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    Methods of using an array of pooled probes in genetic analysis
    12.
    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：US06852490B2

    公开(公告)日：2005-02-08

    申请号：US09930536

    申请日：2001-08-14

    Applicant: Erik Gentalen ,  Mark Chee

    Inventor： Erik Gentalen ,  Mark Chee

    IPC: G01N33/53 ,  C12M1/00 ,  C12M1/34 ,  C12N15/09 ,  C12Q1/68 ,  G01N33/566 ,  G01N37/00 ,  C07H21/02 ,  C07H21/04 ,  C12P19/34

    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 provide 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。

    Nucleic acid analysis techniques
    13.
    发明授权
    Nucleic acid analysis techniques 失效
    核酸分析技术

    公开(公告)号：US06344316B1

    公开(公告)日：2002-02-05

    申请号：US08882649

    申请日：1997-06-25

    Applicant: David J. Lockhart ,  Mark Chee ,  Kevin Gunderson ,  Lai Chaoqiang ,  Lisa Wodicka ,  Maureen T. Cronin ,  Danny Lee ,  Huu M. Tran ,  Hajime Matsuzaki

    Inventor： David J. Lockhart ,  Mark Chee ,  Kevin Gunderson ,  Lai Chaoqiang ,  Lisa Wodicka ,  Maureen T. Cronin ,  Danny Lee ,  Huu M. Tran ,  Hajime Matsuzaki

    IPC: C12Q168

    CPC classification number: C07H19/052 ,  C07H19/12 ,  C07H21/00 ,  C12Q1/6809 ,  C12Q1/6837 ,  C12Q2600/156 ,  C40B40/00 ,  G06F19/20 ,  G06F19/22 ,  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
    20.
    发明授权
    Expression monitoring by hybridization to high density oligonucleotide arrays 失效
    通过与高密度寡核苷酸阵列杂交进行表达监测

    公开(公告)号：US06927032B2

    公开(公告)日：2005-08-09

    申请号：US10353792

    申请日：2003-01-28

    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: G01N33/53 ,  C12N15/09 ,  C12Q1/68 ,  G01N15/14 ,  G01N37/00 ,  C07H21/02 ,  C07H21/04 ,  C12M1/34 ,  C12P19/34

    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 探针与衍生自RNA转录物的RNA转录物或核酸互补; 并定量阵列中的杂交核酸。

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