Patents by Inventor Scott Kuersten
Scott Kuersten 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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Patent number: 10240191Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.Type: GrantFiled: November 3, 2017Date of Patent: March 26, 2019Assignee: Applied Biosystems, LLCInventor: R. Scott Kuersten
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Publication number: 20180298356Abstract: Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same.Type: ApplicationFiled: June 28, 2018Publication date: October 18, 2018Applicant: ILLUMINA, INC.Inventors: Christian Gloeckner, Amirali Kia, Erin Bomati, Molly He, Haiying Li Grunenwald, Scott Kuersten, Trina Faye Osothprarop, Darin Haskins, Joshua Burgess, Anupama Khanna, Daniel Schlingman, Ramesh Vaidyanathan
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Patent number: 10035992Abstract: Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same.Type: GrantFiled: October 12, 2017Date of Patent: July 31, 2018Assignee: ILLUMINA, INC.Inventors: Christian Gloeckner, Amirali Kia, Erin Bomati, Molly He, Haiying Li Grunenwald, Scott Kuersten, Trina Faye Osothprarop, Darin Haskins, Joshua Burgess, Anupama Khanna, Daniel Schlingman, Ramesh Vaidyanathan
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Publication number: 20180171311Abstract: Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same.Type: ApplicationFiled: October 12, 2017Publication date: June 21, 2018Applicant: ILLUMINA, INC.Inventors: Christian GLOECKNER, Amirali KIA, Erin BOMATI, Molly HE, Haiying Li Grunenwald, Scott Kuersten, Trina Faye Osothprarop, Darin Haskins, Joshua Burgess, Anupama Khanna, Daniel Schlingman, Ramesh Vaidyanathan
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Publication number: 20180148767Abstract: Presented herein are methods and compositions for analyzing rare nucleic acid species. Some methods presented herein use DNA reassociation kinetics following thermal denaturation to define populations of nucleic acid sequences, e.g., highly abundant (e.g., cDNA from rRNA), moderately abundant, and less abundant or rare sequences (e.g., cDNA from mRNA).Type: ApplicationFiled: May 27, 2016Publication date: May 31, 2018Applicant: EPICENTRE TECHNOLOGIES CORPORATIONInventors: Scott KUERSTEN, Agnes RADEK, Ramesh VAIDYANATHAN, Haiying Li GRUNENWALD
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Publication number: 20180051328Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.Type: ApplicationFiled: November 3, 2017Publication date: February 22, 2018Inventor: R. Scott KUERSTEN
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Patent number: 9834816Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.Type: GrantFiled: March 6, 2017Date of Patent: December 5, 2017Assignee: APPLIED BIOSYSTEMS, LLCInventor: R. Scott Kuersten
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Patent number: 9790476Abstract: Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same.Type: GrantFiled: April 15, 2015Date of Patent: October 17, 2017Assignee: ILLUMINA, INC.Inventors: Christian Gloeckner, Amirali Kia, Erin Bomati, Molly He, Haiying Li Grunenwald, Scott Kuersten, Trina Faye Osothprarop, Darin Haskins, Joshua Burgess, Anupama Khanna, Daniel Schlingman, Ramesh Vaidyanathan
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Patent number: 9790540Abstract: The present innovation provides methods and kits that enable rapid and efficient dual end-tagging of RNA to prepare libraries for analysis by applications such as next-generation RNA sequencing, qPCR, microarray analysis, or cloning. The methods do not require time-consuming and inefficient gel-purification steps that are common to methods known in the art. In addition, the present invention provides methods and kits for rapid, high-throughput enzymatic preparation of 5?-activated, 3?-blocked DNA oligonucleotides from standard, single-stranded DNA oligonucleotides.Type: GrantFiled: September 13, 2013Date of Patent: October 17, 2017Assignee: EPICENTRE TECHNOLOGIES CORPORATIONInventors: Ramesh Vaidyanathan, Scott Kuersten, Ken Doyle
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Publication number: 20170175180Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.Type: ApplicationFiled: March 6, 2017Publication date: June 22, 2017Inventor: R. Scott KUERSTEN
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Patent number: 9624534Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.Type: GrantFiled: July 13, 2016Date of Patent: April 18, 2017Assignee: APPLIED BIOSYSTEMS, LLCInventor: R. Scott Kuersten
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Publication number: 20160312277Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.Type: ApplicationFiled: July 13, 2016Publication date: October 27, 2016Inventor: R. Scott KUERSTEN
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Patent number: 9416406Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.Type: GrantFiled: December 15, 2014Date of Patent: August 16, 2016Assignee: Applied Biosystems, LLCInventor: R. Scott Kuersten
