Patents by Inventor Jian-Bing Fan
Jian-Bing Fan has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Publication number: 20220033915Abstract: 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.Type: ApplicationFiled: August 18, 2021Publication date: February 3, 2022Applicants: Illumina, Inc., University of Southern CaliforniaInventors: Mariana Carla Stern, Jacek Pinski, Jian-Bing Fan
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Patent number: 11098372Abstract: 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.Type: GrantFiled: July 29, 2019Date of Patent: August 24, 2021Assignees: Illumina, Inc., University of Southern CaliforniaInventors: Mariana Carla Stern, Jacek Pinski, Jian-Bing Fan
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Publication number: 20210198659Abstract: 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).Type: ApplicationFiled: March 10, 2021Publication date: July 1, 2021Applicant: Illumina, Inc.Inventors: Neeraj Salathia, Jian-Bing Fan, Fiona Kaper, Gordon M. Cann, Arash Jamshidi, Alex Aravanis
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Publication number: 20210129107Abstract: 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.Type: ApplicationFiled: November 16, 2020Publication date: May 6, 2021Inventors: Jian-Bing Fan, Kevin L. Gunderson, Frank J. Steemers, Dmitry K. Pokholok, Fiona Kaper
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Patent number: 10975371Abstract: 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).Type: GrantFiled: September 15, 2015Date of Patent: April 13, 2021Assignee: Illumina, Inc.Inventors: Neeraj Salathia, Jian-Bing Fan, Fiona Kaper, Gordon M. Cann, Arash Jamshidi, Alex Aravanis
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Publication number: 20210087625Abstract: 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.Type: ApplicationFiled: September 28, 2020Publication date: March 25, 2021Inventors: Jian-Bing Fan, Kun Zhang
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Publication number: 20210079386Abstract: 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).Type: ApplicationFiled: October 23, 2020Publication date: March 18, 2021Applicant: ILLUMINA, INC.Inventors: Fiona KAPER, Jian-Bing FAN, Neeraj SALATHIA, Gordon M. CANN, Arash JAMSHIDI, Alex ARAVANIS
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Patent number: 10870099Abstract: 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.Type: GrantFiled: February 21, 2013Date of Patent: December 22, 2020Assignee: Illumina, Inc.Inventors: Jian-Bing Fan, Kevin L. Gunderson, Frank J. Steemers, Dmitry K. Pokholok, Fiona Kaper
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Patent number: 10837059Abstract: 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.Type: GrantFiled: November 30, 2017Date of Patent: November 17, 2020Assignee: Illumina, Inc.Inventors: Arnold Oliphant, John R. Stuelpnagel, Mark S. Chee, Scott L. Butler, Jian-Bing Fan, Min-Jui Richard Shen
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Patent number: 10829814Abstract: 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.Type: GrantFiled: June 17, 2015Date of Patent: November 10, 2020Assignees: Illumina, Inc., The Regents of the University of CaliofrniaInventors: Jian-Bing Fan, Kun Zhang
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Publication number: 20200071770Abstract: 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.Type: ApplicationFiled: July 29, 2019Publication date: March 5, 2020Applicants: Illumina, Inc., University of Southern CaliforniaInventors: Mariana Carla Stern, Jacek Pinski, Jian-Bing Fan
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Patent number: 10364469Abstract: 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.Type: GrantFiled: January 16, 2015Date of Patent: July 30, 2019Assignee: ILLUMINA, INCInventors: Mariana Carla Stern, Jacek Pinski, Jian-Bing Fan
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Patent number: 10262104Abstract: 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.Type: GrantFiled: October 8, 2015Date of Patent: April 16, 2019Assignee: ILLUMINA, INC.Inventors: Thomas Royce, Craig April, Fiona Kaper, Jian-Bing Fan
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Publication number: 20180094316Abstract: 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.Type: ApplicationFiled: November 30, 2017Publication date: April 5, 2018Inventors: Arnold Oliphant, John R. Stuelpnagel, Mark S. Chee, Scott L. Butler, Jian-Bing Fan, Min-Jui Richard Shen
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Publication number: 20180044724Abstract: The disclosure provides methods of DNA amplification mediated by DNA ligase. Specifically disclosed is a method of amplifying a target region at DNA level, which comprises repeating cycles of amplification comprising the following steps: denaturing DNA template to obtain single target DNA strands; hybridizing a primer pair comprising an upstream primer and a downstream primer to the target DNA strand, wherein the upstream primer is hybridized to a first nucleic acid sequence of the target region, and the downstream primer is hybridized to a second nucleic acid sequence of the target region; the first nucleic acid sequence is downstream to the second nucleic acid sequence on the target DNA strand, with the downstream primer containing a phosphorylated 5? end; ligating the upstream primer or extension product thereof to the downstream primer or extension product thereof, to obtain a semi-amplification product. This disclosure also discloses a kit used to amplify a target region at DNA level.Type: ApplicationFiled: April 1, 2017Publication date: February 15, 2018Inventors: Jian-Bing FAN, Yangbin GAO, Weihong XU
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Patent number: 9850536Abstract: 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.Type: GrantFiled: November 13, 2014Date of Patent: December 26, 2017Assignee: Illumina, Inc.Inventors: Arnold Oliphant, John R. Stuelpnagel, Mark S. Chee, Scott L. Butler, Jian-Bing Fan, Min-Jui Richard Shen
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Publication number: 20170218458Abstract: The present application discloses a method of detecting the methylation of specific genome regions in a DNA fragment from a sample containing DNA. The method includes treating the DNA fragment containing specific genome regions with sodium bisulfite and obtaining single-strand DNA fragment; attaching an adapter to one or both ends of the single-strand DNA fragment; optionally cyclizing the adapter-attached single-strand DNA fragment; preparing the single-strand DNA fragment with attached adapter into a DNA sequencing library containing the specific genome regions; sequencing the DNA sequencing library to identify the sequence of the single-strand DNA fragment. The present application also discloses a kit for detecting the methylation of specific genome regions in a DNA fragment from a sample containing DNA, and the use of single strand ligating agent in preparing a kit for detecting the methylation of specific genome regions in a DNA fragment.Type: ApplicationFiled: February 3, 2017Publication date: August 3, 2017Inventors: Jian-Bing FAN, Xuyu CAI, Yangbin GAO
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Publication number: 20170051340Abstract: 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.Type: ApplicationFiled: August 31, 2016Publication date: February 23, 2017Inventors: Kevin Gunderson, John R. Stuelpnagel, Mark S. Chee, Jian-Bing Fan
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Publication number: 20170044525Abstract: 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).Type: ApplicationFiled: April 28, 2015Publication date: February 16, 2017Inventors: Fiona KAPER, Jian-Bing FAN, Neeraj SALATHIA, Gordon M. CANN, Arash JAMSHIDI, Alex ARAVANIS
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Publication number: 20160333420Abstract: 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.Type: ApplicationFiled: January 16, 2015Publication date: November 17, 2016Applicants: Illumina, Inc., University of Southern CaliforniaInventors: Mariana Carla Stern, Jacek Pinski, Jian-Bing Fan