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).

  • Patent number: 10428363
    Abstract: Methods for amplifying nucleic acids are provided. The methods can be used to minimize sequence specific bias caused by the preferential amplification of certain nucleic acid sequences. Methods are described which can lower the efficiency of AT rich templates relative to GC rich templates, thereby minimizing GC bias during amplification reactions with multiple templates of different sequence. The methods are suited to solid phase amplification, for example, utilizing flow cells.
    Type: Grant
    Filed: October 17, 2016
    Date of Patent: October 1, 2019
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Roberto Rigatti, Jonathan Mark Boutell, Min-Jui Richard Shen
  • Publication number: 20190292594
    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: June 10, 2019
    Publication date: September 26, 2019
    Applicant: Illumina Cambridge Limited
    Inventors: Roberto Rigatti, Niall Anthony Gormley, Jonathan Mark Boutell
  • Publication number: 20190264279
    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: May 7, 2019
    Publication date: August 29, 2019
    Applicant: 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: 10392655
    Abstract: The invention provides methods for amplifying nucleic acids, particularly methods for reducing density-dependent GC bias and for reducing nucleic acid damage in a bridge amplification of a nucleic acid template. The invention also provides methods for evaluating the effect of reagents and/or additives on nucleic acid damage during bridge amplification of nucleic acid template strands. The methods are suited to solid phase amplification, for example, utilizing flow cells.
    Type: Grant
    Filed: June 2, 2015
    Date of Patent: August 27, 2019
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Jonathan Mark Boutell, Susan Shanahan, Roberto Rigatti
  • Patent number: 10385384
    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 8, 2017
    Date of Patent: August 20, 2019
    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
  • 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
  • Publication number: 20190219835
    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: Application
    Filed: June 20, 2017
    Publication date: July 18, 2019
    Inventors: Gary Mark SKINNER, Geraint Wyn EVANS, Stanley S. HONG, John A. MOON, M. Shane BOWEN, Jonathan Mark BOUTELL, Jasori Richard BETLEY
  • Patent number: 10351846
    Abstract: An apparatus and method for applying a chemistry to samples of interest are provided. The apparatus and method include a flexible tape mounted on an arrangement of guide rollers. Samples of interest (e.g., clusters of DNA templates) are bound to at least one surface of the flexible tape. The method and apparatus further comprise one or more read heads in relation to the flexible tape and a plurality of reservoirs along a path of the flexible tape. The reservoirs comprise liquids comprising chemical reagents for performing the chemistry on the samples of interest bound to the at least one surface of the flexible tape. The method and apparatus further comprise a drive system for driving at least one of the guide rollers to advance the flexible tape into and out of the reservoirs.
    Type: Grant
    Filed: September 11, 2015
    Date of Patent: July 16, 2019
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Jonathan Mark Boutell, Gary Mark Skinner, Gareth Jenkins
  • Patent number: 10344269
    Abstract: Presented herein are recombinases for improved recombinase-mediated amplification of nucleic acids, such as a PCR-library having single-stranded adapter regions, on a patterned flow cell surface for improved cluster amplification, as well as methods and kits using the same.
    Type: Grant
    Filed: May 11, 2018
    Date of Patent: July 9, 2019
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Erin Bomati, Matthew William Kellinger, Jonathan Mark Boutell
  • 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: 10287577
    Abstract: The present invention provides methods for creating an array of features on a surface based on content transferred from a plurality of beads to the surface. Nucleic acid content can be transferred using a method including the steps of (a) providing a surface having one or more primer oligonucleotides attached to the surface; (b) providing a pool of beads, wherein beads in the pool have a plurality of templates attached thereto, the plurality comprising multiple copies of a single nucleic acid template sequence; (c) arraying the beads onto the surface by hybridizing the templates to the primer oligonucleotides; and (d) extending the primers to produce copies of the templates attached to the surface.
    Type: Grant
    Filed: June 12, 2017
    Date of Patent: May 14, 2019
    Assignee: ILLUMINA CAMBRIDGE LTD.
