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    Nucleic acid analysis techniques
    52.
    发明申请
    Nucleic acid analysis techniques 审中-公开
    核酸分析技术

    公开(公告)号：US20050191646A1

    公开(公告)日：2005-09-01

    申请号：US10961341

    申请日：2004-10-07

    Applicant: David Lockhart ,  Mark Chee ,  Kevin Gunderson ,  Lai Chaoqiang ,  Lisa Wodicka ,  Maureen Cronin ,  Danny Lee ,  Huu Tran ,  Hajime Matsuzaki ,  Glenn McGall ,  Anthony Barone

    Inventor： David Lockhart ,  Mark Chee ,  Kevin Gunderson ,  Lai Chaoqiang ,  Lisa Wodicka ,  Maureen Cronin ,  Danny Lee ,  Huu Tran ,  Hajime Matsuzaki ,  Glenn McGall ,  Anthony Barone

    IPC: C07B61/00 ,  C07H19/052 ,  C07H19/12 ,  C07H21/00 ,  C12Q1/00 ,  C12Q1/68

    CPC classification number: C07H19/052 ,  C07H19/12 ,  C07H21/00 ,  C12Q1/6809 ,  C12Q1/6837 ,  C12Q2600/156 ,  C40B40/00 ,  G16B25/00 ,  G16B30/00 ,  C12Q2525/161 ,  C12Q2565/501 ,  C12Q2561/125

    Abstract: The present invention provides a simplified method for identifying differences in nucleic acid abundances (e.g., expression levels) between two or more samples. The methods involve providing an array containing a large number (e.g. greater than 1,000) of arbitrarily selected different oligonucleotide probes where the sequence and location of each different probe is known. Nucleic acid samples (e.g. mRNA) from two or more samples are hybridized to the probe arrays and the pattern of hybridization is detected. Differences in the hybridization patterns between the samples indicates differences in expression of various genes between those samples. This invention also provides a method of end-labeling a nucleic acid. In one embodiment, the method involves providing a nucleic acid, providing a labeled oligonucleotide and then enzymatically ligating the oligonucleotide to the nucleic acid. Thus, for example, where the nucleic acid is an RNA, a labeled oligoribonucleotide can be ligated using an RNA ligase. In another embodiment, the end labeling can be accomplished by providing a nucleic acid, providing labeled nucleoside triphosphates, and attaching the nucleoside triphosphates to the nucleic acid using a terminal transferase.

    Abstract translation: 本发明提供用于鉴定两个或多个样品之间的核酸丰度差异（例如，表达水平）的简化方法。 所述方法包括提供包含大量（例如大于1,000个）任意选择的不同寡核苷酸探针的阵列，其中每个不同探针的序列和位置是已知的。 来自两个或更多个样品的核酸样品（例如mRNA）与探针阵列杂交，并检测杂交模式。 样本之间的杂交模式的差异表明这些样品之间各种基因的表达差异。 本发明还提供了一种终止标记核酸的方法。 在一个实施方案中，该方法包括提供核酸，提供标记的寡核苷酸，然后将寡核苷酸酶连接到核酸上。 因此，例如，当核酸是RNA时，可以使用RNA连接酶连接标记的寡核糖核苷酸。 在另一个实施方案中，末端标记可以通过提供核酸，提供标记的核苷三磷酸和使用末端转移酶将核苷三磷酸与核酸连接来实现。

    Expression monitoring by hybridization to high density oligonucleotide arrays
    53.
    发明申请
    Expression monitoring by hybridization to high density oligonucleotide arrays 审中-公开

    公开(公告)号：US20050158746A1

    公开(公告)日：2005-07-21

    申请号：US10998518

    申请日：2004-11-23

    Applicant: David Lockhart ,  Eugene Brown ,  Gordon Wong ,  Mark Chee ,  Thomas Gingeras

    Inventor： David Lockhart ,  Eugene Brown ,  Gordon Wong ,  Mark Chee ,  Thomas Gingeras

    IPC: G01N33/53 ,  C12N15/09 ,  C12Q1/68 ,  G01N15/14 ,  G01N37/00

    CPC classification number: C12Q1/6809 ,  C12Q1/6837 ,  G01N15/1475 ,  C12Q2565/507

    Abstract: This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample. In one embodiment, the method involves providing a pool of target nucleic acids comprising RNA transcripts of one or more target genes, or nucleic acids derived from the RNA transcripts, hybridizing said pool of nucleic acids to an array of oligonucleotide probes immobilized on surface, where the array comprising more than 100 different oligonucleotides and each different oligonucleotide is localized in a predetermined region of the surface, the density of the different oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and the olignucleotide probes are complementary to the RNA transcripts or nucleic acids derived from the RNA transcripts; and quantifying the hybridized nucleic acids in the array.

