公开(公告)号：US06383754B1

公开(公告)日：2002-05-07

申请号：US09637751

申请日：2000-08-11

申请人： Joseph C. Kaufman ,  Matthew E. Roth ,  Paul M. Lizardi ,  Li Feng ,  Darin R. Latimer

发明人： Joseph C. Kaufman ,  Matthew E. Roth ,  Paul M. Lizardi ,  Li Feng ,  Darin R. Latimer

IPC分类号： C12Q168

CPC分类号： C12Q1/6853 ,  A61K38/00 ,  C07K14/70578 ,  C12Q1/6809 ,  C12Q1/6837 ,  Y10T436/143333 ,  C12Q2565/513 ,  C12Q2525/191 ,  C12Q2521/313

摘要： Disclosed is a method for the comprehensive analysis of nucleic acid samples and a detector composition for use in the method. The method, referred to as Binary Encoded Sequence Tags (BEST), involves generation of a set of nucleic acid fragments; adding an adaptor to the ends containing recognition site for cleavage at a site offset from the recognition site; cleaving the fragment to generate fragments having a plurality sticky ends; indexing of the fragments into sets based on the sequence of sticky ends. The fragments are indexed by adding a offset adaptor to newly generated ends. A different adaptor will be coupled to each different sticky end. The resulting fragments—which will have defined ends, be of equal lengths (in preferred embodiment), and a central sequence derived from the source nucleic acid molecule—are binary sequence tags. The binary sequence tags can be used and further analyzed in numerous ways. For example, the binary sequence tags can be captured by hybridization and coupling, preferably by ligation, to a probe. The probe is preferably immobilized in an array or on sortable beads. One form of the BEST method, referred to as modification assisted analysis of binary sequence tags (MAABST), assesses modification of sequences in nucleic acid molecules by detecting differential cleavage based on the presence or absence of modification in the molecules.

摘要翻译： 公开了用于综合分析核酸样品的方法和用于该方法的检测器组合物。 称为二进制编码序列标签（BEST）的方法涉及产生一组核酸片段; 在包含识别位点的末端添加适配器以在与识别位点偏移的位点处切割; 切割片段以产生具有多个粘性末端的碎片; 基于粘性末端的顺序将片段索引到集合中。 通过向新生成的末尾添加偏移适配器来索引碎片。 不同的适配器将连接到每个不同的粘性端。 所得到的片段（其将具有定义的末端）具有相同的长度（在优选实施方案中），并且源自源核酸分子的中心序列是二进制序列标签。 二进制序列标签可以以多种方式使用和进一步分析。 例如，二元序列标签可以通过杂交和偶联（优选通过连接）到探针来捕获。 探针优选固定在阵列中或可排序的珠粒上。 BEST方法的一种形式，称为二元序列标签（MAABST）的修饰辅助分析，通过基于分子中存在或不存在修饰来检测差异切割来评估核酸分子中序列的修饰。

公开(公告)号：US06824981B2

公开(公告)日：2004-11-30

申请号：US09929266

申请日：2001-08-13

申请人： Brian T. Chait ,  Darin R. Latimer ,  Paul M. Lizardi ,  Eric R. Kershnar ,  Jon S. Morrow ,  Matthew E. Roth ,  Martin J. Mattessich ,  Kevin J. McConnell

发明人： Brian T. Chait ,  Darin R. Latimer ,  Paul M. Lizardi ,  Eric R. Kershnar ,  Jon S. Morrow ,  Matthew E. Roth ,  Martin J. Mattessich ,  Kevin J. McConnell

IPC分类号： C12Q168

CPC分类号： G01N33/6842 ,  C07K1/047 ,  C07K1/1077 ,  C07K1/13 ,  C07K7/06 ,  C07K7/08 ,  G01N33/6803

摘要： Disclosed are compositions and methods for sensitive detection of one or multiple analytes. In general, the methods involve the use of special label components, referred to as reporter signals, that can be associated with, incorporated into, or otherwise linked to the analytes. In some embodiments, the reporter signals can be altered such that the altered forms of different reporter signals can be distinguished from each other. In some embodiments, sets of reporter signals can be used where two or more of the reporter signals in a set have one or more common properties that allow the reporter signals having the common property to be distinguished and/or separated from other molecules lacking the common property. In other embodiments, sets of reporter signal/analyte conjugates can be used where two or more of the reporter signal/analyte conjugates in a set have one or more common properties that allow the reporter signal/analyte conjugates having the common property to be distinguished and/or separated form other molecules lacking the common property. Reporter signals can also be in conjunction with analytes (such as in mixtures of reporter signals and analytes), where no significant physical association between the reporter signals and analytes occurs; or alone, where no analyte is present.

