Patents by Inventor Niall Gormley
Niall 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).
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Patent number: 11970695Abstract: 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: GrantFiled: March 10, 2021Date of Patent: April 30, 2024Assignee: Illumina Cambridge LimitedInventors: Niall Gormley, Geoffrey Paul Smith
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Publication number: 20230383284Abstract: Provided is a method, including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments. Also provided is a method including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments.Type: ApplicationFiled: August 10, 2023Publication date: November 30, 2023Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Maria Candelaria Rogert BACIGALUPO, Frank STEEMERS, Jeffrey FISHER, Andrew SLATTER, Lewis KRAFT, Niall GORMLEY, M. Shane BOWEN
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Patent number: 11827927Abstract: The invention relates to a method of preparing and using a library of template polynucleotides suitable for use as templates in solid-phase nucleic acid amplification and sequencing reactions to determine the methylation status of the cytosine bases in the library. In particular, the invention relates to a method of preparing and analysing a library of template polynucleotides suitable for methylation analysis.Type: GrantFiled: February 17, 2021Date of Patent: November 28, 2023Assignees: ILLUMINA CAMBRIDGE LIMITED, MASSACHUSETTS INSTITUTE OF TECHNOLOGYInventors: Niall Gormley, Andreas Gnirke, David Jaffe, Harris Nusbaum
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Patent number: 11760994Abstract: Provided is a method, including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments. Also provided is a method including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments.Type: GrantFiled: June 25, 2021Date of Patent: September 19, 2023Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Maria Candelaria Rogert Bacigalupo, Frank Steemers, Jeffrey Fisher, Andrew Slatter, Lewis Kraft, Niall Gormley, M. Shane Bowen
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Publication number: 20220331770Abstract: The present disclosure relates to a composition comprising a shell surrounding a core, wherein the core comprises one or more lyophilised microspheres. Also described herein is a method comprising providing one or more lyophilised microspheres; and coating the one or more lyophilised microspheres with a shell under conditions effective to encapsulate the one or more lyophilised microspheres. The present disclosure further relates to a system comprising one or more composition as described herein, and one or more lyophilised cake, wherein the one or more composition and the one or more lyophilised cake are combined under conditions effective to form a rehydration system. Also described herein is a method of controlling release of one or more encapsulated microspheres comprising providing a composition as described herein and mixing the composition with a rehydration solution under a first condition effective to control release of one or more lyophilised microspheres from the composition.Type: ApplicationFiled: April 13, 2022Publication date: October 20, 2022Inventors: Sébastien RICOULT, Pascale MATHONET, Elliot LAWRENCE, Niall GORMLEY, Justin DAVIDSON, Kim SCHNEIDER, Antoine FRANCAIS, Jessica WALSH, Johan Sebastian BASUKI, Shima GHOLIZADEH
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Publication number: 20220333178Abstract: A method for seeding and amplifying target nucleic acids derived from a sample in a cluster at a site on a surface of a substrate includes retaining at least a portion of the target nucleic acids in an inactive form that cannot seed to provide a relatively low concentration of active form target nucleic acids available for seeding. As the active form target nucleic acids seed on the surface of the substrate, they may be amplified. Because the concentration of active form target nucleic acids is low, the likelihood is low that a second active form target nucleic acid will seed at the same site within the same cluster before the first active form target nucleic acid is sufficiently amplified to dominate. Accordingly, the likelihood that the cluster will pass filters is increased relative to traditional seeding and amplification methods employing a higher concentration of active form target nucleic acids.Type: ApplicationFiled: March 21, 2022Publication date: October 20, 2022Inventors: Gary Mark Skinner, Geraint Evans, Niall Gormley, Jonathan Boutell, Matthew W. Kellinger, Michael Previte, Molly He
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Publication number: 20220290234Abstract: Examples provided herein are related to detecting methylcytosine and its derivatives using S-adenosyl-L-methionine analogs (xSAMs). Compositions and methods for performing such detection are disclosed. A target polynucleotide may include cytosine (C) and methylcytosine (mC). The method may include (a) protecting the C in the target polynucleotide from deamination; and (b) after step (a), deaminating the mC in the target polynucleotide to form thymine (T). Protecting the C from deamination may include adding a protective group to the 5 position of the C, e.g., using a methyltransferase enzyme that adds the first protective group from an xSAM.Type: ApplicationFiled: March 14, 2022Publication date: September 15, 2022Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Sarah Shultzaberger, Xiaolin Wu, Eric Brustad, Niall Gormley
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Publication number: 20220002711Abstract: Provided is a method, including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments. Also provided is a method including stretching a polynucleotide over a substrate including a plurality of equally spaced cleavage regions including a plurality of transposases, cleaving the polynucleotide with two or more of the plurality of transposases to form a plurality of polynucleotide fragments, and separating, within the plurality of polynucleotide fragments, a population of longer polynucleotide fragments from a population of shorter polynucleotide fragments.Type: ApplicationFiled: June 25, 2021Publication date: January 6, 2022Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITEDInventors: Maria Candelaria Rogert BACIGALUPO, Frank STEEMERS, Jeffrey FISHER, Andrew SLATTER, Lewis KRAFT, Niall GORMLEY, M. Shane BOWEN
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Publication number: 20210277459Abstract: The invention relates to a method of preparing and using a library of template polynucleotides suitable for use as templates in solid-phase nucleic acid amplification and sequencing reactions to determine the methylation status of the cytosine bases in the library. In particular, the invention relates to a method of preparing and analysing a library of template polynucleotides suitable for methylation analysis.Type: ApplicationFiled: February 17, 2021Publication date: September 9, 2021Inventors: Niall Gormley, Andreas Gnirke, David Jaffe, Harris Nusbaum
