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公开(公告)号：US20050059046A1
公开(公告)日：2005-03-17
申请号：US10871081
申请日：2004-06-18
申请人： James LaBrenz , Jon Sorenson , Curtis Gehman
发明人： James LaBrenz , Jon Sorenson , Curtis Gehman
CPC分类号： G16B30/00 , G01N27/44721 , G16B40/00
摘要： Nucleic acid sequence determination is a method whereby peaks in data traces representing the detection of labeled nucleotides are classified as either noise or specific nucleotides. Embodiments are described herein that formulate this classification as a graph theory problem whereby graph edges encode peak characteristics. The graph can then be traversed to find the shortest path. Various embodiments formulate the graph in such a way as to minimize computational time. In various cases it is desirable that such classification allow for the possibility of mixed bases in the nucleotide sequence. Embodiments are described herein that address the classification of mixed-bases. Embodiments are also described that detail methods and systems for processing the data in order to make the classification step robust and reliable.
摘要翻译： 核酸序列测定是将代表标记的核苷酸检测的数据踪迹中的峰分类为噪声或特定核苷酸的方法。 本文描述了将该分类制定为图论的问题，其中图形边缘编码峰值特性。 然后可以遍历图形以找到最短路径。 各种实施例以使得计算时间最小化的方式来制定图形。 在各种情况下，希望这种分类允许在核苷酸序列中混合碱基的可能性。 本文描述了解混合基底的分类的实施例。 还描述了用于处理数据以便使分类步骤稳健和可靠的详细方法和系统的实施例。
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2.发明授权公开(公告)号：US09194772B2
公开(公告)日：2015-11-24
申请号：US12557488
申请日：2009-09-10
申请人： Linda Lee , Sam Woo , Congcong Ma , Richard Reel , Mark Oldham , David Cox , Benjamin Schroeder , Jon Sorenson , Willy Wiyatno
发明人： Linda Lee , Sam Woo , Congcong Ma , Richard Reel , Mark Oldham , David Cox , Benjamin Schroeder , Jon Sorenson , Willy Wiyatno
IPC分类号： C12Q1/68 , C12M1/34 , G01N1/14 , B01L3/00 , F15C5/00 , F16K99/00 , G01N35/08 , B01L3/02 , B01L7/00
CPC分类号： C12Q1/6869 , B01J2219/00353 , B01J2219/0036 , B01J2219/00364 , B01J2219/00608 , B01J2219/0061 , B01J2219/00612 , B01J2219/00619 , B01J2219/00626 , B01J2219/00637 , B01J2219/00653 , B01J2219/00657 , B01J2219/00659 , B01L3/0293 , B01L3/502715 , B01L3/502784 , B01L7/52 , B01L2200/0673 , B01L2200/10 , B01L2300/0864 , B01L2300/0867 , B01L2400/0421 , B01L2400/0487 , C12Q1/6806 , C12Q1/6874 , F15C5/00 , F16K99/0001 , F16K99/0011 , F16K99/0013 , F16K2099/0084 , G01N1/14 , G01N27/44743 , G01N27/44769 , G01N35/08 , Y10T137/0318 , Y10T137/4259 , Y10T137/85978 , Y10T137/85986 , Y10T137/86863 , Y10T436/2575 , C12Q2535/101
摘要： Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure.
摘要翻译： 本发明的各种实施方案涉及生物化学或分子生物学程序中用于样品制备或分析的系统或方法。 样品制备可以涉及在离散部分或段或块中的小体积处理，在本文中称为离散体积。 分子生物学程序可以是核酸分析。 核酸分析可以是一个综合的DNA扩增/ DNA测序程序。
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公开(公告)号：US20130138358A1
公开(公告)日：2013-05-30
申请号：US13468347
申请日：2012-05-10
申请人： Susan Tang , Jon Sorenson
发明人： Susan Tang , Jon Sorenson
IPC分类号： G06F19/22
CPC分类号： G16B30/00
摘要： The present invention is generally directed to powerful and flexible methods and systems for consensus sequence determination from replicate biomolecule sequence data. It is an object of the present invention to improve the accuracy of consensus biomolecule sequence determination from replicate sequence data by providing methods for assimilating replicate sequence into a final consensus sequence more accurately than any one-pass sequence analysis system.