    Detection of nucleic acid reactions on bead arrays
    54.
    发明申请
    Detection of nucleic acid reactions on bead arrays 审中-公开
    检测珠阵列上的核酸反应

    公开(公告)号：US20050100893A1

    公开(公告)日：2005-05-12

    申请号：US10272384

    申请日：2002-10-15

    Applicant: Kevin Gunderson ,  John Stuelpnagel ,  Mark Chee

    Inventor： Kevin Gunderson ,  John Stuelpnagel ,  Mark Chee

    IPC: C12P19/34 ,  C12Q1/68

    CPC classification number: C12Q1/6874 ,  C12Q2565/537 ,  C12Q2565/518 ,  C12Q2521/501

    Abstract: The present invention is directed to methods and compositions for the use of microsphere arrays to detect and quantify a number of nucleic acid reactions. The invention finds use in genotyping, i.e. the determination of the sequence of nucleic acids, particularly alterations such as nucleotide substitutions (mismatches) and single nucleotide polymorphisms (SNPs). Similarly, the invention finds use in the detection and quantification of a nucleic acid target using a variety of amplification techniques, including both signal amplification and target amplification. The methods and compositions of the invention can be used in nucleic acid sequencing reactions as well. All applications can include the use of adapter sequences to allow for universal arrays.

    Abstract translation: 本发明涉及使用微球阵列来检测和定量许多核酸反应的方法和组合物。 本发明用于基因分型，即确定核酸序列，特别是改变，例如核苷酸取代（错配）和单核苷酸多态性（SNP）。 类似地，本发明用于使用多种扩增技术检测和定量核酸靶，包括信号放大和靶扩增两者。 本发明的方法和组合物也可用于核酸测序反应。 所有应用程序可以包括使用适配器序列来允许通用阵列。

    Methods of identifying nucleic acid probes to quantify the expression of a target nucleic acid
    55.
    发明授权
    Methods of identifying nucleic acid probes to quantify the expression of a target nucleic acid 有权
    鉴定核酸探针以量化靶核酸的表达的方法

    公开(公告)号：US06548257B2

    公开(公告)日：2003-04-15

    申请号：US09935365

    申请日：2001-08-22

    Applicant: David J. Lockhart ,  Eugene L. Brown ,  Gordon G. Wong ,  Mark Chee ,  Thomas R. Gingeras

    Inventor： David J. Lockhart ,  Eugene L. Brown ,  Gordon G. Wong ,  Mark Chee ,  Thomas R. Gingeras

    IPC: C12Q168

    CPC classification number: C12Q1/6809 ,  C12Q1/6837 ,  G01N15/1475 ,  C12Q2565/507

    Abstract: This invention provides methods of monitoring the expression levels of a multiplicity of genes. The methods involve hybridizing a nucleic acid sample to a high density array of oligonucleotide probes where the high density array contains oligonucleotide probes complementary to subsequences of target nucleic acids in the nucleic acid sample. In one embodiment, the method involves providing a pool of target nucleic acids comprising RNA transcripts of one or more target genes, or nucleic acids derived from the RNA transcripts, hybridizing said pool of nucleic acids to an array of oligonucleotide probes immobilized on surface, where the array comprising more than 100 different oligonucleotides and each different oligonucleotide is localized in a predetermined region of the surface, the density of the different oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2, and the olignucleotide probes are complementary to the RNA transcripts or nucleic acids derived from the RNA transcripts; and quantifying the hybridized nucleic acids in the array.

    Abstract translation: 本发明提供监测多种基因的表达水平的方法。 所述方法包括将核酸样品与寡核苷酸探针的高密度阵列杂交，其中高密度阵列含有与核酸样品中靶核酸的子序列互补的寡核苷酸探针。 在一个实施方案中，所述方法包括提供包含一个或多个靶基因的RNA转录物或衍生自RNA转录物的核酸的靶核酸库，将所述核酸库与固定在表面上的寡核苷酸探针阵列杂交，其中 包含超过100种不同寡核苷酸的阵列和每种不同的寡核苷酸被定位在表面的预定区域中，不同寡核苷酸的密度大于每1cm 2大约60个不同的寡核苷酸，并且寡核苷酸探针与RNA转录物互补 衍生自RNA转录物的核酸; 并定量阵列中的杂交核酸。

    Methods of using an array of pooled probes in genetic analysis
    57.
    发明授权
    Methods of using an array of pooled probes in genetic analysis 有权
    在遗传分析中使用汇集探针阵列的方法

