides methodologies that do not utilize bacterial amplification of phage. Alternatively or additionally, the present invention provides phage display systems that rapidly identify ligands. Alternatively or additionally, the present invention provides phage display methodologies for use in human subjects. Alternatively or additionally, the present invention provides phage display systems that allow detection and/or characterization of low abundance ligands.
摘要翻译：本公开提供了新的和改进的噬菌体展示方法。除其他之外，本发明提供了不利用噬菌体的细菌扩增的方法。或者或另外，本发明提供了快速鉴定配体的噬菌体展示系统。或者或另外，本发明提供用于人类受试者的噬菌体展示方法。或者或另外，本发明提供允许检测和/或表征低丰度配体的噬菌体展示系统。

7. 发明申请

WO2011156707A3 ALTERNATIVE NUCLEOTIDE FLOWS IN SEQUENCING-BY-SYNTHESIS METHODS 审中-公开
标题翻译：序列合成方法中的替代核酸流
公开(公告)号：WO2011156707A3
公开(公告)日：2012-03-29
申请号：PCT/US2011039973
申请日：2011-06-10
申请人： LIFE TECHNOLOGIES CORP , SCHULTZ JONATHAN , DAVIDSON JOHN F
发明人： SCHULTZ JONATHAN , DAVIDSON JOHN F
IPC分类号： C12Q1/68 , G01N33/48 , G01N33/50
CPC分类号： C12Q1/6869 , B01L3/5027 , C12Q1/6874 , C12Q2537/155 , C12Q2563/149 , C12Q2565/301 , C12Q2565/629
摘要： A method for sequencing a polynucleotide strand by using sequencing-by-synthesis techniques. To address the problem of incomplete extension (IE) and/or carry forward (CF) errors that can occur in sequencing-by-synthesis reactions, an alternative flow ordering of dNTPs is used. In contrast to conventional flow orderings, the dNTPs are flowed in an ordering that is not a continuous repeat of an ordering of the four different dNTPs. This alternate flow ordering may reduce the loss of phasic synchrony in the population of template polynucleotide strands that result from IE and/or CF errors.
摘要翻译：通过使用按顺序合成技术测序多核苷酸链的方法。为了解决在逐个合成反应中可能发生的不完全扩展（IE）和/或结转（CF）错误的问题，使用了dNTP的替代流顺序。与常规流顺序相反，dNTP以不是四种不同dNTP的顺序的连续重复的顺序流动。这种交替流顺序可以减少由IE和/或CF错误导致的模板多核苷酸链群体中的相位同步损失。

8. 发明申请

WO2011102808A1 INTEGRATED MICROFLUIDIC AND SOLID STATE PYROSEQUENCING SYSTEMS 审中-公开
标题翻译：综合微流体和固体状态聚合体系
公开(公告)号：WO2011102808A1
公开(公告)日：2011-08-25
申请号：PCT/SG2011/000070
申请日：2011-02-21
申请人： AGENCY FOR SCIENCE, TECHNOLOGY AND RESEARCH , GOEL, Sanket , GONG, Min , RAHMAN, Abdur Rub Abdur , FOO, Shihui
发明人： GOEL, Sanket , GONG, Min , RAHMAN, Abdur Rub Abdur , FOO, Shihui
IPC分类号： C12Q1/68 , C12N9/12
CPC分类号： C12Q1/6869 , B01L3/502761 , B01L7/52 , B01L2200/0642 , B01L2400/0415 , B01L2400/0487 , C12Q2565/301
摘要： The invention provides for sequencing a nucleic acid molecule based on the detection of base incorporation by the release of pyrophosphate (PPi) using a new enzyme system comprising adenosine diphosphate (ADP)-glucose pyrophosphorylase (AGPase) and its substrate ADP-glucose.
摘要翻译：本发明提供了基于通过使用包含二磷酸腺苷（ADP） - 葡萄糖焦磷酸化酶（AGPase）和其底物ADP-葡萄糖的新酶系统释放焦磷酸盐（PPi）来检测碱基掺入的测序。