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Publication number: 20210222157Abstract: 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: ApplicationFiled: March 10, 2021Publication date: July 22, 2021Applicant: Illumina Cambridge LimitedInventors: Niall Gormley, Geoffrey Paul Smith
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Patent number: 10954554Abstract: The invention relates to a kit for preparing a library of template polynucleotides suitable for use as templates in solid-phase nucleic acid amplification and sequencing reactions to determine the methylation status of the cytosine bases in the library. In particular, the invention relates to a kit for preparing a library of template polynucleotides suitable for methylation analysis.Type: GrantFiled: January 10, 2018Date of Patent: March 23, 2021Assignees: Massachusetts Institute of TechnologyInventors: Niall Gormley, Andreas Gnirke, David Jaffe, Harris Nusbaum
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Publication number: 20180237844Abstract: The invention relates to a kit for preparing a library of template polynucleotides suitable for use as templates in solid-phase nucleic acid amplification and sequencing reactions to determine the methylation status of the cytosine bases in the library. In particular, the invention relates to a kit for preparing a library of template polynucleotides suitable for methylation analysis.Type: ApplicationFiled: January 10, 2018Publication date: August 23, 2018Inventors: Niall Gormley, Andreas Gnirke, David Jaffe, Harris Nusbaum
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Patent number: 9868982Abstract: The invention relates to a method of preparing and using a library of template polynucleotides suitable for use as templates in solid-phase nucleic acid amplification and sequencing reactions to determine the methylation status of the cytosine bases in the library. In particular, the invention relates to a method of preparing and analyzing a library of template polynucleotides suitable for methylation analysis.Type: GrantFiled: February 7, 2008Date of Patent: January 16, 2018Assignees: ILLUMINA CAMBRIDGE LIMITED, MASSACHUSETTS INSTITUTE OF TECHNOLOGYInventors: Niall Gormley, Andreas Gnirke, David Jaffe, Harris Nusbaum
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Publication number: 20090148842Abstract: The invention relates to a method of preparing and using a library of template polynucleotides suitable for use as templates in solid-phase nucleic acid amplification and sequencing reactions to determine the methylation status of the cytosine bases in the library. In particular, the invention relates to a method of preparing and analysing a library of template polynucleotides suitable for methylation analysis.Type: ApplicationFiled: February 7, 2008Publication date: June 11, 2009Inventors: Niall Gormley, Andreas Gnirke, David Jaffe, Harris Nusbaum
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Publication number: 20080207460Abstract: The invention relates to a method of detecting the precise locations of methyl-cytosines in a given nucleic acid sequence. In particular, the invention features a method which includes sequencing a template nucleic acid that is attached to a hairpin nucleic acid or double-stranded nucleic acid anchor, which contain specifically-designed sites for nicking or other endonucleases. The template nucleic acid is then regenerated to single-stranded form via methods described herein, and then treated to convert either the methylated cytosines, or non-methylated cytosines, and the template nucleic acid is then re-sequenced The results of the first and second sequencing reactions are then compared.Type: ApplicationFiled: December 20, 2007Publication date: August 28, 2008Inventor: Niall Gormley
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Publication number: 20080108515Abstract: The present invention is concerned with methods of producing fabricated arrays comprising clusters of clonal copies of one or more target molecules. In particular the invention relates to methods comprising providing clonal copies of a single target molecule within a vesicle or on the surface of a solid support within a chamber defined by a vesicle in contact with a solid support to produce clonal copies thereof and immobilising the copies on the solid support.Type: ApplicationFiled: August 27, 2007Publication date: May 8, 2008Inventors: Niall Gormley, Adrian Horgan, Darren Ellis, Jean-Ernest Sohna
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Publication number: 20070141604Abstract: The present invention is directed to a method for reducing the complexity of a nucleic acid sample in a reproducible manner by enriching for specific nucleic acid target sequences in the population of nucleic acids. More specifically, the invention relates to a method for enriching specific target sequences in a population using libraries of oligonucleotides.Type: ApplicationFiled: November 14, 2006Publication date: June 21, 2007Inventors: Niall Gormley, John West
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Publication number: 20070128624Abstract: 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: ApplicationFiled: July 14, 2006Publication date: June 7, 2007Inventors: Niall Gormley, Geoffrey Smith, David Bentley, Roberto Rigatti
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Publication number: 20060094016Abstract: The invention relates to a method of detecting the precise locations of methyl-cytosines in a given nucleic acid sequence. In particular, the invention features a method which includes sequencing a template nucleic acid that is attached to a hairpin nucleic acid or double-stranded nucleic acid anchor, which contain specifically-designed sites for nicking or other endonucleases. The template nucleic acid is then regenerated to single-stranded form via methods described herein, and then treated to convert either the methylated cytosines, or non-methylated cytosines, and the template nucleic acid is then re-sequenced The results of the first and second sequencing reactions are then compared.Type: ApplicationFiled: December 2, 2003Publication date: May 4, 2006Inventor: Niall Gormley
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Publication number: 20060035233Abstract: The present invention relates to methods for regenerating a single-stranded nucleic acid template following its conversion to a double-stranded product, e.g., during a polymerase reaction, and also to regenerating a hairpin or anchoring sequence by removal of the template and its synthesized complement, by design of enzyme restriction sites into the hairpin or anchoring sequence.Type: ApplicationFiled: December 2, 2003Publication date: February 16, 2006Inventors: Niall Gormley, Shankar Balasubramanian