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).

  • Patent number: 10385323
    Abstract: 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: Grant
    Filed: June 28, 2018
    Date of Patent: August 20, 2019
    Assignee: 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
  • Publication number: 20190161749
    Abstract: 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: Application
    Filed: December 5, 2018
    Publication date: May 30, 2019
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
  • Patent number: 10184122
    Abstract: 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: Grant
    Filed: July 21, 2015
    Date of Patent: January 22, 2019
    Assignee: Epicentre Technologies Corporation
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
  • Publication number: 20180298356
    Abstract: 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: Application
    Filed: June 28, 2018
    Publication date: October 18, 2018
    Applicant: 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
  • Publication number: 20180230458
    Abstract: 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: Application
    Filed: November 12, 2015
    Publication date: August 16, 2018
    Inventors: Haiying Li Grunenwald, Stephen Paul Bruinsma, Anupama Khanna, Ramesh Vaidyanathan
  • Patent number: 10035992
    Abstract: 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: Grant
    Filed: October 12, 2017
    Date of Patent: July 31, 2018
    Assignee: 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
  • Publication number: 20180171311
    Abstract: 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: Application
    Filed: October 12, 2017
    Publication date: June 21, 2018
    Applicant: 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
  • Publication number: 20180148767
    Abstract: 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: Application
    Filed: May 27, 2016
    Publication date: May 31, 2018
    Applicant: EPICENTRE TECHNOLOGIES CORPORATION
    Inventors: Scott KUERSTEN, Agnes RADEK, Ramesh VAIDYANATHAN, Haiying Li GRUNENWALD
  • Patent number: 9790476
    Abstract: 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: Grant
    Filed: April 15, 2015
    Date of Patent: October 17, 2017
    Assignee: 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
  • Publication number: 20150353925
    Abstract: 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: Application
    Filed: July 21, 2015
    Publication date: December 10, 2015
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
  • Publication number: 20150291942
    Abstract: 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: Application
    Filed: April 15, 2015
    Publication date: October 15, 2015
    Applicant: 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
  • Patent number: 9115396
    Abstract: Compositions of transposome complexes for generating DNA fragments with specific 5?- and 3?-tags. Kits for generating libraries for sequencing, with transposome complexes, enzymes, oligonucleotides or other components.
    Type: Grant
    Filed: July 7, 2011
    Date of Patent: August 25, 2015
    Assignee: Epicentre Technologies Corporation
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
  • Patent number: 9085801
    Abstract: Compositions of transposome complexes for generating DNA fragments with specific 5?- and 3?-tags. Kits for generating libraries for sequencing, with transposome complexes, enzymes, oligonucleotides or other components.
    Type: Grant
    Filed: June 5, 2012
    Date of Patent: July 21, 2015
    Assignee: EPICENTRE TECHNOLOGIES CORPORATION
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
  • Patent number: 9080211
    Abstract: 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: Grant
    Filed: October 24, 2009
    Date of Patent: July 14, 2015
    Assignee: Epicentre Technologies Corporation
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
  • Patent number: 9040256
    Abstract: 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: Grant
    Filed: January 6, 2014
    Date of Patent: May 26, 2015
    Assignee: EPICENTRE TECHNOLOGIES CORPORATION
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
  • Publication number: 20140162897
    Abstract: 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: Application
    Filed: January 6, 2014
    Publication date: June 12, 2014
    Applicant: ILLUMINA, INC.
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
  • Publication number: 20130196860
    Abstract: Compositions of transposome complexes for generating DNA fragments with specific 5?- and 3?-tags. Kits for generating libraries for sequencing, with transposome complexes, enzymes, oligonucleotides or other components.
    Type: Application
    Filed: June 5, 2012
    Publication date: August 1, 2013
    Applicant: EPICENTRE TECHNOLOGIES CORPORATION
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
  • Publication number: 20110287435
    Abstract: Compositions of transposome complexes for generating DNA fragments with specific 5?- and 3?-tags. Kits for generating libraries for sequencing, with transposome complexes, enzymes, oligonucleotides or other components.
    Type: Application
    Filed: July 7, 2011
    Publication date: November 24, 2011
    Applicant: EPICENTRE TECHNOLOGIES CORPORATION
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl
  • Publication number: 20100120098
    Abstract: 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: Application
    Filed: October 24, 2009
    Publication date: May 13, 2010
    Applicant: Epicentre Technologies Corporation
    Inventors: Haiying Li Grunenwald, Nicholas Caruccio, Jerome Jendrisak, Gary Dahl