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4.发明申请公开(公告)号：US20070141593A1
公开(公告)日：2007-06-21
申请号：US11507735
申请日：2006-08-22
申请人： Linda Lee , Sam Woo , Congcong Ma , Richard Reel , Mark Oldham , David Cox , Benjamin Schroeder , Jon Sorenson , Willy Wiyatno
发明人： Linda Lee , Sam Woo , Congcong Ma , Richard Reel , Mark Oldham , David Cox , Benjamin Schroeder , Jon Sorenson , Willy Wiyatno
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , B01J2219/00353 , B01J2219/0036 , B01J2219/00364 , B01J2219/00608 , B01J2219/0061 , B01J2219/00612 , B01J2219/00619 , B01J2219/00626 , B01J2219/00637 , B01J2219/00653 , B01J2219/00657 , B01J2219/00659 , B01L3/0293 , B01L3/502715 , B01L3/502784 , B01L7/52 , B01L2200/0673 , B01L2200/10 , B01L2300/0864 , B01L2300/0867 , B01L2400/0421 , B01L2400/0487 , C12Q1/6806 , C12Q1/6874 , C12Q2535/101 , F15C5/00 , F16K99/0001 , F16K99/0011 , F16K99/0013 , F16K2099/0084 , G01N1/14 , G01N27/44743 , G01N27/44769 , G01N35/08 , Y10T137/0318 , Y10T137/4259 , Y10T137/85978 , Y10T137/85986 , Y10T137/86863 , Y10T436/2575
摘要： Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure.
摘要翻译： 本发明的各种实施方案涉及生物化学或分子生物学程序中用于样品制备或分析的系统或方法。 样品制备可以涉及在离散部分或段或块中的小体积处理，在本文中称为离散体积。 分子生物学程序可以是核酸分析。 核酸分析可以是一个综合的DNA扩增/ DNA测序程序。
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公开(公告)号：US08383369B2
公开(公告)日：2013-02-26
申请号：US12561221
申请日：2009-09-16
申请人： Kenneth Mark Maxham , Jon Sorenson , John Eid , Patrick Marks , Kevin Travers , Donald Gray , Robin Emig , Mark Chaisson , Benjamin Flusberg
发明人： Kenneth Mark Maxham , Jon Sorenson , John Eid , Patrick Marks , Kevin Travers , Donald Gray , Robin Emig , Mark Chaisson , Benjamin Flusberg
CPC分类号： G01N21/6452 , C12Q1/6869 , G01N21/6428 , G01N2201/0635 , Y10T436/143333 , C12Q2525/119 , C12Q2521/125 , C12Q2537/149
摘要： Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
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公开(公告)号：US08143030B2
公开(公告)日：2012-03-27
申请号：US12413226
申请日：2009-03-27
申请人： Kenneth Mark Maxham , Jon Sorenson , John Eid , Patrick Marks , Kevin Travers
发明人： Kenneth Mark Maxham , Jon Sorenson , John Eid , Patrick Marks , Kevin Travers
CPC分类号： C12Q1/6869 , G01N2021/7786 , Y10T436/143333 , C12Q2525/301 , C12Q2533/101 , C12Q2537/149 , C12Q2565/631 , C12Q2525/307 , C12Q2525/191
摘要： Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
摘要翻译： 提供了在分析反应期间执行间歇检测的方法，装置和系统。 这种方法有助于从不同的反应时间收集反应数据。 此外，这样的方法可用于在给定的反应时间下降低照明分析反应中的一种或多种反应物的光致损伤。 在优选的实施方案中，将反应混合物经受至少一个照明和非照射期，并允许进行，使得反应混合物被照射的时间小于光诱导的损伤阈值期。
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公开(公告)号：US20100331194A1
公开(公告)日：2010-12-30
申请号：US12757789
申请日：2010-04-09
申请人： Stephen Turner , Benjamin Flusberg , Mathieu Foquet , Hans Callebaut , Robert Sebra , Bidhan Chaudhuri , Jon Sorenson , Keith Bjornson , Adrian Fehr , Jonas Korlach , Robin Emig
发明人： Stephen Turner , Benjamin Flusberg , Mathieu Foquet , Hans Callebaut , Robert Sebra , Bidhan Chaudhuri , Jon Sorenson , Keith Bjornson , Adrian Fehr , Jonas Korlach , Robin Emig
CPC分类号： G01N33/48721 , B82Y5/00 , B82Y15/00 , C12Q1/6869 , C12Q1/6874 , C12Q2565/631 , G01N27/447 , G01N27/44791 , C12Q2563/116 , C12Q2527/113
摘要： The invention relates to devices and methods for nanopore sequencing. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS. In some cases, the arrays of nanopores comprise resistive openings for isolating the electronic signals for improved sequencing. Methods for controlling translocation of through the nanopore are disclosed.
