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1. 发明授权

US06897023B2 Method for determining relative abundance of nucleic acid sequences 失效
标题翻译：确定核酸序列相对丰度的方法
公开(公告)号：US06897023B2
公开(公告)日：2005-05-24
申请号：US09967238
申请日：2001-09-27
申请人： Rongdian Fu , Sydney Brenner , Glenn Albrecht
发明人： Rongdian Fu , Sydney Brenner , Glenn Albrecht
IPC分类号： C07H21/00 , C07H21/02 , C07H21/04 , C12N15/10 , C12P19/34 , C12Q1/68
CPC分类号： C12Q1/6809 , C12Q2545/114 , C12Q2563/179 , C12Q2565/626
摘要： Disclosed are methods for identifying nucleic acid sequences which are of different abundances in different nucleic acid source populations, e.g. differentially expressed genes or genomic variations among individuals or populations of individuals. In one embodiment, probes derived from the source nucleic acid populations are derivatized with a terminal sample ID (SID) sequence characteristic of that population. Upon competitive hybridization of the probes to a reference or index nucleic acid library containing all the sequences in the populations being compared, the SID tags remain single stranded, and those from the different sources are then annealed to one another. Unhybridized (remainder) SID sequences are then quantified. By labeling such remainder SID sequences with a fluorescent dye, FACS sorting of beads containing the hybridized probes can be carried out. The signal ratio upon which such sorting is based is enhanced compared to competitive hybridization using labeled probes without SID sequences.
摘要翻译：公开了用于鉴定在不同核酸源群体中具有不同丰度的核酸序列的方法，例如，差异表达基因或个体个体或个体群体的基因组变异。在一个实施方案中，衍生自源核酸群体的探针用该群体特征的终端样品ID（SID）序列衍生化。当探针与包含正在比较的群体中的所有序列的参考或指数核酸文库竞争性杂交时，SID标签保持单链，然后来自不同来源的那些序列彼此退火。然后对未杂交（其余）SID序列进行定量。通过用荧光染料标记这些剩余的SID序列，可以进行含有杂交探针的珠的FACS分选。与使用没有SID序列的标记探针的竞争性杂交相比，这种分选所基于的信号比率增加。

2. 发明授权

US06175002B1 Adaptor-based sequence analysis 有权
标题翻译：基于适配器的序列分析
公开(公告)号：US06175002B1
公开(公告)日：2001-01-16
申请号：US09225652
申请日：1999-01-05
申请人： Robert B. DuBridge , Glenn Albrecht , Sydney Brenner , Sergei M. Gryaznov , Sarah N. McCurdy
发明人： Robert B. DuBridge , Glenn Albrecht , Sydney Brenner , Sergei M. Gryaznov , Sarah N. McCurdy
IPC分类号： C07H2100
CPC分类号： C12Q1/6869 , C12Q2525/15 , C12Q2521/525 , C12Q2525/191
摘要： An improvement in adaptor-based sequence analysis is provided that addresses the problems created by self-ligation of target polynucleotides that have complementary ends. The improvement includes preparation of target polynucleotides with dephosphorylated 5′ strands and the use of adaptors having a 3′ blocking group. In a preferred embodiment, adaptors are ligated to target polynucleotides by a single strand, 3′ blocking groups are removed, the adjacent 5′ hydroxyl of the target polynucleotide is phosphorylated, and the ligation of the adaptor is completed by treatment with a ligase.
摘要翻译：提供了基于衔接子的序列分析的改进，其解决了具有互补末端的靶多核苷酸的自连接产生的问题。改进包括制备具有脱磷酸化的5'链的靶多核苷酸，以及使用具有3'阻断基团的衔接子。在优选的实施方案中，衔接子通过单链连接到靶多核苷酸，除去3'阻断基团，靶多核苷酸的相邻5'羟基被磷酸化，并且衔接子的连接通过用连接酶处理完成。

