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1. 发明授权

US08407554B2 Method and apparatus for quantification of DNA sequencing quality and construction of a characterizable model system using Reed-Solomon codes 有权
标题翻译：用于定量DNA测序质量的方法和设备，以及使用里德 - 所罗门码的特征化模型系统的构建
公开(公告)号：US08407554B2
公开(公告)日：2013-03-26
申请号：US12697995
申请日：2010-02-01
申请人： Bahram Ghaffarzadeh Kermani , Karen W. Shannon
发明人： Bahram Ghaffarzadeh Kermani , Karen W. Shannon
IPC分类号： H03M13/03 , H03M13/15
CPC分类号： H03M13/1515 , G06F19/22
摘要： Data extracted from fluorosphore responses of fluorophore labeled bases in genetic material used in sequencing of unknown fragments from a defined set of for example a model system are converted into a class of block codes that are then employed in a computer-based process to compare and correct preliminary calls of calls of the categorically known genetic material. In a specific embodiment, the Reed-Solomon codes are employed to identify one or more errors as may occur in a finite block of codes. The methodology is also useful to identify elements of a real system containing known elements in the form of a tag. Reed-Solomon sensors may be employed with and in addition to other types of genome sensors.
摘要翻译：从用于例如模型系统的定义的组中对未知片段测序中使用的遗传物质中的荧光团标记碱基的荧光反应提取的数据被转换成一类块代码，然后将其用于基于计算机的过程中进行比较和校正对这些明确已知遗传物质的呼叫的初步呼吁。在特定实施例中，使用里德 - 所罗门码来识别可能在有限的代码块中发生的一个或多个错误。该方法对于识别包含标签形式的已知元素的真实系统的元素也是有用的。里德 - 所罗门传感器可以与其他类型的基因组传感器一起使用，也可以与其他类型的基因组传感器一起使用。

2. 发明授权

US06558908B2 Methods and kits for indirect labeling of nucleic acids 失效
公开(公告)号：US06558908B2
公开(公告)日：2003-05-06
申请号：US09861035
申请日：2001-05-18
申请人： Paul K. Wolber , Karen W. Shannon
发明人： Paul K. Wolber , Karen W. Shannon
IPC分类号： C12Q168
CPC分类号： C12Q1/6806 , C12Q1/6837 , C12Q2563/179 , C12Q2531/143 , C12Q2525/185
摘要： Methods and kits for labeling nucleic acids are provided. In the subject methods, an oligonucleotide tagged nucleic acid comprising an oligonucleotide tag is first generated. The oligonucleotide tagged nucleic acid is then contacted under hybridization conditions with a labeled oligonucleotide complementary to the oligonucleotide tag, yielding a labeled nucleic acid. The kits of the subject invention at least include a primer for use in enzymatically generating an oligonucleotide tagged target nucleic acid, where the primer generally at least includes an oligo dT region and the oligonucleotide tag, and a labeled oligonucleotide complementary to the oligonucleotide tag. The subject methods and kits find use in a variety of applications, and are particularly suited for use in gene expression analysis applications.

3. 发明授权

US06235483B1 Methods and kits for indirect labeling of nucleic acids 失效
标题翻译：间接标记核酸的方法和试剂盒
公开(公告)号：US06235483B1
公开(公告)日：2001-05-22
申请号：US09495152
申请日：2000-01-31
申请人： Paul K. Wolber , Karen W. Shannon
发明人： Paul K. Wolber , Karen W. Shannon
IPC分类号： C12Q168
CPC分类号： C12Q1/6806 , C12Q1/6837 , C12Q2563/179 , C12Q2531/143 , C12Q2525/185
摘要： Methods and kits for labeling nucleic acids are provided. In the subject methods, an oligonucleotide tagged nucleic acid comprising an oligonucleotide tag is first generated. The oligonucleotide tagged nucleic acid is then contacted under hybridization conditions with a labeled oligonucleotide complementary to the oligonucleotide tag, yielding a labeled nucleic acid. The kits of the subject invention at least include a primer for use in enzymatically generating an oligonucleotide tagged target nucleic acid, where the primer generally at least includes an oligo dT region and the oligonucleotide tag, and a labeled oligonucleotide complementary to the oligonucleotide tag. The subject methods and kits find use in a variety of applications, and are particularly suited for use in gene expression analysis applications.
摘要翻译：提供了用于标记核酸的方法和试剂盒。在本方法中，首先生成包含寡核苷酸标签的寡核苷酸标记的核酸。然后将寡核苷酸标记的核酸在杂交条件下与与寡核苷酸标签互补的标记的寡核苷酸接触，产生标记的核酸。本发明的试剂盒至少包括用于酶促产生寡核苷酸标记的靶核酸的引物，其中引物通常至少包含寡聚dT区和寡核苷酸标签，以及与寡核苷酸标签互补的标记的寡核苷酸。主题方法和试剂盒可用于各种应用，特别适用于基因表达分析应用。

