Patents by Inventor Niall Anthony Gormley

Niall Anthony Gormley 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: 10370709
    Abstract: Disclosed herein are compositions and methods for sequencing nucleic acids.
    Type: Grant
    Filed: September 12, 2016
    Date of Patent: August 6, 2019
    Assignee: Illumina Cambridge Limited
    Inventors: Roberto Rigatti, Jonathan Mark Boutell, Jason Betley, Niall Anthony Gormley
  • Patent number: 10329613
    Abstract: Provided herein is a method for sequencing a polynucleotide molecules. The method includes the steps of providing a plurality of polynucleotide molecules attached to a surface, wherein a first portion of each polynucleotide molecule is attached to a first location of the surface and a second portion of each polynucleotide molecule is attached to a second location of the surface, the relative proximity of the first and second locations being correlated with the probability that the first and second portions are paired, separating the first and second portions of the polynucleotide molecules on the surface, determining the sequences of the first and second portions of the polynucleotide molecules and comparing the relative proximities and the sequences to determine which first and second portions are paired and to determine the sequence of the target polynucleotide molecules.
    Type: Grant
    Filed: April 10, 2015
    Date of Patent: June 25, 2019
    Assignee: Illumina Cambridge Limited
    Inventors: Roberto Rigatti, Niall Anthony Gormley, Jonathan Mark Boutell
  • Patent number: 10267804
    Abstract: Provided herein is a method of using transposition to improve methods of sequencing RNA molecules. Provided herein is a method of tagging nucleic acid duplexes, such as DNA:RNA duplexes or DNA:DNA duplexes. The method includes the steps of providing a transposase and a transposon composition, providing one or more nucleic acid duplexes immobilized on a support, and contacting the transposase and transposon composition with the one or more nucleic acid duplexes under conditions wherein the one or more nucleic acid duplexes and transposon composition undergo a transposition reaction to produce one or more tagged nucleic acid duplexes, wherein the transposon composition comprises a double stranded nucleic acid molecule comprising a transferred strand and a non-transferred strand.
    Type: Grant
    Filed: February 1, 2017
    Date of Patent: April 23, 2019
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Niall Anthony Gormley, Louise Fraser, Paula Kokko-Gonzales
  • Patent number: 10253359
    Abstract: The present invention relates to a method for preparing a library of template polynucleotides and use thereof in methods of solid-phase nucleic acid amplification. More specifically, the invention relates to a method for preparing a library of template polynucleotides that have common sequences at their 5? ends and at their 3? ends.
    Type: Grant
    Filed: June 3, 2016
    Date of Patent: April 9, 2019
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Niall Anthony Gormley, Geoffrey Paul Smith, David Bentley, Roberto Rigatti, Shujun Luo
  • Publication number: 20190048332
    Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.
    Type: Application
    Filed: October 29, 2018
    Publication date: February 14, 2019
    Inventors: Frank J. Steemers, Kevin L. Gunderson, Fan Zhang, Jason Richard Betley, Niall Anthony Gormley, Wouter Meuleman, Jacqueline Weir, Avgousta Ioannou, Gareth Jenkins, Rosamond Jackson, Natalie Morrell, Dmitry K. Pokholok, Steven J. Norberg, Molly He, Amirali Kia, Igor Goryshin, Rigo Pantoja
  • Publication number: 20190040382
    Abstract: Embodiments provided herein relate to methods and compositions for preparing an immobilized library of barcoded DNA fragments of a target nucleic acid, identifying genomic variants, determining the contiguity information, phasing information, and methylation status of the target nucleic acid.
    Type: Application
    Filed: October 16, 2015
    Publication date: February 7, 2019
    Applicant: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Frank J. Steemers, Kevin L. Gunderson, Fan Zhang, Jason Richard Betley, Niall Anthony Gormley, Wouter Meuleman, Jacqueline Weir, Avgousta Ioannou, Gareth Jenkins, Rosamond Jackson, Natalie Morrell, Dmitry K. Pokholok, Steven J. Norberg, Molly He, Amirali Kia, Igor Goryshin, Rigo Pantoja
  • Publication number: 20180363047
    Abstract: The invention provides methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template.