    Inventors: Roberto Rigatti, Geoffrey Paul Smith, Jonathan Mark Boutell
  • Patent number: 10287629
    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: July 12, 2016
    Date of Patent: May 14, 2019
    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
  • Publication number: 20190112730
    Abstract: A method of characterizing candidate agents including steps of (a) providing a library of candidate agents attached to nucleic acid tags; (b) contacting the library with a solid support to attach the candidate agents to the solid support, whereby an array of candidate agents is formed; (c) contacting the array with a screening agent, wherein one or more candidate agents in the array react with the screening agent; (d) detecting the array to determine that at least one candidate agent in the array reacts with the screening agent; (e) sequencing the nucleic acid tag to determine the tag sequences attached to candidate agents in the array; and (f) identifying the at least one candidate agent in the array that reacts with the screening agent based on the tag sequence that is attached to the at least one candidate agent.
    Type: Application
    Filed: October 11, 2018
    Publication date: April 18, 2019
    Applicant: Illumina, Inc.
    Inventors: Molly He, Michael Previte, Misha Golynskiy, Matthew William Kellinger, Sergio Peisajovich, Jonathan Mark Boutell
  • 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: 20180322243
    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: May 11, 2018
    Publication date: November 8, 2018
    Inventors: Roberto Rigatti, Jonathan Mark Boutell
  • Publication number: 20180305753
    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: Application
    Filed: April 23, 2018
    Publication date: October 25, 2018
    Applicant: Illumina Cambridge Limited
    Inventors: Michael Chesney, Vincent Peter Smith, Claire Bevis-Mott, Jonathan Mark Boutell, Angela Kalbande
  • Publication number: 20180305840
    Abstract: Protein arrays and their use to assay, in a parallel fashion, the protein products of highly homologous or related DNA coding sequences and described. By highly homologous or related it is meant those DNA coding sequences which share a common sequence and which differ only by one or more naturally occurring mutations such as single nucleotide polymorphisms, deletions or insertions, or those sequences which are considered to be haplotypes. Such highly homologous or related DNA coding sequences are generally naturally occurring variants of the same gene. Arrays according to the invention have two or more individual proteins deposited in a spatially defined pattern on a surface in a form whereby a property such as an activity or function of the proteins can be investigated or assayed in parallel by interrogation of the array.
    Type: Application
    Filed: April 3, 2018
    Publication date: October 25, 2018
    Inventors: Jonathan Mark BOUTELL, Benjamin Leslie James GODBER, Darren James HART, Jonathan Michael BLACKBURN
  • Publication number: 20180305750
    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: Application
    Filed: April 23, 2018
    Publication date: October 25, 2018
    Applicant: Illumina Cambridge Limited
    Inventors: Vincent Peter Smith, Claire Bevis-Mott, Jonathan Mark Boutell
  • Publication number: 20180258409
    Abstract: Presented herein are recombinases for improved recombinase-mediated amplification of nucleic acids, such as a PCR-library having single-stranded adapter regions, on a patterned flow cell surface for improved cluster amplification, as well as methods and kits using the same.
    Type: Application
    Filed: May 11, 2018
    Publication date: September 13, 2018
    Applicant: Illumina Cambridge Limited
    Inventors: Erin Bomati, Matthew William Kellinger, Jonathan Mark Boutell
  • Publication number: 20180187251
    Abstract: The invention provides methods for amplifying nucleic acids, particularly methods for reducing density-dependent GC bias and for reducing nucleic acid damage in a bridge amplification of a nucleic acid template. The invention also provides methods for evaluating the effect of reagents and/or additives on nucleic acid damage during bridge amplification of nucleic acid template strands. The methods are suited to solid phase amplification, for example, utilizing flow cells.
    Type: Application
    Filed: June 2, 2015
    Publication date: July 5, 2018
    Inventors: Jonathan Mark BOUTELL, Susan SHANAHAN, Roberto RIGATTI