4. 发明申请

US20060008836A1 Composite arrays 审中-公开
公开(公告)号：US20060008836A1
公开(公告)日：2006-01-12
申请号：US11193107
申请日：2005-07-29
申请人： Douglas A. Amorese , Karen W. Shannon , Patrick J. Collins , Paul K. Wolber
发明人： Douglas A. Amorese , Karen W. Shannon , Patrick J. Collins , Paul K. Wolber
IPC分类号： C12Q1/68 , C12M1/34
CPC分类号： B82Y30/00 , B01J19/0046 , B01J2219/00527 , B01J2219/00585 , B01J2219/00596 , B01J2219/00605 , B01J2219/00608 , B01J2219/00612 , B01J2219/00659 , B01J2219/00675 , B01J2219/00707 , C40B50/14
摘要： A polynucleotide array, and methods of making and using such arrays. The array may include a first set of multiple features each of which has first polynucleotide molecules of at least 400 nucleotides in length, and a second set of features each of which has second polynucleotide molecules of no more than 100 nucleotides in length. The second set of features can be used as control features, or to replace failed sequences in an enzymatic amplification to produce first polynucleotides, or to detect polymorphisms or splice variants which may not be detected by a particular first polynucleotide.

5. 发明授权

US06753145B2 Buffer composition and method for hybridization of microarrays on adsorbed polymer siliceous surfaces 失效
标题翻译：缓冲液组合物和微阵列在吸附聚合物硅质表面上的杂交方法
公开(公告)号：US06753145B2
公开(公告)日：2004-06-22
申请号：US09900084
申请日：2001-07-05
申请人： Nelson R. Holcomb , Patrick J. Collins , Karen W. Shannon , Steven M. Lefkowitz
发明人： Nelson R. Holcomb , Patrick J. Collins , Karen W. Shannon , Steven M. Lefkowitz
IPC分类号： C12Q168
CPC分类号： C12Q1/689
摘要： A buffer composition, method and kit for hybridizing microarrays of nucleic acids bound to an adsorbed polymer surface of a siliceous substrate provide an envelope of conditions to hybridize nucleic acid targets, while preserving theintactness of the adsorbed polymer surface of the array. The buffer composition comprises a non-chelating buffering agent, a pH within a range of pH 6.4 and 7.5, a monovalent cation having a monovalent cation concentration that ranges from about 0.01 M to about 2.0 M, and optionally relatively lower concentrations of a chelating agent and an ionic surfactant. The total cation concentration of the buffer composition ranges from about 0.02 M to about 2.0 M. The method comprises incubating the targets with the microarray in the buffer composition at a temperature between about 55° C. and 70° C.
摘要翻译：用于杂交与硅质底物的吸附的聚合物表面结合的核酸的微阵列的缓冲组合物，方法和试剂盒提供了与核酸靶标杂交的条件的包络线，同时保持阵列的吸附的聚合物表面的活性。缓冲剂组合物包含非螯合缓冲剂，pH在6.4和7.5范围内的pH，一价阳离子浓度范围为约0.01M至约2.0M，任选相对较低浓度的螯合剂和离子表面活性剂。缓冲剂组合物的总阳离子浓度范围为约0.02M至约2.0M。该方法包括在约55℃至70℃的温度下将靶标与缓冲液组合物中的微阵列温育。