摘要翻译： 公开了用于敏感检测一种或多种分析物的组合物和方法。 通常，这些方法涉及使用称为报告信号的特殊标记成分，其可以与分析物相关联，并入或以其它方式连接到分析物上。 在一些实施方案中，可以改变报道信号，使得不同报道信号的改变形式可以彼此区分。 在一些实施方案中，可以使用一组报告信号，其中一组中的两个或更多个报告基因信号具有一个或多个共同性质，其允许具有共同性质的报道信号被区分和/或与其他分子不相同 属性。 在其它实施方案中，可以使用组的报告信号/分析物缀合物，其中组中的两个或多个报道信号/分析物缀合物具有一个或多个共同性质，其允许区分具有共同性质的报道信号/分析物缀合物， /或分离形成其他缺乏共同性质的分子。 记者信号也可以与分析物（例如报告信号和分析物的混合物）结合，其中报告信号和分析物之间不存在明显的物理结合; 或单独存在，其中不存在分析物。

公开(公告)号：US06677121B2

公开(公告)日：2004-01-13

申请号：US09855793

申请日：2001-05-15

申请人： Paul M. Lizardi ,  Matthew E. Roth ,  Li Feng ,  Cesar E. Guerra ,  Shane C. Weber ,  Joseph C. Kaufman ,  Darin R. Latimer

发明人： Paul M. Lizardi ,  Matthew E. Roth ,  Li Feng ,  Cesar E. Guerra ,  Shane C. Weber ,  Joseph C. Kaufman ,  Darin R. Latimer

IPC分类号： C12Q168

CPC分类号： C12Q1/6855 ,  C12Q1/6809 ,  C12Q1/6837 ,  Y10S977/924 ,  C12Q2525/191 ,  C12Q2525/179 ,  C12Q2521/313 ,  C12Q2565/513

摘要： Disclosed is a method for the comprehensive analysis of nucleic acid samples and a detector composition for use in the method. The method, referred to as Fixed Address Analysis of Sequence Tags (FAAST), involves generation of a set of nucleic acid fragments having a variety of sticky end sequences; indexing of the fragments into sets based on the sequence of sticky ends; associating a detector sequence with the fragments; sequence-based capture of the indexed fragments on a detector array; and detection of the fragment labels. Generation of the multiple sticky end sequences is accomplished by incubating the nucleic acid sample with one or more nucleic acid cleaving reagents. The indexed fragments are captured by hybridization and coupling, preferably by ligation, to a probe. The method allows a complex sample of nucleic acid to be quickly and easily cataloged in a reproducible and sequence-specific manner. One form of the method allows determination of associations, in a nucleic acid molecule, of different combinations of known or potential sequences. Another form of the method assesses modification of sequences in nucleic acid molecules by basing cleavage of the molecules on the presence or absence of modification.

摘要翻译： 公开了用于综合分析核酸样品的方法和用于该方法的检测器组合物。 称为序​​列标签的固定地址分析（FAAST）的方法涉及产生具有各种粘性末端序列的一组核酸片段; 基于粘性末端的顺序将片段索引到集合中; 将检测器序列与片段相关联; 检测器阵列上索引片段的基于序列的捕获; 并检测片段标签。 通过将核酸样品与一种或多种核酸切割试剂孵育来实现多粘性末端序列的产生。 索引的片段通过杂交和偶联，优选通过连接被捕获到探针。 该方法允许复制的核酸样品以可再现和序列特异性方式快速且容易地编目。 该方法的一种形式允许确定核酸分子中已知或潜在序列的不同组合的缔合。 该方法的另一种形式通过在存在或不存在修饰的基础上分解裂解来评估核酸分子中序列的修饰。

公开(公告)号：US06261782B1

公开(公告)日：2001-07-17

申请号：US09544713

申请日：2000-04-06

申请人： Paul M. Lizardi ,  Matthew E. Roth ,  Li Feng ,  Cesar E. Guerra ,  Shane C. Weber ,  Joseph C. Kaufman ,  Darin R. Latimer

发明人： Paul M. Lizardi ,  Matthew E. Roth ,  Li Feng ,  Cesar E. Guerra ,  Shane C. Weber ,  Joseph C. Kaufman ,  Darin R. Latimer

IPC分类号： C12Q168

CPC分类号： C12Q1/6855 ,  C12Q1/6809 ,  C12Q1/6837 ,  Y10S977/924 ,  C12Q2525/191 ,  C12Q2525/179 ,  C12Q2521/313 ,  C12Q2565/513