9. 发明申请

WO2010008480A3 METHODS AND APPARATUS FOR MEASURING ANALYTES USING LARGE SCALE FET ARRAYS 审中-公开
标题翻译：用大尺寸FET阵列测量分析物的方法和设备
公开(公告)号：WO2010008480A3
公开(公告)日：2010-06-03
申请号：PCT/US2009003766
申请日：2009-06-25
申请人： ION TORRENT SYSTEMS INC , ROTHBERG JONATHAN M , HINZ WOLFGANG , JOHNSON KIM L , BUSTILLO JAMES M , LEAMON JOHN H , SCHULTZ JONATHAN
发明人： ROTHBERG JONATHAN M , HINZ WOLFGANG , JOHNSON KIM L , BUSTILLO JAMES M , LEAMON JOHN H , SCHULTZ JONATHAN
IPC分类号： C12Q1/68 , G01N27/414
CPC分类号： C12Q1/6874 , B01L3/502761 , B01L2300/046 , B01L2300/0663 , B01L2300/0851 , B01L2400/086 , C12Q1/6869 , G01N27/4145 , G01N27/4148 , C12Q2565/607 , C12Q2565/301 , C12Q2565/629
摘要： Methods and apparatus relating to very large scale FET arrays for analyte measurements. ChemFET (e.g., ISFET) arrays may be fabricated using conventional CMOS processing techniques based on improved FET pixel and array designs that increase measurement sensitivity and accuracy, and at the same time facilitate significantly small pixel sizes and dense arrays. Improved array control techniques provide for rapid data acquisition from large and dense arrays. Such arrays may be employed to detect a presence and/or concentration changes of various analyte types in a wide variety of chemical and/or biological processes. In one example, chemFET arrays facilitate DNA sequencing techniques based on monitoring changes in the concentration of inorganic pyrophosphate (PPi), hydrogen ions, and nucleotide triphosphates.
摘要翻译：涉及用于分析物测量的超大规模FET阵列的方法和装置。可以使用基于改善的FET像素和阵列设计的常规CMOS处理技术来制造ChemFET（例如，ISFET）阵列，这些技术增加了测量灵敏度和准确度，并且同时促进了显着小的像素尺寸和密集阵列。改进的阵列控制技术可以从大型密集阵列中快速获取数据。这种阵列可用于检测各种化学和/或生物过程中各种分析物类型的存在和/或浓度变化。在一个实例中，chemFET阵列基于监测无机焦磷酸（PPi），氢离子和三磷酸核苷酸浓度的变化来促进DNA测序技术。

10. 发明申请

WO2009029728A1 ALTERNATIVE NUCLEIC ACID SEQUENCING METHODS 审中-公开
标题翻译：替代核酸序列方法
公开(公告)号：WO2009029728A1
公开(公告)日：2009-03-05
申请号：PCT/US2008/074678
申请日：2008-08-28
申请人： APPLIED BIOSYSTEMS INC. , BORTNER, Scott, R.
发明人： BORTNER, Scott, R.
IPC分类号： C07H21/00
CPC分类号： C12Q1/6874 , C12Q1/6869 , C40B20/08 , G06F19/22 , C12Q2565/301 , C12Q2537/149 , C12Q2535/101 , C12Q2565/627 , C12Q2533/107
摘要： Embodiments are provided that provide for parallel sequencing of nucleic acid segments. In some embodiments, a single sequence is sequenced by at least two different sequencing techniques and the results compared, allowing for deficiencies or strengths of one technique to be complemented by the second technique.
摘要翻译：提供了提供核酸片段的并行测序的实施方案。在一些实施方案中，通过至少两种不同的测序技术对单个序列进行测序，并且比较结果，允许通过第二种技术补充一种技术的缺陷或强度。

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