6. 发明授权

US5710029A Methods for determining pre-amplification levels of a nucleic acid target sequence from post-amplification levels of product 失效
标题翻译：从产物的扩增后水平确定核酸靶序列的预扩增水平的方法
公开(公告)号：US5710029A
公开(公告)日：1998-01-20
申请号：US486705
申请日：1995-06-07
申请人： Thomas Brendan Ryder , Karen W. Shannon , Daniel Louis Kacian , Richard C. Harvey , Sherrol H. McDonough , Frank R. Gonzales , Maria R. Castillo , Elizabeth R. Billyard , Nancy Lau Liu Shen
发明人： Thomas Brendan Ryder , Karen W. Shannon , Daniel Louis Kacian , Richard C. Harvey , Sherrol H. McDonough , Frank R. Gonzales , Maria R. Castillo , Elizabeth R. Billyard , Nancy Lau Liu Shen
IPC分类号： C12Q1/68 , C07H19/00 , C07H21/02 , C12P19/34
CPC分类号： C12Q1/6851 , C12Q1/6865
摘要： Methods and kits for relating initial amounts of target nucleic acids present in a sample to target-specific amplification products. It has been discovered that the transcription-mediated amplification system is capable of producing a quantitative relationship between target input and target-specific output. Further, the present invention relates to methods for carefully controlling this relationship resulting in an unexpectedly high degree of reproducability. Also described are useful methods for extending the dynamic range of transcription-based amplification systems.
摘要翻译：用于将样品中存在的目标核酸的初始量与靶特异性扩增产物相关联的方法和试剂盒。已经发现，转录介导的扩增系统能够产生目标输入和目标特异性输出之间的定量关系。此外，本发明涉及仔细控制这种关系的方法，导致意想不到的高再现性。还描述了扩展基于转录的扩增系统的动态范围的有用方法。

7. 发明授权

US07029854B2 Methods designing multiple mRNA transcript nucleic acid probe sequences for use in nucleic acid arrays 失效
标题翻译：设计用于核酸阵列的多个mRNA转录核酸探针序列的方法
公开(公告)号：US07029854B2
公开(公告)日：2006-04-18
申请号：US10303151
申请日：2002-11-22
申请人： Patrick J. Collins , Keith C. Butler , Peter G. Webb , Karen W. Shannon , Sandra L. Tang
发明人： Patrick J. Collins , Keith C. Butler , Peter G. Webb , Karen W. Shannon , Sandra L. Tang
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6876 , G06F19/22
摘要： Methods of identifying a sequence of a nucleic acid that is suitable for use as a surface immobilized probe for two or more mRNA transcripts encoded by the same gene are provided. In practicing the subject methods, a consensus region for the two or more transcripts is first identified, and this identified consensus region is then employed to identify the suitable nucleic acid sequence, e.g., by using a probe design protocol. The subject invention also includes algorithms for performing the subject methods recorded on a computer readable medium, as well as computational analysis systems that include the same. Also provided are nucleic acid arrays produced with probes having sequences identified by the subject methods, as well as methods for using the same.
摘要翻译：提供了鉴定适合用作由相同基因编码的两个或更多个mRNA转录物的表面固定化探针的核酸序列的方法。在实施本发明方法时，首先鉴定两个或多个转录物的共有区域，然后使用该鉴定的共有区域来鉴定合适的核酸序列，例如通过使用探针设计方案。本发明还包括用于执行记录在计算机可读介质上的主题方法的算法，以及包括其的计算分析系统。还提供了由具有由本发明方法鉴定的序列的探针产生的核酸阵列，以及使用该序列的方法。

8. 发明授权

US06251588B1 Method for evaluating oligonucleotide probe sequences 失效
标题翻译：评价寡核苷酸探针序列的方法
公开(公告)号：US06251588B1
公开(公告)日：2001-06-26
申请号：US09021701
申请日：1998-02-10
申请人： Karen W. Shannon , Paul K. Wolber , Glenda C. Delenstarr , Peter G. Webb , Robert H. Kincaid
发明人： Karen W. Shannon , Paul K. Wolber , Glenda C. Delenstarr , Peter G. Webb , Robert H. Kincaid
IPC分类号： C12Q168
CPC分类号： G06F19/20 , G06F19/24
摘要： Methods are disclosed for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined number of unique oligonucleotides is identified. The unique oligonucleotides are chosen to sample the entire length of a nucleotide sequence that is hybridizable with the target nucleotide sequence. At least one parameter that is independently predictive of the ability of each of the oligonucleotides of the set to hybridize to the target nucleotide sequence is determined and evaluated for each of the above oligonucleotides. A subset of oligonucleotides within the predetermined number of unique oligonucleotides is identified based on the evaluation of the parameter. Oligonucleotides in the subset are identified that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence. The method may be carried out with the aid of a computer.
摘要翻译：公开了用于预测寡核苷酸与靶核苷酸序列杂交的潜力的方法。鉴定出预定数量的唯一寡核苷酸。选择独特的寡核苷酸来对可与靶核苷酸序列杂交的核苷酸序列的整个长度进行采样。确定并评估每种上述寡核苷酸的至少一个独立地预测该组寡核苷酸与靶核苷酸序列杂交的能力的参数。基于参数的评估来鉴定预定数量的唯一寡核苷酸内的寡核苷酸的子集。鉴定了亚群中的寡核苷酸，其沿着与靶核苷酸序列可杂交的核苷酸序列的区域聚集。该方法可以借助于计算机进行。

