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    GENE EXPRESSION PANEL FOR PROGNOSIS OF PROSTATE CANCER RECURRENCE
    4.
    发明申请
    GENE EXPRESSION PANEL FOR PROGNOSIS OF PROSTATE CANCER RECURRENCE 审中-公开
    用于预防癌症复发的基因表达板

    公开(公告)号：US20160333420A1

    公开(公告)日：2016-11-17

    申请号：US15111946

    申请日：2015-01-16

    Applicant: ILLUMINA, INC. ,  UNIVERSITY OF SOUTHERN CALIFORNIA

    Inventor： Mariana Carla Stern ,  Jacek Pinski ,  Jian-Bing Fan

    IPC: C12Q1/68

    CPC classification number: C12Q1/6886 ,  C12Q2600/118 ,  C12Q2600/158

    Abstract: Disclosed is a gene expression panel that can be used to predict prostate cancer (PCa) progression. Some embodiments provide methods for predicting clinical recurrence of PCa. Some embodiments provide a method for predicting progression of prostate cancer in an individual, the method comprising: (a) receiving expression levels of a collection of signature genes from a biological sample taken from said individual, wherein said collection of signature genes comprises at least two genes selected from the group consisting of: NKX2-1, UPK1A, ADRA2C, ABCC11, MMP11, CPVL, ZYG11A, CLEC4F, OAS2, PGC, UPK3B, PCBP3, ABLIM1, EDARADD, GPR81, MYBPC1, F10, KCNA3, GLDC, KCNQ2, RAPGEF1, TUBB2B, MB, DUOXA1, C2orf43, DUOX1, PCA3 and NPR3; (b) applying the expression levels to a predictive model relating expression levels of said collection of signature genes with prostate cancer progression; and (c) evaluating an output of said predictive model to predict progression of prostate cancer in said individual. Systems are also provided for predicting progression and/or recurrence of PCa.

    Abstract translation: 公开了可用于预测前列腺癌（PCa）进展的基因表达小组。 一些实施方案提供了用于预测PCa的临床复发的方法。 一些实施方案提供了预测个体中前列腺癌进展的方法，所述方法包括：（a）接收来自所述个体的生物样品的特征基因集合的表达水平，其中所述签名基因的收集包括至少两个 选自NKX2-1，UPK1A，ADRA2C，ABCC11，MMP11，CPVL，ZYG11A，CLEC4F，OAS2，PGC，UPK3B，PCBP3，ABLIM1，EDARADD，GPR81，MYBPC1，F10，KCNA3，GLDC，KCNQ2， RAPGEF1，TUBB2B，MB，DUOXA1，C2orf43，DUOX1，PCA3和NPR3; （b）将所述表达水平应用于将所述特征基因集合的表达水平与前列腺癌进展相关联的预测模型; 和（c）评估所述预测模型的输出以预测所述个体中前列腺癌的进展。 还提供了用于预测PCa进展和/或复发的系统。

    METHODS AND COMPOSITIONS FOR SINGLE CELL GENOMICS
    6.
    发明申请
    METHODS AND COMPOSITIONS FOR SINGLE CELL GENOMICS 审中-公开
    单细胞基因组学的方法和组合

    公开(公告)号：US20150368704A1

    公开(公告)日：2015-12-24

    申请号：US14742027

    申请日：2015-06-17

    Applicant: ILLUMINA, INC.

    Inventor： Jian-Bing Fan ,  Kun Zhang

    IPC: C12Q1/68

    Abstract: Presented are methods and compositions for obtaining sequence information from one or more individual cells. The methods are useful for obtaining sequence information for a single nucleotide sequence, and for multiplex generation of sequence information from one or more individual cells.

    Abstract translation: 提出了用于从一个或多个单个细胞获得序列信息的方法和组合物。 该方法对于获得单个核苷酸序列的序列信息以及从一个或多个单个细胞多次生成序列信息是有用的。

    MULTIPLEX NUCLEIC ACID REACTIONS
    7.
    发明申请
    MULTIPLEX NUCLEIC ACID REACTIONS 有权
    多重核酸反应

    公开(公告)号：US20150203913A1

    公开(公告)日：2015-07-23

    申请号：US14540832

    申请日：2014-11-13

    Applicant: ILLUMINA, INC.

    Inventor： Arnold Oliphant ,  John R. Stuelpnagel ,  Mark S. Chee ,  Scott L. Butler ,  Jian-Bing Fan ,  Min-Jui Richard Shen

    IPC: C12Q1/68

    CPC classification number: C12Q1/6876 ,  C12Q1/6834 ,  C12Q1/6837 ,  C12Q2600/16 ,  Y10T436/143333 ,  C12Q2525/155 ,  C12Q2563/131 ,  C12Q2563/179

    Abstract: A method for detecting nucleic acids by (a) providing a sample having target nucleic acids, each nucleic acid having contiguous first, second, and third domains; (b) contacting the sample with probe sets to form hybridization complexes, wherein each probe set includes (i) a first probe having a sequence that is complementary to the first domain; and (ii) a second probe having a sequence substantially complementary to the third domain; (c) extending the first probes along the second domains of the complexes while the complexes are immobilized on a solid support; (d) ligating the extended first probes to the second probes to form templates; (e) amplifying the templates with primers that are complementary to the first and second priming sequences to produce amplicons; and (f) detecting the amplicons on the surface of a nucleic acid array.

    Abstract translation: 一种用于通过（a）提供具有靶核酸的样品来检测核酸的方法，每个核酸具有连续的第一，第二和第三结构域; （b）使样品与探针组接触以形成杂交复合物，其中每个探针组包括（i）具有与第一结构域互补的序列的第一探针; 和（ii）具有与第三结构域基本上互补的序列的第二探针; （c）沿络合物的第二结构域扩展第一探针，同时将复合物固定在固体支持物上; （d）将扩展的第一探针连接到第二探针以形成模板; （e）用与第一和第二引物序列互补的引物扩增模板以产生扩增子; 和（f）检测核酸阵列表面上的扩增子。

    DETECTION OF NUCLEIC ACID REACTIONS ON BEAD ARRAYS
    9.
    发明申请
    DETECTION OF NUCLEIC ACID REACTIONS ON BEAD ARRAYS 审中-公开
    检测珠粒阵列上的核酸反应

    公开(公告)号：US20170051340A1

    公开(公告)日：2017-02-23

    申请号：US15252630

    申请日：2016-08-31

    Applicant: Illumina, Inc

    Inventor： Kevin Gunderson ,  John R. Stuelpnagel ,  Mark S. Chee ,  Jian-Bing Fan

    IPC: C12Q1/68

    CPC classification number: C12Q1/6837 ,  C12Q1/6858 ,  C12Q1/6874 ,  C12Q2535/131 ,  C12Q2525/191 ,  C12Q2531/137 ,  C12Q2563/149

    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。

    Detection of nucleic acid reactions on bead arrays
    10.
    发明授权
    Detection of nucleic acid reactions on bead arrays 有权

    公开(公告)号：US09441267B2

    公开(公告)日：2016-09-13

    申请号：US14322529

    申请日：2014-07-02

    Applicant: Illumina, Inc.

    Inventor： Kevin Gunderson ,  John R. Stuelpnagel ,  Mark S. Chee ,  Jian-Bing Fan

    IPC: C12Q1/68

    CPC classification number: C12Q1/6837 ,  C12Q1/6858 ,  C12Q1/6874 ,  C12Q2535/131 ,  C12Q2525/191 ,  C12Q2531/137 ,  C12Q2563/149

    Abstract: The present invention is directed to methods and compositions for the use of micro sphere 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.

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