3. 发明授权

US06511802B1 Solid phase selection of differentially expressed genes 有权
标题翻译：差异表达基因的固相选择
公开(公告)号：US06511802B1
公开(公告)日：2003-01-28
申请号：US09227694
申请日：1999-01-08
申请人： Glenn Albrecht , Sydney Brenner , Robert B. DuBridge
发明人： Glenn Albrecht , Sydney Brenner , Robert B. DuBridge
IPC分类号： C12Q168
CPC分类号： C12Q1/6834 , C12N15/1096 , C12Q1/6809 , C12Q2565/518 , C12Q2521/313 , C12Q2525/191
摘要： The invention provides a method and materials for monitoring and isolating differentially expressed genes. In accordance with the method of the invention, differently labeled populations of DNAs from sources to be compared are competitively hybridized with reference DNA cloned on solid phase supports, e.g. microparticles, to provide a differential expression library which, in the preferred embodiment, may be manipulated by fluorescence-activated cell sorting (FACS). Monitoring the relative signal intensity of the different fluorescent labels on the microparticles permits quantitative analysis of expression levels relative to the reference DNA. The invention also provides a method for identifying and isolating rare genes. Populations of microparticles having relative signal intensities of interest can be isolated by FACS and the attached DNAs identified by sequencing, such as with massively parallel signature sequencing (MPSS), or with conventional DNA sequencing protocols.
摘要翻译：本发明提供了用于监测和分离差异表达基因的方法和材料。根据本发明的方法，来自待比较来源的不同标记的DNA群体与克隆在固相载体上的参考DNA竞争性杂交，例如，微粒，以提供在优选实施方案中可以通过荧光激活细胞分选（FACS）操纵的差异表达文库。监测微粒上不同荧光标记的相对信号强度允许相对于参照DNA的表达水平进行定量分析。本发明还提供了鉴定和分离稀有基因的方法。具有感兴趣的相对信号强度的微粒的群体可以通过FACS和通过测序鉴定的所连接的DNA进行分离，例如通过大规模并行签名测序（MPSS）或常规DNA测序方案。

4. 再颁专利

USRE43097E1 Massively parallel signature sequencing by ligation of encoded adaptors 有权
标题翻译：通过编码适配器的连接进行大规模并行签名排序
公开(公告)号：USRE43097E1
公开(公告)日：2012-01-10
申请号：US12782008
申请日：2010-05-18
申请人： Glenn Albrecht , Sydney Brenner , Robert B. DuBridge , David H. Lloyd , Michael C. Pallas
发明人： Glenn Albrecht , Sydney Brenner , Robert B. DuBridge , David H. Lloyd , Michael C. Pallas
IPC分类号： C12Q1/68 , C07H21/02
CPC分类号： C12Q1/6869 , C12Q1/6837 , C12Q2525/191 , C12Q2563/149 , C12Q2563/179
摘要： The invention provides a method of nucleic acid sequence analysis based on the ligation of one or more sets of encoded adaptors to the terminus of a target polynucleotide. Encoded adaptors whose protruding strands form perfectly matched duplexes with the complementary protruding strands of the target polynucleotide are ligated, and the identity of the nucleotides in the protruding strands is determined by an oligonucleotide tag carried by the encoded adaptor. Such determination, or “decoding” is carried out by specifically hybridizing a labeled tag complement to its corresponding tag on the ligated adaptor.
摘要翻译：本发明提供了基于将一组或多组编码衔接子连接到靶多核苷酸末端的核酸序列分析方法。将其突出的链与靶多核苷酸的互补突出链形成完全匹配的双链体的编码适配子连接，突出的链中的核苷酸的身份由编码的适配器携带的寡核苷酸标签确定。这样的确定或“解码”是通过将标记的标签补体与连接的适配器上的相应标签进行特异性杂交来进行的。

5. 发明授权

US06265163B1 Solid phase selection of differentially expressed genes 有权
标题翻译：差异表达基因的固相选择
公开(公告)号：US06265163B1
公开(公告)日：2001-07-24
申请号：US09130546
申请日：1998-08-06
申请人： Glenn Albrecht , Sydney Brenner , Robert B. DuBridge
发明人： Glenn Albrecht , Sydney Brenner , Robert B. DuBridge
IPC分类号： C12Q168
CPC分类号： C12Q1/6834 , C12N15/1096 , C12Q1/6809 , C12Q2565/518 , C12Q2521/313 , C12Q2525/191
摘要： The invention provides a method and materials for monitoring and isolating differentially expressed genes. In accordance with the method of the invention, differently labeled populations of DNAs from sources to be compared are competitively hybridized with reference DNA cloned on solid phase supports, e.g. microparticles, to provide a differential expression library which, in the preferred embodiment, may be manipulated by fluorescence-activated cell sorting (FACS). Monitoring the relative signal intensity of the different fluoresent labels on the microparticles permits quantitative analysis of expression levels relative to the reference DNA. Populations of microparticles having relative signal intensities of interest can be isolated by FACS and the attached DNAs identified by sequencing, such as with massively parallel signature sequencing (MPSS), or with conventional DNA sequencing protocols.
摘要翻译：本发明提供了用于监测和分离差异表达基因的方法和材料。根据本发明的方法，来自待比较来源的不同标记的DNA群体与克隆在固相载体上的参考DNA竞争性杂交，例如，微粒，以提供在优选实施方案中可以通过荧光激活细胞分选（FACS）操纵的差异表达文库。监测微粒上不同荧光标记的相对信号强度允许相对于参照DNA的表达水平进行定量分析。具有感兴趣的相对信号强度的微粒的群体可以通过FACS和通过测序鉴定的所连接的DNA进行分离，例如通过大规模并行签名测序（MPSS）或常规DNA测序方案。

