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).

  • Publication number: 20240026348
    Abstract: Materials and methods for preparing nucleic acid libraries for next-generation sequencing are described herein. A variety of approaches are described relating to the use of unique molecular identifiers with transposon-based technology in the preparation of sequencing libraries. Also described herein are sequencing materials and methods for identifying and correcting amplification and sequencing errors.
    Type: Application
    Filed: September 28, 2023
    Publication date: January 25, 2024
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Susan C. Verity, Robert Scott Kuersten, Niall Anthony Gormley, Andrew B. Kennedy, Sarah E. Shultzaberger, Andrew Slatter, Emma Bell, Sebastien Georg Gabriel Ricoult, Grace DeSantis, Fiona Kaper, Han-Yu Chuang, Oliver Jon Miller, Jason Richard Betley, Stephen M. Gross, Mats Ekstrand
  • Patent number: 11873480
    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: Grant
    Filed: October 16, 2015
    Date of Patent: January 16, 2024
    Assignee: 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: 20230407388
    Abstract: Described herein is a polynucleotide for use as a sequencing template comprising multiple inserts. Also described herein are method of generating and using these polynucleotides and methods of use of such templates, including analysis of contiguity information. Further, sequencing templates comprising an insert sequence and a copy of the insert sequence can be used to correct for random errors generated during sequencing or amplification or to identify nucleobase damage or other mutation that leads to non-canonical base pairing in a double-stranded nucleic acid. Methods of performing methylation analysis are also described herein.
    Type: Application
    Filed: April 20, 2023
    Publication date: December 21, 2023
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Tarun Khurana, Yir-Shyuan Wu, Niall Anthony Gormley, Jonathan Mark Boutell
  • Patent number: 11834699
    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: April 1, 2019
    Date of Patent: December 5, 2023
    Assignee: Illumina Cambridge Limited
    Inventors: Niall Anthony Gormley, Louise Fraser, Paula Kokko-Gonzales
  • Publication number: 20230340568
    Abstract: The present disclosure relates to methods, compositions, and kits for generating a library of tagged nucleic acid fragments without using PCR amplification, including methods and compositions for fragmenting and tagging nucleic acids (e.g., DNA) using transposome complexes immobilized on solid support.
    Type: Application
    Filed: May 12, 2023
    Publication date: October 26, 2023
    Applicant: Illumina Cambridge Limited
    Inventors: Andrew Slatter, Esther Musgrave-Brown, Susan C. Verity, Niall Anthony Gormley
  • Publication number: 20230279385
    Abstract: A variety of different types of targeted transposome complexes are described herein that may be used to mediate sequence-specific targeted transposition of nucleic acids.
    Type: Application
    Filed: February 16, 2023
    Publication date: September 7, 2023
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Frank J. STEEMERS, Jonathan Mark BOUTELL, Pietro GATTI LAFRANCONI, Oliver Jon MILLER, Emma BELL, Sebastien Georg Gabriel RICOULT, Niall Anthony GORMLEY, Kim SCHNEIDER
  • Publication number: 20230279469
    Abstract: An example of a flow cell includes a substrate having depressions separated by interstitial regions. First and second primers are immobilized within the depressions. First transposome complexes are immobilized within the depressions, and the first transposome complexes include a first amplification domain. Second transposome complexes are also immobilized within the depressions, and the second transposome complexes include a second amplification domain. Some of the first transposome complexes, or some of the second transposome complexes, or some of both of the first and second transposome complexes include a modification to reduce tagmentation efficiency.
    Type: Application
    Filed: December 23, 2022
    Publication date: September 7, 2023
    Inventors: Johan Sebastian Basuki, Jonathan Mark Boutell, Jeffrey S. Fisher, Louise Jane Fraser, Wayne N. George, Niall Anthony Gormley, David Jones, Xiaoyu Ma, Maria Ines Martins Vitoriano, Zhong Mei, Oliver Jon Miller, Andrew Price, Sebastien Georg Gabriel Ricoult, Vicki S. Thomson, Jacqueline C. Weir, Xiaoy Ma, Weihua Chang, Hui Han
  • Patent number: 11685946
    Abstract: The present disclosure relates to methods, compositions, and kits for generating a library of tagged nucleic acid fragments without using PCR amplification, including methods and compositions for fragmenting and tagging nucleic acids (e.g., DNA) using transposome complexes immobilized on solid support.