摘要： Disclosed is a method for the comprehensive analysis of nucleic acid samples and a detector composition for use in the method. The method, referred to as Fixed Address Analysis of Sequence Tags (FAAST), involves generation of a set of nucleic acid fragments having a variety of sticky end sequences; indexing of the fragments into sets based on the sequence of sticky ends; associating a detector sequence with the fragments; sequence-based capture of the indexed fragments on a detector array; and detection of the fragment labels. Generation of the multiple sticky end sequences is accomplished by incubating the nucleic acid sample with one or more nucleic acid cleaving reagents. The indexed fragments are captured by hybridization and coupling, preferably by ligation, to a probe. The method allows a complex sample of nucleic acid to be quickly and easily cataloged in a reproducible and sequence-specific manner. One form of the method allows determination of associations, in a nucleic acid molecule, of different combinations of known or potential sequences. Another form of the method assesses modification of sequences in nucleic acid molecules by basing cleavage of the molecules on the presence or absence of modification.

摘要翻译： 公开了用于综合分析核酸样品的方法和用于该方法的检测器组合物。 称为序​​列标签的固定地址分析（FAAST）的方法涉及产生具有各种粘性末端序列的一组核酸片段; 基于粘性末端的序列将片段索引到集合中; 将检测器序列与片段相关联; 检测器阵列上索引片段的基于序列的捕获; 并检测片段标签。 通过将核酸样品与一种或多种核酸切割试剂孵育来实现多粘性末端序列的产生。 索引的片段通过杂交和偶联，优选通过连接被捕获到探针。 该方法允许复制的核酸样品以可再现和序列特异性方式快速且容易地编目。 该方法的一种形式允许确定核酸分子中已知或潜在序列的不同组合的缔合。 该方法的另一种形式通过在存在或不存在修饰的基础上分解裂解来评估核酸分子中序列的修饰。

公开(公告)号：US06773886B2

公开(公告)日：2004-08-10

申请号：US09994311

申请日：2001-11-26

申请人： Joseph C. Kaufman ,  Matthew E. Roth ,  Paul M. Lizardi ,  Li Feng ,  Darin R. Latimer

发明人： Joseph C. Kaufman ,  Matthew E. Roth ,  Paul M. Lizardi ,  Li Feng ,  Darin R. Latimer

IPC分类号： C12Q168

CPC分类号： C12Q1/6853 ,  A61K38/00 ,  C07K14/70578 ,  C12Q1/6809 ,  C12Q1/6837 ,  Y10T436/143333 ,  C12Q2565/513 ,  C12Q2525/191 ,  C12Q2521/313

摘要： Disclosed is a method for the comprehensive analysis of nucleic acid samples and a detector composition for use in the method. The method, referred to as Binary Encoded Sequence Tags (BEST), involves generation of a set of nucleic acid fragments; adding an adaptor to the ends containing recognition site for cleavage at a site offset from the recognition site; cleaving the fragment to generate fragments having a plurality sticky ends; indexing of the fragments into sets based on the sequence of sticky ends. The fragments are indexed by adding a offset adaptor to newly generated ends. A different adaptor will be coupled to each different sticky end. The resulting fragments—which will have defined ends, be of equal lengths (in preferred embodiment), and a central sequence derived from the source nucleic acid molecule—are binary sequence tags. The binary sequence tags can be used and further analyzed in numerous ways. For example, the binary sequence tags can be captured by hybridization and coupling, preferably by ligation, to a probe. The probe is preferably immobilized in an array or on sortable beads. One form of the BEST method, referred to as modification assisted analysis of binary sequence tags (MAABST), assesses modification of sequences in nucleic acid molecules by detecting differential cleavage based on the presence or absence of modification in the molecules.

摘要翻译： 公开了用于综合分析核酸样品的方法和用于该方法的检测器组合物。 称为二进制编码序列标签（BEST）的方法涉及产生一组核酸片段; 在包含识别位点的末端添加适配器以在与识别位点偏移的位点处切割; 切割片段以产生具有多个粘性末端的碎片; 基于粘性末端的顺序将片段索引到集合中。 通过向新生成的末尾添加偏移适配器来索引碎片。 不同的适配器将连接到每个不同的粘性端。 所得到的片段（其将具有定义的末端）具有相同的长度（在优选实施方案中），并且源自源核酸分子的中心序列是二进制序列标签。 二进制序列标签可以以多种方式使用和进一步分析。 例如，二元序列标签可以通过杂交和偶联（优选通过连接）到探针来捕获。 探针优选固定在阵列中或可排序的珠粒上。 BEST方法的一种形式，称为二元序列标签（MAABST）的修饰辅助分析，通过基于分子中存在或不存在修饰来检测差异切割来评估核酸分子中序列的修饰。