6. 发明授权

US5888737A Adaptor-based sequence analysis 失效
标题翻译：基于适配器的序列分析
公开(公告)号：US5888737A
公开(公告)日：1999-03-30
申请号：US842608
申请日：1997-04-15
申请人： Robert B. DuBridge , Glenn Albrecht , Sydney Brenner , Sergei M. Gryaznov , Sarah N. McCurdy
发明人： Robert B. DuBridge , Glenn Albrecht , Sydney Brenner , Sergei M. Gryaznov , Sarah N. McCurdy
IPC分类号： C12N15/09 , C12Q1/68
CPC分类号： C12Q1/6869
摘要： An improvement in adaptor-based sequence analysis is provided that addresses the problems created by self-ligation of target polynucleotides that have complementary ends. The improvement includes preparation of target polynucleotides with dephosphorylated 5' strands and the use of adaptors having a 3' blocking group. In a preferred embodiment, adaptors are ligated to target polynucleotides by a single strand, 3' blocking groups are removed, the adjacent 5' hydroxyl of the target polynucleotide is phosphorylated, and the ligation of the adaptor is completed by treatment with a ligase.
摘要翻译：提供了基于衔接子的序列分析的改进，其解决了具有互补末端的靶多核苷酸的自连接产生的问题。改进包括制备具有脱磷酸化的5'链的靶多核苷酸，以及使用具有3'阻断基团的衔接子。在优选的实施方案中，衔接子通过单链连接到靶多核苷酸，除去3'阻断基团，靶多核苷酸的相邻5'羟基被磷酸化，并且衔接子的连接通过用连接酶处理完成。

7. 发明授权

US5846719A Oligonucleotide tags for sorting and identification 失效
公开(公告)号：US5846719A
公开(公告)日：1998-12-08
申请号：US659453
申请日：1996-06-06
申请人： Sydney Brenner , Glenn Albrecht , Stephen C. Macevicz
发明人： Sydney Brenner , Glenn Albrecht , Stephen C. Macevicz
IPC分类号： G01N33/53 , A61K49/00 , B01J19/00 , C07H21/00 , C12N15/09 , C12N15/10 , C12Q1/68 , C40B40/06 , C40B70/00 , G01N33/566 , G01N37/00 , C07H21/04
CPC分类号： B01J19/0046 , C12N15/10 , C12N15/1034 , C12N15/1065 , C12Q1/6809 , C12Q1/6827 , C12Q1/6837 , C12Q1/6839 , C12Q1/6855 , C12Q1/6874 , C40B80/00 , B01J2219/005 , B01J2219/00572 , B01J2219/00605 , B01J2219/00612 , B01J2219/00626 , B01J2219/00648 , B01J2219/00659 , B01J2219/00722 , C40B40/06 , C40B70/00
摘要： The invention provides a method of tracking, identifying, and/or sorting classes or subpopulations of molecules by the use of oligonucleotide tags. Oligonucleotide tags of the invention comprise oligonucleotides selected from a minimally cross-hybridizing set. Preferably, such oligonucleotides each consist of a plurality of subunits 3 to 9 nucleotides in length. A subunit of a minimally cross-hybridizing set forms a duplex or triplex having two or more mismatches with the complement of any other subunit of the same set. The number of oligonucleotide tags available in a particular embodiment depends on the number of subunits per tag and on the length of the subunit. An important aspect of the invention is the use of the oligonucleotide tags for sorting polynucleotides by specifically hybridizing tags attached to the polynucleotides to their complements on solid phase supports. This embodiment provides a readily automated system for manipulating and sorting polynucleotides, particularly useful in large-scale parallel operations, such as large-scale DNA sequencing, mRNA fingerprinting, and the like, wherein many target polynucleotides or many segments of a single target polynucleotide are sequenced simultaneously.

