Patents by Inventor Haiying Li Grunenwald
Haiying Li Grunenwald 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: 20240003055Abstract: 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: September 6, 2023Publication date: January 4, 2024Applicant: ILLUMINA, INC.Inventors: Scott Kuersten, Agnes Radek, Ramesh Vaidyanathan, Haiying Li Grunenwald
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Patent number: 11795578Abstract: 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: GrantFiled: April 25, 2022Date of Patent: October 24, 2023Assignee: Illumina, Inc.Inventors: Scott Kuersten, Agnes Radek, Ramesh Vaidyanathan, Haiying Li Grunenwald
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Publication number: 20220275428Abstract: 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: April 25, 2022Publication date: September 1, 2022Applicant: Epicentre Technologies CorporationInventors: Scott Kuersten, Agnes Radek, Ramesh Vaidyanathan, Haiying Li Grunenwald
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Patent number: 11339422Abstract: 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: GrantFiled: March 26, 2020Date of Patent: May 24, 2022Assignee: Illumina, Inc.Inventors: Scott Kuersten, Agnes Radek, Ramesh Vaidyanathan, Haiying Li Grunenwald
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Publication number: 20220042007Abstract: The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5?-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5?- and 3?-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on the 5?-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on the 3?-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing (so-called “next generation sequencing”).Type: ApplicationFiled: August 26, 2021Publication date: February 10, 2022Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
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Patent number: 11118175Abstract: The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5?-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5?- and 3?-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on the 5?-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on the 3?-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing so-called “next generation sequencing”).Type: GrantFiled: December 5, 2018Date of Patent: September 14, 2021Assignee: Illumina, Inc.Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
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Patent number: 10640809Abstract: 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: GrantFiled: May 27, 2016Date of Patent: May 5, 2020Assignee: EPICENTRE TECHNOLOGIES CORPORATIONInventors: Scott Kuersten, Agnes Radek, Ramesh Vaidyanathan, Haiying Li Grunenwald
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Patent number: 10544403Abstract: 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 29, 2019Date of Patent: January 28, 2020Assignee: 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: 20190359955Abstract: 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 29, 2019Publication date: November 28, 2019Inventors: 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: 10385323Abstract: 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: June 28, 2018Date of Patent: August 20, 2019Assignee: 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: 20190161749Abstract: The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5?-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5?- and 3?-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on the 5?-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on the 3?-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing (so-called “next generation sequencing.Type: ApplicationFiled: December 5, 2018Publication date: May 30, 2019Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
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Patent number: 10184122Abstract: The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5?-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5?- and 3?-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on the 5?-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on the 3?-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing (so-called “next generation sequencing).Type: GrantFiled: July 21, 2015Date of Patent: January 22, 2019Assignee: Epicentre Technologies CorporationInventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
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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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Publication number: 20180230458Abstract: Some embodiments of the present invention relate to the enrichment of non-host nucleic acids in a mixture of host and non-host nucleic acids. Some embodiments include methods for detecting pathogenic organisms from a nucleic acid sample comprising host nucleic acids and nucleic acids indicative of the pathogenic organism.Type: ApplicationFiled: November 12, 2015Publication date: August 16, 2018Inventors: Haiying Li Grunenwald, Stephen Paul Bruinsma, Anupama Khanna, 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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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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Publication number: 20150353925Abstract: The present invention provides methods, compositions and kits for using a transposase and a transposon end for generating extensive fragmentation and 5?-tagging of double-stranded target DNA in vitro, then using a DNA polymerase for generating 5?- and 3?-tagged single-stranded DNA fragments without performing a PCR amplification reaction, wherein the first tag on the 5?-ends exhibits the sequence of the transferred transposon end and optionally, an additional arbitrary sequence, and the second tag on the 3?-ends exhibits a different sequence from the sequence exhibited by the first tag. The method is useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including processes for metagenomic analysis of DNA in environmental samples, copy number variation (CNV) analysis of DNA, and comparative genomic sequencing (CGS), including massively parallel DNA sequencing (so-called “next generation sequencing.Type: ApplicationFiled: July 21, 2015Publication date: December 10, 2015Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
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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