Patents by Inventor Jonathan Mark Boutell

Jonathan Mark Boutell 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: 20220316003
    Abstract: The present invention relates to improvements in methods of high throughput nucleic acid sequencing, and in particular to improvements to methods of carrying out extension reactions during pairwise sequencing. The present invention relates to a method for carrying out a strand resynthesis extension reaction during pairwise sequencing, wherein said strand resynthesis extension reaction is carried out between a first sequencing read and a second sequencing read, and wherein said strand resynthesis extension reaction extends one or more immobilised primers to copy a first template strand to generate a second immobilised template strand; characterised in that the strand resynthesis extension reaction is carried out using a non-thermostable strand displacement polymerase at a temperature of less than 55° C., preferably at 38° C.
    Type: Application
    Filed: March 9, 2021
    Publication date: October 6, 2022
    Inventors: Jared Peace, Klara Bojanovic Machado, Peter McInerney, Jonathan Mark Boutell
  • Patent number: 11459610
    Abstract: The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by exonuclease treatment and optionally blocking the 3? ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing.
    Type: Grant
    Filed: April 23, 2018
    Date of Patent: October 4, 2022
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Michael Chesney, Vincent Peter Smith, Claire Bevis-Mott, Jonathan Mark Boutell, Angela Kalbande
  • 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: 20220243261
    Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
    Type: Application
    Filed: January 13, 2022
    Publication date: August 4, 2022
    Applicant: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
  • Publication number: 20220180970
    Abstract: The present disclosure provides methods and systems for determining and/or characterizing one or more haplotypes and/or phasing of haplotypes in a nucleic acid sample. In particular, the disclosure provides methods for determining a haplotype and/or phasing of haplotypes in a nucleic acid sample by incorporating synthetic polymorphisms into fragments of a nucleic acid sample and utilizing the synthetic polymorphisms in determining one or more haplotypes and/or phasing of haplotypes.
    Type: Application
    Filed: February 18, 2022
    Publication date: June 9, 2022
    Inventors: Roberto Rigatti, Jonathan Mark Boutell
  • Publication number: 20220180969
    Abstract: The present disclosure provides methods and systems for determining and/or characterizing one or more haplotypes and/or phasing of haplotypes in a nucleic acid sample. In particular, the disclosure provides methods for determining a haplotype and/or phasing of haplotypes in a nucleic acid sample by incorporating synthetic polymorphisms into fragments of a nucleic acid sample and utilizing the synthetic polymorphisms in determining one or more haplotypes and/or phasing of haplotypes.
    Type: Application
    Filed: December 15, 2021
    Publication date: June 9, 2022
    Inventors: Roberto Rigatti, Jonathan Mark Boutell
  • Patent number: 11279975
    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: June 10, 2019
    Date of Patent: March 22, 2022
    Assignee: Illumina Cambridge Limited
    Inventors: Roberto Rigatti, Niall Anthony Gormley, Jonathan Mark Boutell
  • Patent number: 11257568
    Abstract: The present disclosure provides methods and systems for determining and/or characterizing one or more haplotypes and/or phasing of haplotypes in a nucleic acid sample. In particular, the disclosure provides methods for determining a haplotype and/or phasing of haplotypes in a nucleic acid sample by incorporating synthetic polymorphisms into fragments of a nucleic acid sample and utilizing the synthetic polymorphisms in determining one or more haplotypes and/or phasing of haplotypes.
    Type: Grant
    Filed: May 11, 2018
    Date of Patent: February 22, 2022
    Assignee: Illumina Cambridge Limited
    Inventors: Roberto Rigatti, Jonathan Mark Boutell
  • Patent number: 11254976
    Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
    Type: Grant
    Filed: August 19, 2019
    Date of Patent: February 22, 2022
    Assignee: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
  • Publication number: 20220049288
    Abstract: The present invention relates to methods of imaging template hybridisation for estimating cluster numbers prior to solid phase amplification and sequencing. More particularly, an initial round of imaging is carried out at the single molecule template hybridisation stage which allows a general estimation of cluster numbers prior to clusters being formed. Amplification of the signal allows single molecule imaging to be carried out using standard sequencing imaging apparatus.
    Type: Application
    Filed: June 14, 2021
    Publication date: February 17, 2022
    Inventors: Isabelle Marie Julia RASOLONJATOVO, Jonathan Mark BOUTELL, Vincent Peter SMITH, Roberto RIGATTI
  • Publication number: 20210230689
    Abstract: The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by blocking the 3? ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing, by exonuclease treatment and optionally blocking the 3? ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing, by exonuclease treatment after protective adapters are ligated to target polynucleotides to degrade unincorporated adapters prior to amplification and sequencing, and/or by modifying or blocking 5? and 3? ends of pooled indexed polynucleotides from multiple samples, with an optional exonuclease treatment, prior to amplification and sequencing.
    Type: Application
    Filed: April 12, 2021
    Publication date: July 29, 2021
    Applicants: Illumina, Inc., Ilumina Cambridge Limited
    Inventors: Eric Vermaas, Mahdieh Khosroheidari, Angela Kalbande, Vincent Peter Smith, Claire Bevis-Mott, Jonathan Mark Boutell, Michael Chesney
  • Patent number: 11060130
    Abstract: The present invention relates to methods of imaging template hybridisation for estimating cluster numbers prior to solid phase amplification and sequencing. More particularly, an initial round of imaging is carried out at the single molecule template hybridisation stage which allows a general estimation of cluster numbers prior to clusters being formed. Amplification of the signal allows single molecule imaging to be carried out using standard sequencing imaging apparatus.