8. 发明授权

US6150516A Kits for sorting and identifying polynucleotides 有权
标题翻译：用于分选和鉴定多核苷酸的试剂盒
公开(公告)号：US6150516A
公开(公告)日：2000-11-21
申请号：US196543
申请日：1998-11-20
申请人： Sydney Brenner , Glenn Albrecht , Stephen C. Macevicz
发明人： Sydney Brenner , Glenn Albrecht , Stephen C. Macevicz
IPC分类号： G01N33/53 , A61K49/00 , B01J19/00 , C07H21/00 , C12N15/09 , C12N15/10 , C12Q1/68 , C40B40/06 , C40B70/00 , G01N33/566 , G01N37/00 , C07H21/04 , C12N15/00 , C12N15/11 , C12N15/63
CPC分类号： B01J19/0046 , C12N15/10 , C12N15/1034 , C12N15/1065 , C12Q1/6809 , C12Q1/6827 , C12Q1/6837 , C12Q1/6839 , C12Q1/6855 , C12Q1/6874 , C40B80/00 , B01J2219/005 , B01J2219/00572 , B01J2219/00605 , B01J2219/00612 , B01J2219/00626 , B01J2219/00648 , B01J2219/00659 , B01J2219/00722 , C40B40/06 , C40B70/00
摘要： The invention provides a method of tracking, identifying, and/or sorting classes or subpopulations of molecules by the use of oligonucleotide tags. Oligonucleotide tags of the invention comprise oligonucleotides selected from a minimally cross-hybridizing set. Preferably, such oligonucleotides each consist of a plurality of subunits 3 to 9 nucleotides in length. A subunit of a minimally cross-hybridizing set forms a duplex or triplex having two or more mismatches with the complement of any other subunit of the same set. The number of oligonucleotide tags available in a particular embodiment depends on the number of subunits per tag and on the length of the subunit.An important aspect of the invention is the use of the oligonucleotide tags for sorting polynucleotides by specifically hybridizing tags attached to the polynucleotides to their complements on solid phase supports. This embodiment provides a readily automated system for manipulating and sorting polynucleotides, particularly useful in large-scale parallel operations, such as large-scale DNA sequencing, mRNA fingerprinting, and the like, wherein many target polynucleotides or many segments of a single target polynucleotide are sequenced simultaneously.
摘要翻译：本发明提供了通过使用寡核苷酸标签来跟踪，鉴定和/或分类分子的分类或亚群的方法。本发明的寡核苷酸标签包含选自最小交叉杂交组的寡核苷酸。优选地，这样的寡核苷酸每个由多个长度为3至9个核苷酸的亚单位组成。最小交叉杂交组的亚基形成具有两个或更多个错配的双链体或三链体，同一组的任何其他亚基的互补体。在特定实施方案中可用的寡核苷酸标签的数量取决于每个标签的亚单位的数目和子单元的长度。本发明的一个重要方面是使用寡核苷酸标签通过将与多核苷酸连接的标签与其固相载体上的互补序列特异性杂交来分选多核苷酸。该实施方案提供了用于操纵和分选多核苷酸的容易自动化系统，特别可用于大规模并行操作，例如大规模DNA测序，mRNA指纹图谱等，其中单个靶多核苷酸的许多靶多核苷酸或多个片段是同时排序。