    Type: Grant
    Filed: January 10, 2020
    Date of Patent: June 27, 2023
    Inventors: Andrew Slatter, Esther Musgrave-Brown, Susan C. Verity, Niall Anthony Gormley
  • Publication number: 20230183682
    Abstract: This application describes methods of preparing an immobilized library of tagged RNA fragments. Also described herein are a number of methods of preparing DNA and RNA sequencing libraries from a single sample. These methods can include library preparation from single cells.
    Type: Application
    Filed: February 2, 2023
    Publication date: June 15, 2023
    Applicants: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Niall Anthony Gormley, Andrew B. Kennedy, Robert Scott Kuersten, Gary Schroth, Carlo Randise-Hinchliff, Sarah E. Shultzaberger, Fiona Kaper, Yir-Shyuan Wu, Tarun Khurana, Foad Mashayekhi
  • Patent number: 11634768
    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: Grant
    Filed: February 26, 2021
    Date of Patent: April 25, 2023
    Assignee: Illumina Cambridge Limited
    Inventors: Helen Bignell, Louise Fraser, Niall Anthony Gormley
  • Publication number: 20220403376
    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: August 18, 2022
    Publication date: December 22, 2022
    Applicant: Illumina Cambridge Limited
    Inventors: Niall Anthony Gormley, Avgousta Ioannou, Rosamond Jackson, Natalie Morrell
  • Patent number: 11453875
    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: Grant
    Filed: May 27, 2016
    Date of Patent: September 27, 2022
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Niall Anthony Gormley, Avgousta Ioannou, Rosamond Jackson, Natalie Morrell
  • Publication number: 20220282242
    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: April 12, 2022
    Publication date: September 8, 2022
    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: 20220259651
    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: Application
    Filed: March 8, 2022
    Publication date: August 18, 2022
    Inventors: Roberto Rigatti, Niall Anthony Gormley, Jonathan Mark Boutell
  • Publication number: 20220259587
    Abstract: A method of generating an asymmetric closed-ended double stranded nucleic acid template from a double stranded nucleic acid template having free 5? and 3? ends by use of hairpin or dumbbell adaptors, and sequencing therefrom.
    Type: Application
    Filed: October 23, 2020
    Publication date: August 18, 2022
    Inventor: Niall Anthony Gormley
  • Publication number: 20220195495
    Abstract: Embodiments provided herein relate to methods and compositions for next generation sequencing. Some embodiments include the preparation of a template library from a target nucleic acid in contact with a surface, and sequencing the library on the surface.
    Type: Application
    Filed: March 8, 2022
    Publication date: June 23, 2022
    Inventors: Roberto Rigatti, Niall Anthony Gormley
  • Publication number: 20220154173
    Abstract: Presented are methods and compositions for using immobilized CRISPR/Cas9 enzymes for generating an immobilized library of randomly fragmented, double-stranded target nucleic acid fragments on a surface. The methods are useful for generating nucleic acid fragments for use in a variety of processes, including massively parallel nucleic acid sequencing.
    Type: Application
    Filed: June 18, 2020
    Publication date: May 19, 2022
    Inventor: Niall Anthony Gormley
  • Publication number: 20220127596
    Abstract: Described herein are methods and systems for performing chemical or enzymatic reactions using electrophoresis. Devices, systems, and methods for preparing a library of tagged nucleic acid fragments from a target double-stranded nucleic acid using electrophoresis are also provided. Application of one or more electric fields causes molecules to migrate through the electrophoresis gel matrix.
    Type: Application
    Filed: July 10, 2020
    Publication date: April 28, 2022
    Applicant: lllumina Cambridge Limited
    Inventor: Niall Anthony GORMLEY
  • Patent number: 11306348
    Abstract: The present disclosure relates to methods, compositions, and kits for generating a library of tagged nucleic acid fragments without using PCR amplification, including methods and compositions for fragmenting and tagging nucleic acids (e.g., DNA) using transposome complexes immobilized on solid support.
    Type: Grant
    Filed: May 3, 2021
    Date of Patent: April 19, 2022
    Assignee: Illumina Cambridge Limited
    Inventors: Andrew Slatter, Esther Musgrave-Brown, Susan C. Verity, Niall Anthony Gormley
  • Patent number: 11299765
    Abstract: Embodiments provided herein relate to methods and compositions for next generation sequencing. Some embodiments include the preparation of a template library from a target nucleic acid in contact with a surface, and sequencing the library on the surface.
    Type: Grant
    Filed: September 5, 2019
    Date of Patent: April 12, 2022
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Roberto Rigatti, Niall Anthony Gormley