    Type: Application
    Filed: June 11, 2018
    Publication date: December 20, 2018
    Applicant: Illumina Cambridge Limited
    Inventors: Geoffrey Paul Smith, Jonathan Mark Boutell, Colin Lloyd Barnes, Roberto Rigatti, Niall Anthony Gormley, David Bentley, Tobias William Barr Ost, Vincent Peter Smith, Graham John Worsley, Eric Hans Vermaas
  • Publication number: 20180312833
    Abstract: Presented are methods and compositions for using immobilized transposase and a transposon end for generating an immobilized library of 5?-tagged double-stranded target DNA on a surface. The methods are useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including massively parallel DNA sequencing.
    Type: Application
    Filed: July 3, 2018
    Publication date: November 1, 2018
    Inventors: Niall Anthony Gormley, Geoffrey Paul Smith
  • Patent number: 10041066
    Abstract: Presented are methods and compositions for using immobilized transposase and a transposon end for generating an immobilized library of 5?-tagged double-stranded target DNA on a surface. The methods are useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including massively parallel DNA sequencing.
    Type: Grant
    Filed: March 27, 2015
    Date of Patent: August 7, 2018
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Niall Anthony Gormley, Geoffrey Paul Smith
  • Patent number: 10006081
    Abstract: The invention relates to a method of preparing a 5? and 3? modified library of template polynucleotides and also the use of the 5? and 3? modified library of templates in methods of solid-phase nucleic acid amplification. In particular, the invention relates to a method of preparing a 5? and 3? modified library of template polynucleotides which have common sequences at their 5? ends and at their 3? ends, wherein over-representation of “end” sequences of the primary polynucleotide molecules from when the 5? and 3? modified library is generated is greatly reduced or prevented.
    Type: Grant
    Filed: March 24, 2015
    Date of Patent: June 26, 2018
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Roberto Rigatti, Niall Anthony Gormley, Helen Rachel Bignell
  • Patent number: 9994896
    Abstract: The invention provides methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template.
    Type: Grant
    Filed: December 17, 2014
    Date of Patent: June 12, 2018
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Geoffrey Paul Smith, Jonathan Mark Boutell, Colin Lloyd Barnes, Roberto Rigatti, Niall Anthony Gormley, David Bentley, Tobias William Barr Ost, Vincent Peter Smith, Graham John Worsley, Eric Hans Vermaas
  • Publication number: 20180155709
    Abstract: Presented herein are methods and compositions surface-based tagmentation. In particular embodiments, methods of preparing an immobilized library of fragmented and tagged DNA molecules on a solid surface are presented. In particular embodiments, the solid surface comprises immobilized transposomes in a dried format, suitable for reconstitution upon contact with liquid, such as a liquid sample.
    Type: Application
    Filed: May 27, 2016
    Publication date: June 7, 2018
    Inventors: Niall Anthony Gormley, Avgousta Ioannou, Rosamond Jackson, Natalie Morrell
  • Patent number: 9944924
    Abstract: The present disclosure relates to the field of molecular biology and more specifically to methods for capturing and amplifying target polynucleotides on a solid surface.
    Type: Grant
    Filed: July 10, 2015
    Date of Patent: April 17, 2018
    Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITED
    Inventors: Roberto Rigatti, Niall Anthony Gormley, Allen E. Eckhardt, Jonathan Mark Boutell
  • Patent number: 9902994
    Abstract: The invention relates to a method of preparing a library of template polynucleotides with uniform sequence representation and to use of a library of templates prepared using this method for solid-phase nucleic acid amplification. In particular, the invention relates to a method of preparing a library of template polynucleotides which have common sequences at their 5? ends and at their 3? ends, which contains even representation of all the fragments present in a starting sample of nucleic acid before fragmentation. The invention is especially applicable to the preparation of short insert libraries, where the sample fragments are less than 150 base pairs in length.