    Type: Grant
    Filed: June 11, 2015
    Date of Patent: July 13, 2021
    Assignee: Illumina Cambridge Limited
    Inventors: Isabelle Marie Julia Rasolonjatovo, Jonathan Mark Boutell, Vincent Peter Smith, Roberto Rigatti
  • Publication number: 20210187469
    Abstract: Provided is a nanoparticle including a scaffold, a single template site for bonding a template polynucleotide to the scaffold, and a plurality of accessory sites for bonding accessory oligonucleotides to the scaffold, wherein the scaffold is selected from one or more scaffold DNA molecules and one or more scaffold polypeptides, the single template site for bonding a template polynucleotide to the scaffold is selected from a covalent template bonding site and a noncovalent template bonding site and the plurality of accessory sites for bonding accessory oligonucleotides to the scaffold are selected from covalent accessory oligonucleotide bonding sites and noncovalent accessory oligonucleotide bonding sites. Also provided are methods of using the nanoparticle.
    Type: Application
    Filed: December 22, 2020
    Publication date: June 24, 2021
    Applicants: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITED, ILLUMINA SINGAPORE PTE. LTD.
    Inventors: Wayne N. GEORGE, Jonathan Mark BOUTELL, Mathieu LESSARD-VIGER, Saurabh NIRANTAR, Pietro GATTI LAFRANCONI, Seth MCDONALD, Yin Nah TEO, Maria Rogert BACIGALUPO, Sergio PEISAJOVICH, Eric BRUSTAD, Michael HOWARD, Xiangyuan YANG, M. Shane Bowen, Alex NEMIROSKI, Jeffrey BRODIN, Ludovic VINCENT, Lorenzo BERTI, Andrew A. BROWN, Fei SHEN, Lena STORMS, Olivia BENICE
  • Publication number: 20210155985
    Abstract: Presented herein are methods and compositions for concatenating template strands during the bridge amplification process. The methods are useful for surface amplification at improved densities. The methods and compositions provided herein enable creation of clusters that are brighter, but at the same densities as currently achieved using standard cluster amplification.
    Type: Application
    Filed: January 20, 2021
    Publication date: May 27, 2021
    Inventor: Jonathan Mark Boutell
  • Publication number: 20210139978
    Abstract: The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected.
    Type: Application
    Filed: January 20, 2021
    Publication date: May 13, 2021
    Inventors: Robert C. Kain, Xiaohai Liu, Wenyi Feng, Bernard Hirschbein, Helmy A. Eltoukhy, Xiaolin Wu, Geoffrey Paul Smith, Jonathan Mark Boutell, Thomas Joseph, Randall Smith, Min-Jui Richard Shen, Carolyn Tregidgo, Kay Klausing
  • Patent number: 10975430
    Abstract: The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by blocking the 3? ends of pooled indexed polynucleotides from multiple samples prior to amplification and sequencing.
    Type: Grant
    Filed: April 23, 2018
    Date of Patent: April 13, 2021
    Assignee: Illumina Cambridge Limited
    Inventors: Vincent Peter Smith, Claire Bevis-Mott, Jonathan Mark Boutell
  • Publication number: 20210086174
    Abstract: In an example of the method, a functionalized coating layer is applied in depressions of a patterned flow cell substrate. The depressions are separated by interstitial regions. A primer is grafted to the functionalized coating layer to form a grafted functionalized coating layer in the depressions. A hydrogel is applied on at least the grafted functionalized coating layer.
    Type: Application
    Filed: December 7, 2020
    Publication date: March 25, 2021
    Inventors: Hongji Ren, Jonathan Mark Boutell, John A. Moon, M. Shane Bowen, Alex Nemiroski, Gary Mark Skinner, Kenny Chen
  • Patent number: 10919033
    Abstract: In an example of the method, a functionalized coating layer is applied in depressions of a patterned flow cell substrate. The depressions are separated by interstitial regions. A primer is grafted to the functionalized coating layer to form a grafted functionalized coating layer in the depressions. A hydrogel is applied on at least the grafted functionalized coating layer.
    Type: Grant
    Filed: December 17, 2018
    Date of Patent: February 16, 2021
    Assignees: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Hongji Ren, Jonathan Mark Boutell, John A. Moon, M. Shane Bowen, Alex Nemiroski, Gary Mark Skinner, Kenny Chen
  • Patent number: 10900077
    Abstract: The present disclosure provides methods and systems for detecting multiple different nucleotides in a sample. In particular, the disclosure provides for detection of multiple different nucleotides in a sample utilizing fewer detection moieties than the number of nucleotides being detected and/or fewer imaging events than the number of nucleotides being detected.
    Type: Grant
    Filed: May 7, 2019
    Date of Patent: January 26, 2021
    Assignee: ILLUMINA, INC.
    Inventors: Robert C. Kain, Xiaohai Liu, Wenyi Feng, Bernard Hirschbein, Helmy A. Eltoukhy, Xiaolin Wu, Geoffrey Paul Smith, Jonathan Mark Boutell, Thomas Joseph, Randall Smith, Min-Jui Richard Shen, Carolyn Tregidgo, Kay Klausing
  • Patent number: 10901230
    Abstract: Example super-resolution microscopy systems are described herein that are configured for relatively high throughput. The disclosed microscopy systems can be to generate an array of sub-diffraction activated areas for imaging. The microscopy systems can be to utilize imaging techniques that employ time delay integration to build up super-resolution images over time. The disclosed microscopy systems can utilize long-lived fluorophores in conjunction with wide field and patterned illumination to generate super-resolution images of a sample with relatively high throughput.
    Type: Grant
    Filed: June 20, 2017
    Date of Patent: January 26, 2021
    Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITED
    Inventors: Gary Mark Skinner, Geraint Wyn Evans, Stanley S. Hong, John A. Moon, M. Shane Bowen, Jonathan Mark Boutell, Jason Richard Betley