9. 发明授权

US6132997A Method for linear mRNA amplification 有权
标题翻译：线性mRNA扩增方法
公开(公告)号：US6132997A
公开(公告)日：2000-10-17
申请号：US322692
申请日：1999-05-28
申请人： Karen W. Shannon
发明人： Karen W. Shannon
IPC分类号： C12N15/10 , C12Q1/68 , C12P19/34
CPC分类号： C12N15/1096 , C12Q1/6806 , C12Q1/6865 , C12Q2600/158
摘要： Methods for linearly amplifying mRNA to produce antisense RNA are provided. In the subject methods, mRNA is converted to double-stranded cDNA using a promoter-primer having a poly-dT primer site linked to a promoter sequence so that the resulting double-stranded cDNA is recognized by an RNA polymerase. The resultant double-stranded cDNA is then transcribed into antisense RNA in the presence of a reverse transcriptase that is rendered incapable of RNA-dependent DNA polymerase activity during this transcription step. The subject methods find use a variety of different applications in which the preparation of linearly amplified amounts of antisense RNA is desired. Also provided are kits for practicing the subject methods.
摘要翻译：提供了线性扩增mRNA以产生反义RNA的方法。在本发明方法中，使用具有与启动子序列连接的poly-dT引物位点的启动子 - 引物将mRNA转化为双链cDNA，从而得到的双链cDNA被RNA聚合酶识别。然后，在逆转录酶存在下，将所得的双链cDNA转录成反义RNA，所述逆转录酶在该转录步骤中不能使其与RNA依赖性DNA聚合酶活性无关。本发明方法发现使用各种不同的应用，其中需要线性扩增量的反义RNA的制备。还提供了用于实践主题方法的工具包。

10. 发明授权

US07927838B2 Method for linear mRNA amplification 有权
标题翻译：线性mRNA扩增方法
公开(公告)号：US07927838B2
公开(公告)日：2011-04-19
申请号：US11179813
申请日：2005-07-11
申请人： Karen W. Shannon
发明人： Karen W. Shannon
IPC分类号： C12Q1/68 , C12P19/34 , C07H21/04
CPC分类号： C12N15/1096 , C12Q1/6806 , C12Q1/6865 , C12Q2600/158 , C12Q2525/173 , C12Q2525/143 , C12Q2521/119 , C12Q2521/107
摘要： Methods for linearly amplifying mRNA to produce antisense RNA are provided. In the subject methods, mRNA is converted to double-stranded cDNA using a promoter-primer having a poly-dT primer site linked to a promoter sequence so that the resulting double-stranded cDNA is recognized by an RNA polymerase. The resultant double-stranded cDNA is then transcribed into antisense RNA in the presence of a reverse transcriptase that is rendered incapable of RNA-dependent DNA polymerase activity during this transcription step. The subject methods find use a variety of different applications in which the preparation of linearly amplified amounts of antisense RNA is desired. Also provided are kits for practicing the subject methods.
摘要翻译：提供了线性扩增mRNA以产生反义RNA的方法。在本发明方法中，使用具有与启动子序列连接的poly-dT引物位点的启动子 - 引物将mRNA转化为双链cDNA，从而得到的双链cDNA被RNA聚合酶识别。然后，在逆转录酶存在下，将所得的双链cDNA转录成反义RNA，所述逆转录酶在该转录步骤中不能使其与RNA依赖性DNA聚合酶活性无关。本发明方法发现使用各种不同的应用，其中需要线性扩增量的反义RNA的制备。还提供了用于实践主题方法的工具包。

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