9. 发明授权

US6013445A Massively parallel signature sequencing by ligation of encoded adaptors 失效
标题翻译：通过编码适配器的连接进行大规模并行签名排序
公开(公告)号：US6013445A
公开(公告)日：2000-01-11
申请号：US946138
申请日：1997-10-07
申请人： Glenn Albrecht , Sydney Brenner , Robert B. DuBridge , David H. Lloyd , Michael C. Pallas
发明人： Glenn Albrecht , Sydney Brenner , Robert B. DuBridge , David H. Lloyd , Michael C. Pallas
IPC分类号： B01J19/00 , C12Q1/68 , C40B60/14 , G01N15/14 , C07H21/02
CPC分类号： C12Q1/6827 , B01J19/0046 , C12Q1/6809 , C12Q1/6874 , G01N15/1456 , G01N15/1484 , B01J2219/00317 , B01J2219/00648 , B01J2219/00659 , C40B60/14 , G01N2015/149
摘要： The invention provides a method of nucleic acid sequence analysis based on the ligation of one or more sets of encoded adaptors to the terminus of a target polynucleotide. Encoded adaptors whose protruding strands form perfectly matched duplexes with the complementary protruding strands of the target polynucleotide are ligated, and the identity of the nucleotides in the protruding strands is determined by an oligonucleotide tag carried by the encoded adaptor. Such determination, or "decoding" is carried out by specifically hybridizing a labeled tag complement to its corresponding tag on the ligated adaptor.
摘要翻译：本发明提供了基于将一组或多组编码衔接子连接到靶多核苷酸末端的核酸序列分析方法。将其突出的链与靶多核苷酸的互补突出链形成完全匹配的双链体的编码适配子连接，突出的链中的核苷酸的身份由编码的适配器携带的寡核苷酸标签确定。这样的确定或“解码”是通过将标记的标签补体与连接的适配器上的相应标签进行特异性杂交来进行的。

10. 发明授权

US06235475B1 Oligonucleotide tags for sorting and identification 有权
标题翻译：用于分类和鉴定的寡核苷酸标签
公开(公告)号：US06235475B1
公开(公告)日：2001-05-22
申请号：US09130862
申请日：1998-08-07
申请人： Sydney Brenner , Glenn Albrecht , Stephen C. Macevicz
发明人： Sydney Brenner , Glenn Albrecht , Stephen C. Macevicz
IPC分类号： C12Q168
CPC分类号： B01J19/0046 , B01J2219/005 , B01J2219/00572 , B01J2219/00605 , B01J2219/00612 , B01J2219/00626 , B01J2219/00648 , B01J2219/00659 , B01J2219/00722 , C12N15/10 , C12N15/1034 , C12N15/1065 , C12Q1/6809 , C12Q1/6827 , C12Q1/6837 , C12Q1/6839 , C12Q1/6855 , C12Q1/6874 , C40B40/06 , C40B70/00 , C40B80/00 , C12Q2525/191 , C12Q2565/519 , C12Q2521/501 , C12Q2565/518 , C12Q2563/107 , C12Q2563/185 , C12Q2565/501 , C12Q2525/161 , C12Q2521/313 , C12Q2525/204
摘要： The invention provides a method of tracking, identifying, and/or sorting classes or subpopulations of molecules by the use of oligonucleotide tags. Oligonucleotide tags of the invention comprise oligonucleotides selected from a minimally cross-hybridizing set. Preferably, such oligonucleotides each consist of a plurality of subunits 3 to 9 nucleotides in length. A subunit of a minimally cross-hybridizing set forms a duplex or triplex having two or more mismatches with the complement of any other subunit of the same set The number of oligonucleotide tags available in a particular embodiment depends on the number of subunits per tag and on the length of the subunit. An important aspect of the invention is the use of the oligonucleotide tags for sorting polynucleotides by specifically hybridizing tags attached to the polynucleotides to their complements on solid phase supports. This embodiment provides a readily automated system for manipulating and sorting polynucleotides, particularly useful in large-scale parallel operations, such as large-scale DNA sequencing, mRNA fingerprinting, and the like, wherein many target polynucleotides or many segments of a single target polynucleotide are sequenced simultaneously.
摘要翻译：本发明提供了通过使用寡核苷酸标签来跟踪，鉴定和/或分类分子的分类或亚群的方法。本发明的寡核苷酸标签包含选自最小交叉杂交组的寡核苷酸。优选地，这样的寡核苷酸每个由多个长度为3至9个核苷酸的亚单位组成。最小交叉杂交组的亚基形成具有两个或更多个错配的双链或三链，其具有相同组的任何其他亚基的互补。特定实施方案中可用的寡核苷酸标签的数量取决于每个标签的亚单位的数量，亚单位的长度。本发明的一个重要方面是使用寡核苷酸标签通过将与多核苷酸连接的标签与其固相载体上的互补序列特异性杂交来分选多核苷酸。该实施方案提供了用于操纵和分选多核苷酸的容易自动化系统，特别可用于大规模并行操作，例如大规模DNA测序，mRNA指纹图谱等，其中单个靶多核苷酸的许多靶多核苷酸或多个片段是同时排序。

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