    Type: Grant
    Filed: December 3, 2014
    Date of Patent: February 27, 2018
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Niall Anthony Gormley, Melanie Anne Smith
  • Publication number: 20170212123
    Abstract: Provided herein is a method of using transposition to improve methods of sequencing RNA molecules. Provided herein is a method of tagging nucleic acid duplexes, such as DNA:RNA duplexes or DNA:DNA duplexes. The method includes the steps of providing a transposase and a transposon composition, providing one or more nucleic acid duplexes immobilized on a support, and contacting the transposase and transposon composition with the one or more nucleic acid duplexes under conditions wherein the one or more nucleic acid duplexes and transposon composition undergo a transposition reaction to produce one or more tagged nucleic acid duplexes, wherein the transposon composition comprises a double stranded nucleic acid molecule comprising a transferred strand and a non-transferred strand.
    Type: Application
    Filed: February 1, 2017
    Publication date: July 27, 2017
    Inventors: Niall Anthony Gormley, Louise Fraser, Paula Kokko-Gonzales
  • Patent number: 9683230
    Abstract: Presented are methods and compositions for using immobilized transposase and a transposon end for generating an immobilized library of 5?-tagged double-stranded target DNA on a surface. The methods are useful for generating 5?- and 3?-tagged DNA fragments for use in a variety of processes, including massively parallel DNA sequencing.
    Type: Grant
    Filed: March 8, 2013
    Date of Patent: June 20, 2017
    Assignee: Illumina Cambridge Limited
    Inventors: Niall Anthony Gormley, Geoffrey Paul Smith
  • Patent number: 9677132
    Abstract: The present disclosure relates to the field of molecular biology and more specifically to methods for capturing and amplifying target polynucleotides on a solid surface.
    Type: Grant
    Filed: December 18, 2014
    Date of Patent: June 13, 2017
    Assignee: Illumina, Inc.
    Inventors: Roberto Rigatti, Niall Anthony Gormley, Allen E. Eckhardt, Jonathan Mark Boutell
  • Publication number: 20170145499
    Abstract: The invention relates to methods for indexing samples during the sequencing of polynucleotide templates, resulting in the attachment of tags specific to the source of each nucleic acid sample such that after a sequencing run, both the source and sequence of each polynucleotide can be determined. Thus, the present invention pertains to analysis of complex genomes (e.g., human genomes), as well as multiplexing less complex genomes, such as those of bacteria, viruses, mitochondria, and the like.
    Type: Application
    Filed: November 30, 2016
    Publication date: May 25, 2017
    Applicant: Illumina Cambridge Limited
    Inventors: Helen Bignell, Louise Fraser, Niall Anthony Gormley
  • Publication number: 20170130260
    Abstract: Embodiments provided herein relate to methods and compositions for next generation sequencing.
    Type: Application
    Filed: June 12, 2014
    Publication date: May 11, 2017
    Inventors: Roberto RIGATTI, Niall Anthony GORMLEY
  • Patent number: 9574226
    Abstract: Provided herein is a method of using transposition to improve methods of sequencing RNA molecules. Provided herein is a method of tagging nucleic acid duplexes, such as DNA:RNA duplexes or DNA:DNA duplexes. The method includes the steps of providing a transposase and a transposon composition, providing one or more nucleic acid duplexes immobilized on a support, and contacting the transposase and transposon composition with the one or more nucleic acid duplexes under conditions wherein the one or more nucleic acid duplexes and transposon composition undergo a transposition reaction to produce one or more tagged nucleic acid duplexes, wherein the transposon composition comprises a double stranded nucleic acid molecule comprising a transferred strand and a non-transferred strand.
    Type: Grant
    Filed: March 6, 2013
    Date of Patent: February 21, 2017
    Assignee: Illumina, Inc.
    Inventors: Niall Anthony Gormley, Louise Fraser, Paula Kokko-Gonzales