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1. 发明申请

US20210198659A1 Nucleic Acid Sequence Analysis from Single Cells 有权
公开(公告)号：US20210198659A1
公开(公告)日：2021-07-01
申请号：US17197836
申请日：2021-03-10
申请人： Illumina, Inc.
发明人： Neeraj Salathia , Jian-Bing Fan , Fiona Kaper , Gordon M. Cann , Arash Jamshidi , Alex Aravanis
IPC分类号： C12N15/10 , C12Q1/6869 , C12Q1/6853 , C12Q1/6806
摘要： Presented herein are methods and compositions for multiplexed single cell gene expression analysis. Some methods and compositions include the use of droplets and/or beads bearing unique barcodes such as unique molecular barcodes (UMI).

2. 发明申请

US20210087625A1 METHODS AND COMPOSITIONS FOR SINGLE CELL GENOMICS 有权
公开(公告)号：US20210087625A1
公开(公告)日：2021-03-25
申请号：US17035436
申请日：2020-09-28
申请人： Illumina, Inc. , The Regents of the University of California
发明人： Jian-Bing Fan , Kun Zhang
IPC分类号： C12Q1/6874 , C12Q1/6841
摘要： 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.

3. 发明申请

US20160333420A1 GENE EXPRESSION PANEL FOR PROGNOSIS OF PROSTATE CANCER RECURRENCE 审中-公开
标题翻译：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
申请人： ILLUMINA, INC. , UNIVERSITY OF SOUTHERN CALIFORNIA
发明人： Mariana Carla Stern , Jacek Pinski , Jian-Bing Fan
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6886 , C12Q2600/118 , C12Q2600/158
摘要： 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.
摘要翻译：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。

4. 发明申请

US20160098518A1 HLA TYPING USING SELECTIVE AMPLIFICATION AND SEQUENCING 审中-公开
标题翻译： HLA型选择性放大和序列化
公开(公告)号：US20160098518A1
公开(公告)日：2016-04-07
申请号：US14878830
申请日：2015-10-08
申请人： Illumina, Inc.
发明人： Thomas Royce , Craig April , Fiona Kaper , Jian-Bing Fan
IPC分类号： G06F19/22 , C12Q1/68
CPC分类号： G06F19/22 , C12Q1/6827 , C12Q1/6853 , C12Q1/6874 , C12Q1/6881 , C12Q1/6883 , C12Q2600/172 , G06F19/16 , C12Q2525/155 , C12Q2525/161 , C12Q2535/122
摘要： Presented herein are methods and compositions for determining haplotypes in a sample. The methods are useful for obtaining sequence information regarding, for example, HLA type and haplotype. Also presented herein are methods of determining haplotypes in a sample based on a plurality sequence reads.
摘要翻译：本文提出了用于确定样品中单倍型的方法和组合物。该方法对于获得关于例如HLA类型和单体型的序列信息是有用的。本文还呈现了基于多个序列读取来确定样品中的单倍型的方法。

5. 发明申请

US20150368704A1 METHODS AND COMPOSITIONS FOR SINGLE CELL GENOMICS 审中-公开
标题翻译：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
申请人： ILLUMINA, INC.
发明人： Jian-Bing Fan , Kun Zhang
IPC分类号： C12Q1/68
摘要： 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.
摘要翻译：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。

6. 发明申请

US20150203913A1 MULTIPLEX NUCLEIC ACID REACTIONS 有权
标题翻译：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
申请人： ILLUMINA, INC.
发明人： Arnold Oliphant , John R. Stuelpnagel , Mark S. Chee , Scott L. Butler , Jian-Bing Fan , Min-Jui Richard Shen
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6876 , C12Q1/6834 , C12Q1/6837 , C12Q2600/16 , Y10T436/143333 , C12Q2525/155 , C12Q2563/131 , C12Q2563/179
摘要： 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.
摘要翻译：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。

7. 发明授权

US10870099B2 Compositions and methods for the amplification of nucleic acids 有权
公开(公告)号：US10870099B2
公开(公告)日：2020-12-22
申请号：US14416563
申请日：2013-02-21
申请人： Illumina, Inc.
发明人： Jian-Bing Fan , Kevin L. Gunderson , Frank J. Steemers , Dmitry K. Pokholok , Fiona Kaper
IPC分类号： B01J19/00 , C12Q1/6844
CPC分类号： B01J19/0046 , C12Q1/6844 , B01J2219/00585 , B01J2219/00722
摘要： The present disclosure relates to systems and methods for the amplification of nucleic acids, including, but not limited to, the amplification of nucleic acid libraries and whole genome amplification.

8. 发明申请

US20180094316A1 MULTIPLEX NUCLEIC ACID REACTIONS 审中-公开
公开(公告)号：US20180094316A1
公开(公告)日：2018-04-05
申请号：US15827141
申请日：2017-11-30
申请人： Illumina, Inc.
发明人： Arnold Oliphant , John R. Stuelpnagel , Mark S. Chee , Scott L. Butler , Jian-Bing Fan , Min-Jui Richard Shen
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6876 , C12Q1/6834 , C12Q1/6837 , C12Q2600/16 , Y10T436/143333 , C12Q2525/155 , C12Q2563/131 , C12Q2563/179
摘要： 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.

9. 发明授权

US09850536B2 Multiplex nucleic acid reactions 有权
公开(公告)号：US09850536B2
公开(公告)日：2017-12-26
申请号：US14540832
申请日：2014-11-13
申请人： ILLUMINA, INC.
发明人： Arnold Oliphant , John R. Stuelpnagel , Mark S. Chee , Scott L. Butler , Jian-Bing Fan , Min-Jui Richard Shen
IPC分类号： C12P19/34 , C12Q1/68 , C12M1/34 , C12M3/00 , C07H21/02 , C07H21/04 , C07H21/00
CPC分类号： C12Q1/6876 , C12Q1/6834 , C12Q1/6837 , C12Q2600/16 , Y10T436/143333 , C12Q2525/155 , C12Q2563/131 , C12Q2563/179
摘要： 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.

10. 发明申请

US20170051340A1 DETECTION OF NUCLEIC ACID REACTIONS ON BEAD ARRAYS 审中-公开
标题翻译：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
申请人： Illumina, Inc
发明人： Kevin Gunderson , John R. Stuelpnagel , Mark S. Chee , Jian-Bing Fan
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6837 , C12Q1/6858 , C12Q1/6874 , C12Q2535/131 , C12Q2525/191 , C12Q2531/137 , C12Q2563/149
摘要： 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.
摘要翻译：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。

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