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Publication number: 20150291942Abstract: Presented herein are transposase enzymes and reaction conditions for improved fragmentation and tagging of nucleic acid samples, in particular altered transposases and reaction conditions which exhibit improved insertion sequence bias, as well as methods and kits using the same.Type: ApplicationFiled: April 15, 2015Publication date: October 15, 2015Applicant: ILLUMINA, INC.Inventors: Christian GLOECKNER, Amirali KIA, Erin BOMATI, Molly HE, Haiying Li Grunenwald, Scott KUERSTEN, Trina Faye OSOTHPRAROP, Darin HASKINS, Joshua BURGESS, Anupama KHANNA, Daniel SCHLINGMAN, Ramesh VAIDYANATHAN
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Publication number: 20150147759Abstract: Ligation-enhanced nucleic acid detection assay embodiments for detection of RNA or DNA are described. The assay embodiments rely on ligation of chimeric oligonucleotide probes to generate a template for amplification and detection. The assay embodiments are substantially independent of the fidelity of a polymerase for copying compromised nucleic acid. Very little background amplification is observed and as few as 1000 copies of target nucleic acid can be detected. Method embodiments are particularly adept for detection of RNA from compromised samples such as formalin-fixed and paraffin-embedded samples. Heavily degraded and cross-linked nucleic acids of compromised samples, in which classic quantitative real time PCR assays typically fail to adequately amplify signal, can be reliably detected and quantified.Type: ApplicationFiled: November 14, 2014Publication date: May 28, 2015Inventors: R. Scott Kuersten, Brittan Pasloske
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Patent number: 9012183Abstract: A method of preparing a DNA copy of a target polynucleotide using template switching is described. The method includes mixing a double stranded template/primer substrate made up of a DNA primer oligonucleotide associated with a complementary oligonucleotide template strand with a target polynucleotide in a reaction medium and adding a suitable amount of a non-retroviral reverse transcriptase to the reaction medium to extend the DNA primer oligonucleotide from its 3? end to provide a DNA copy polynucleotide. The DNA copy polynucleotide includes a complementary target DNA polynucleotide that is synthesized using the target polynucleotide as a template. Methods of adding nucleotides to the double stranded template/primer substrate are also described. The method can be used to facilitate detection, PCR amplification, cloning, and determination of RNA and DNA sequences.Type: GrantFiled: February 23, 2012Date of Patent: April 21, 2015Assignee: Board of Regents, The University of Texas SystemInventors: Alan M. Lambowitz, Sabine Mohr, Travis B. White, Scott Kuersten
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Publication number: 20150099268Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.Type: ApplicationFiled: December 15, 2014Publication date: April 9, 2015Inventor: R. Scott KUERSTEN
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Patent number: 8932816Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.Type: GrantFiled: August 6, 2013Date of Patent: January 13, 2015Assignee: Applied Biosystems, LLCInventor: R. Scott Kuersten
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Patent number: 8889355Abstract: Ligation-enhanced nucleic acid detection assay embodiments for detection of RNA or DNA are described. The assay embodiments rely on ligation of chimeric oligonucleotide probes to generate a template for amplification and detection. The assay embodiments are substantially independent of the fidelity of a polymerase for copying compromised nucleic acid. Very little background amplification is observed and as few as 1000 copies of target nucleic acid can be detected. Method embodiments are particularly adept for detection of RNA from compromised samples such as formalin-fixed and paraffin-embedded samples. Heavily degraded and cross-linked nucleic acids of compromised samples, in which classic quantitative real time PCR assays typically fail to adequately amplify signal, can be reliably detected and quantified.Type: GrantFiled: April 26, 2013Date of Patent: November 18, 2014Assignee: Applied Biosystems, LLCInventors: R. Scott Kuersten, Brittan Pasloske
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Publication number: 20140179562Abstract: The present innovation provides methods and kits that enable rapid and efficient dual end-tagging of RNA to prepare libraries for analysis by applications such as next-generation RNA sequencing, qPCR, microarray analysis, or cloning. The methods do not require time-consuming and inefficient gel-purification steps that are common to methods known in the art. In addition, the present invention provides methods and kits for rapid, high-throughput enzymatic preparation of 5?-activated, 3?-blocked DNA oligonucleotides from standard, single-stranded DNA oligonucleotides.Type: ApplicationFiled: September 13, 2013Publication date: June 26, 2014Applicant: Epicentre Technologies CorporationInventors: Ramesh Vaidyanathan, Scott Kuersten, Ken Doyle