Patents by Inventor Kathryn M. Stephens
Kathryn M. Stephens 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: 20240117336Abstract: The present disclosure in some aspects relates to performing DNA based kinship analysis involving analysis of between 5,000 and 50,000 SNPs, including sample preparation and sequencing technologies and methods that can be used to calculate the degree of relationship of a DNA profile to one or more reference DNA profiles.Type: ApplicationFiled: February 10, 2022Publication date: April 11, 2024Applicant: Verogen, Inc.Inventors: Cydne L. HOLT, Paulina WALICHIEWICZ, Elmira FOROUZMAND, Kathryn M. STEPHENS, Seth STADICK, Tim FENNELL
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Patent number: 11530446Abstract: Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences.Type: GrantFiled: September 19, 2019Date of Patent: December 20, 2022Assignee: Illumina, Inc.Inventors: Kathryn M. Stephens, Cydne Holt, Carey Davis, Anne Jager, Paulina Walichiewicz, Yonmee Han, David Silva, Min-Jui Richard Shen, Sasan Amini, Frank J. Steemers
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Publication number: 20220243261Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: ApplicationFiled: January 13, 2022Publication date: August 4, 2022Applicant: Illumina, Inc.Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Patent number: 11254976Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: GrantFiled: August 19, 2019Date of Patent: February 22, 2022Assignee: Illumina, Inc.Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Publication number: 20210130885Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.Type: ApplicationFiled: January 11, 2021Publication date: May 6, 2021Inventors: Alex So, Li Liu, Min-Jui Richard Shen, Neeraj Salathia, Kathryn M. Stephens, Anne Jager, Timothy Wilson, Justin Fullerton, Sean M. Ramirez, Shannon Kaplan, Rigo Pantoja, Bala Murali Venkatesan, Steven Modiano
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Patent number: 10913975Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.Type: GrantFiled: July 21, 2016Date of Patent: February 9, 2021Assignee: Illumina, Inc.Inventors: Alex So, Li Liu, Min-Jui Richard Shen, Neeraj Salathia, Kathryn M. Stephens, Anne Jager, Timothy Wilson, Justin Fullerton, Sean M. Ramirez, Shannon Kaplan, Rigo Pantoja, Bala Murali Venkatesan, Steven Modiano
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Publication number: 20200224268Abstract: Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences.Type: ApplicationFiled: September 19, 2019Publication date: July 16, 2020Inventors: Kathryn M. Stephens, Cydne Holt, Carey Davis, Anne Jager, Paulina Walichiewicz, Yonmee Han, David Silva, Min-Jui Richard Shen, Sasan Amini, Frank J. Steemers
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Publication number: 20200040386Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: ApplicationFiled: August 19, 2019Publication date: February 6, 2020Applicant: Illumina, Inc.Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Patent number: 10422002Abstract: Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences.Type: GrantFiled: February 13, 2015Date of Patent: September 24, 2019Assignee: ILLUMINA, INC.Inventors: Kathryn M. Stephens, Cydne Holt, Carey Davis, Anne Jager, Paulina Walichiewicz, Yonmee Han, David Silva, Min-Jui Richard Shen, Sasan Amini, Frank J. Steemers
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Patent number: 10385384Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: GrantFiled: August 8, 2017Date of Patent: August 20, 2019Assignee: Illumina, Inc.Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Publication number: 20180245142Abstract: Presented are methods and compositions for spatial detection and analysis of nucleic acids in a tissue sample. The methods can enable the characterization of transcriptomes and/or genomic variations in tissues while preserving spatial information about the tissue.Type: ApplicationFiled: July 21, 2016Publication date: August 30, 2018Inventors: Alex SO, Li LIU, Min-Jui Richard SHEN, Neeraj SALATHIA, Kathryn M. STEPHENS, Anne JAGER, Timothy WILSON, Justin FULLERTON, Sean M. RAMIREZ, Shannon KAPLAN, Rigo PANTOJA, Bala Murali VENKATESAN, Steven MODIANO
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Patent number: 10047359Abstract: The present system provides novel methods and compositions for selecting a particular strand of RNA and/or producing a cDNA library that results in an unbiased representation of RNA in a sample.Type: GrantFiled: January 12, 2016Date of Patent: August 14, 2018Assignee: ILLUMINA, INC.Inventors: Kathryn M. Stephens, Marcus Burch
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Publication number: 20170335380Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: ApplicationFiled: August 8, 2017Publication date: November 23, 2017Applicant: Illumina, Inc.Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Patent number: 9758816Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: GrantFiled: October 9, 2015Date of Patent: September 12, 2017Assignee: Illumina, Inc.Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Publication number: 20160194628Abstract: The present system provides novel methods and compositions for selecting a particular strand of RNA and/or producing a cDNA library that results in an unbiased representation of RNA in a sample.Type: ApplicationFiled: January 12, 2016Publication date: July 7, 2016Inventors: Kathryn M. Stephens, Marcus Burch
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Publication number: 20160053310Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: ApplicationFiled: October 9, 2015Publication date: February 25, 2016Applicant: ILLUMINA, INC.Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Patent number: 9255265Abstract: The present system provides novel methods and compositions for selecting a particular strand of RNA and/or producing a cDNA library that results in an unbiased representation of RNA in a sample.Type: GrantFiled: March 15, 2013Date of Patent: February 9, 2016Assignee: Illumina, Inc.Inventors: Kathryn M. Stephens, Marcus Burch
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Patent number: 9169513Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: GrantFiled: October 13, 2014Date of Patent: October 27, 2015Assignee: ILLUMINA, INC.Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
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Publication number: 20150232929Abstract: Embodiments disclosed herein provide methods for constructing a DNA profile comprising: providing a nucleic acid sample, amplifying the nucleic acid sample with a plurality of primers that specifically hybridize to at least one target sequence comprising a SNP and at least one target sequence comprising a tandem repeat, and determining the genotypes of the at least one SNP and at least one tandem repeat in the amplification products, thereby constructing the DNA profile of the nucleic acid sample. Embodiments disclosed herein further provide a plurality of primers that specifically hybridize to at least one short target sequence and at least one long target sequence in a nucleic acid sample, wherein amplifying the nucleic acid sample using the plurality of primers in a single reaction results in a short amplification product and a long amplification product, wherein each of the plurality of primers comprises one or more tag sequences.Type: ApplicationFiled: February 13, 2015Publication date: August 20, 2015Applicant: ILLUMINA, INC.Inventors: Kathryn M. Stephens, Cydne Holt, Carey Davis, Anne Jager, Paulina Walichiewicz, Yonmee Han, David Silva, Min-Jui Richard Shen, Sasan Amini, Frank J. Steemers
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Publication number: 20150080230Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.Type: ApplicationFiled: October 13, 2014Publication date: March 19, 2015Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan