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。

公开(公告)号：US20220033915A1

公开(公告)日：2022-02-03

申请号：US17405686

申请日：2021-08-18

Applicant: Illumina, Inc. ,  University of Southern California

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

IPC: C12Q1/6886

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.

公开(公告)号：US11098372B2

公开(公告)日：2021-08-24

申请号：US16524617

申请日：2019-07-29

Applicant: Illumina, Inc. ,  University of Southern California

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

IPC: C12Q1/6886

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 treating a patient with prostate cancer, the method comprising: detecting expression levels of a collection of signature genes from a biological sample taken from said patient, wherein said collection of signature genes comprises at least NKX2-1; and correlating expression levels of said collection of signature genes with prostate cancer-related mortality to identify whether the patient is at risk of prostate cancer-related mortality.

公开(公告)号：US20200071770A1

公开(公告)日：2020-03-05

申请号：US16524617

申请日：2019-07-29

Applicant: Illumina, Inc. ,  University of Southern California

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

IPC: C12Q1/6886

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.

公开(公告)号：US10364469B2

公开(公告)日：2019-07-30

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: C12Q1/6886

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.

公开(公告)号：US20180094316A1

公开(公告)日：2018-04-05

申请号：US15827141

申请日：2017-11-30

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.

公开(公告)号：US20210198659A1

公开(公告)日：2021-07-01

申请号：US17197836

申请日：2021-03-10

Applicant: Illumina, Inc.

Inventor： Neeraj Salathia ,  Jian-Bing Fan ,  Fiona Kaper ,  Gordon M. Cann ,  Arash Jamshidi ,  Alex Aravanis

IPC: C12N15/10 ,  C12Q1/6869 ,  C12Q1/6853 ,  C12Q1/6806

Abstract: 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).

公开(公告)号：US20210087625A1

公开(公告)日：2021-03-25

申请号：US17035436

申请日：2020-09-28

Applicant: Illumina, Inc. ,  The Regents of the University of California

Inventor： Jian-Bing Fan ,  Kun Zhang

IPC: C12Q1/6874 ,  C12Q1/6841

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.

公开(公告)号：US20160098518A1

公开(公告)日：2016-04-07

申请号：US14878830

申请日：2015-10-08

Applicant: Illumina, Inc.

Inventor： Thomas Royce ,  Craig April ,  Fiona Kaper ,  Jian-Bing Fan

IPC: G06F19/22 ,  C12Q1/68

CPC classification number: G06F19/22 ,  C12Q1/6827 ,  C12Q1/6853 ,  C12Q1/6874 ,  C12Q1/6881 ,  C12Q1/6883 ,  C12Q2600/172 ,  G06F19/16 ,  C12Q2525/155 ,  C12Q2525/161 ,  C12Q2535/122

Abstract: 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.

Abstract translation: 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。

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。