摘要翻译： 本发明涉及纳米孔测序的装置和方法。 本发明包括纳入电子电路的纳米孔阵列，例如在CMOS中。 在一些情况下，纳米孔阵列包括用于隔离电子信号的电阻开口以改善测序。 公开了通过纳米孔控制易位的方法。
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公开(公告)号：US20100075327A1
公开(公告)日：2010-03-25
申请号：US12561221
申请日：2009-09-16
申请人： Kenneth Mark Maxham , Jon Sorenson , John Eid , Patrick Marks , Kevin Travers , Donald Gray , Robin Emig , Mark Chaisson , Benjamin Flusberg
发明人： Kenneth Mark Maxham , Jon Sorenson , John Eid , Patrick Marks , Kevin Travers , Donald Gray , Robin Emig , Mark Chaisson , Benjamin Flusberg
CPC分类号： G01N21/6452 , C12Q1/6869 , G01N21/6428 , G01N2201/0635 , Y10T436/143333 , C12Q2525/119 , C12Q2521/125 , C12Q2537/149
摘要： Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
摘要翻译： 提供了在分析反应期间执行间歇检测的方法，装置和系统。 这种方法有助于从不同的反应时间收集反应数据。 此外，这样的方法可用于在给定的反应时间下降低照明分析反应中一种或多种反应物的光诱导损伤。 在优选的实施方案中，将反应混合物经受至少一个照明和非照射期，并允许进行，使得反应混合物被照射的时间小于光诱导的损伤阈值期。
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公开(公告)号：US09175338B2
公开(公告)日：2015-11-03
申请号：US12945767
申请日：2010-11-12
申请人： Benjamin Flusberg , Jonas Korlach , Jeffrey Wegener , Tyson A. Clark , Igor Vilfan , Andrey Kislyuk , Stephen Turner , Jon Sorenson , Kevin Travers , Cheryl Heiner , Austin B. Tomaney , Patrick Marks , Jessica Lee , Lei Jia , Dale Webster , John Lyle , Jeremiah Hanes , Joseph Puglisi
发明人： Benjamin Flusberg , Jonas Korlach , Jeffrey Wegener , Tyson A. Clark , Igor Vilfan , Andrey Kislyuk , Stephen Turner , Jon Sorenson , Kevin Travers , Cheryl Heiner , Austin B. Tomaney , Patrick Marks , Jessica Lee , Lei Jia , Dale Webster , John Lyle , Jeremiah Hanes , Joseph Puglisi
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , C12Q1/6837 , C12Q1/6858 , C12Q1/6874 , C12Q1/689 , C12Q2600/154 , C12Q2537/164 , C12Q2527/113 , C12Q2521/101 , C12Q2525/307 , C12Q2525/117
摘要： Methods, compositions, and systems are provided for characterization of modified nucleic acids. In certain preferred embodiments, single molecule sequencing methods are provided for identification of modified nucleotides within nucleic acid sequences. Modifications detectable by the methods provided herein include chemically modified bases, enzymatically modified bases, abasic sites, non-natural bases, secondary structures, and agents bound to a template nucleic acid.
摘要翻译： 提供了方法，组合物和系统用于表征修饰的核酸。 在某些优选实施方案中，提供单分子测序方法用于鉴定核酸序列内的修饰的核苷酸。 通过本文提供的方法可检测的修饰物包括化学修饰的碱基，酶修饰的碱基，脱碱基位点，非天然碱基，二级结构和与模板核酸结合的试剂。
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公开(公告)号：US08986928B2
公开(公告)日：2015-03-24
申请号：US12757789
申请日：2010-04-09
申请人： Stephen Turner , Benjamin Flusberg , Mathieu Foquet , Hans Callebaut , Robert Sebra , Bidhan Chaudhuri , Jon Sorenson , Keith Bjornson , Adrian Fehr , Jonas Korlach , Robin Emig
发明人： Stephen Turner , Benjamin Flusberg , Mathieu Foquet , Hans Callebaut , Robert Sebra , Bidhan Chaudhuri , Jon Sorenson , Keith Bjornson , Adrian Fehr , Jonas Korlach , Robin Emig
IPC分类号： C12Q1/68 , G01N27/447 , G01N33/487 , G01N33/50
CPC分类号： G01N33/48721 , B82Y5/00 , B82Y15/00 , C12Q1/6869 , C12Q1/6874 , C12Q2565/631 , G01N27/447 , G01N27/44791 , C12Q2563/116 , C12Q2527/113
摘要： The invention relates to devices and methods for nanopore sequencing. The invention includes arrays of nanopores having incorporated electronic circuits, for example, in CMOS. In some cases, the arrays of nanopores comprise resistive openings for isolating the electronic signals for improved sequencing. Methods for controlling translocation of through the nanopore are disclosed.
摘要翻译： 本发明涉及纳米孔测序的装置和方法。 本发明包括纳入电子电路的纳米孔阵列，例如在CMOS中。 在一些情况下，纳米孔阵列包括用于隔离电子信号的电阻开口以改善测序。 公开了通过纳米孔控制易位的方法。
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