    公开(公告)号：US08586312B2

    公开(公告)日：2013-11-19

    申请号：US12858237

    申请日：2010-08-17

    Applicant: Erik Gentalen ,  Mark Chee

    Inventor： Erik Gentalen ,  Mark Chee

    IPC: C12Q1/68 ,  C12P19/34 ,  C07H21/04

    CPC classification number: C12Q1/6837 ,  C12Q1/6827 ,  C12Q1/6874 ,  C12Q2565/543 ,  C12Q2565/513

    Abstract: The invention provides arrays of polynucleotide probes having at least one pooled position. A typical array comprises a support having at least three discrete regions. A first region bears a pool of polynucleotide probes comprising first and second probes. A second region bears the first probe without the second probe and a third region bears the second probe without the first probe. A target nucleic acid having segments complementary to both the first and second probes shows stronger normalized binding to the first region than to the aggregate of binding to the second and third regions due to cooperative binding of pooled probes in the first region. The invention provides methods of using such arrays for e.g., linkage analysis, sequence analysis, and expression monitoring.

    Abstract translation: 本发明提供具有至少一个合并位置的多核苷酸探针阵列。 典型的阵列包括具有至少三个离散区域的支撑件。 第一区域具有包含第一和第二探针的多核苷酸探针池。 第二区域承载第一探针而没有第二探针，第三区域承载第二探针而没有第一探针。 具有与第一和第二探针两者互补的区段的靶核酸由于在第一区域中的合并探针的协同结合而显示比第一区域更强的标准化结合，而不是与第二和第三区域结合的聚集体。 本发明提供了使用这种阵列进行例如连锁分析，序列分析和表达监测的方法。

    Methods of enzymatic discrimination enhancement and surface bound double-stranded DNA
    60.
    发明申请
    Methods of enzymatic discrimination enhancement and surface bound double-stranded DNA 审中-公开
    酶鉴别增强方法和表面结合双链DNA

    公开(公告)号：US20060292579A1

    公开(公告)日：2006-12-28

    申请号：US11176012

    申请日：2005-07-05

    Applicant: David Lockhart ,  Mark Chee ,  Dirk Vetter ,  Martin Digglemann

    Inventor： David Lockhart ,  Mark Chee ,  Dirk Vetter ,  Martin Digglemann

    IPC: C12Q1/68

    CPC classification number: C12N15/1093 ,  B01J19/0046 ,  B01J2219/00529 ,  B01J2219/00608 ,  B01J2219/00612 ,  B01J2219/00626 ,  B01J2219/0063 ,  B01J2219/00659 ,  B01J2219/00722 ,  C07B2200/11 ,  C07H21/00 ,  C12Q1/6827 ,  C12Q1/683 ,  C12Q1/6837 ,  C12Q1/6874 ,  C40B40/06 ,  C40B80/00 ,  G01N33/5308 ,  G01N33/551

    Abstract: Methods for discriminating between fully complementary hybrids and those that differ by one or more base pairs and libraries of unimolecular, double-stranded oligonucleotides on a solid support. In one embodiment, the present invention provides methods of using nuclease treatment to improve the quality of hybridization signals on high density oligonucleotide arrays. In another embodiment, the present invention provides methods of using ligation reactions to improve the quality of hybridization signals on high density oligonucleotide arrays. In yet another embodiment, the present invention provides libraries of unimolecular or intermolecular, double-stranded oligonucleotides on a solid support. These libraries are useful in pharmaceutical discovery for the screening of numerous biological samples for specific interactions between the double-stranded oligonucleotides, and peptides, proteins, drugs and RNA. In a related aspect, the present invention provides libraries of conformationally restricted probes on a solid support. The probes are restricted in their movement and flexibility using double-stranded oligonucleotides as scaffolding. The probes are also useful in various screening procedures associated with drug discovery and diagnosis. The present invention further provides methods for the preparation and screening of the above libraries.

    Abstract translation: 用于区分完全互补的杂交体与通过一个或多个碱基对不同的那些的方法和在固体支持物上的单分子双链寡核苷酸的文库。 在一个实施方案中，本发明提供了使用核酸酶处理来提高高密度寡核苷酸阵列上杂交信号质量的方法。 在另一个实施方案中，本发明提供了使用连接反应来提高高密度寡核苷酸阵列上杂交信号质量的方法。 在另一个实施方案中，本发明提供了在固体支持物上的单分子或分子间双链寡核苷酸的文库。 这些文库在药物发现中可用于筛选许多生物样品，用于双链寡核苷酸与肽，蛋白质，药物和RNA之间的特异性相互作用。 在相关方面，本发明提供了在固体支持物上的构象限制探针的文库。 使用双链寡核苷酸作为脚手架，探针的运动和灵活性受到限制。 探针也可用于与药物发现和诊断相关的各种筛选程序。 本发明还提供了制备和筛选上述文库的方法。

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