Patents Assigned to Illumina Cambridge Limited
  • MODIFIED POLYMERASES FOR IMPROVED INCORPORATION OF NUCLEOTIDE ANALOGUES
    Publication number: 20180298358
    Abstract: The invention relates to modified polymerase enzymes which exhibit improved incorporation of nucleotide analogues bearing substituents at the 3? position of the sugar moiety that are larger in size than the naturally occurring 3? hydroxyl group. Also described are methods of using the polymerases to incorporate nucleotides into polynucleotides, particularly in the context of DNA sequencing.
    Type: Application
    Filed: June 26, 2018
    Publication date: October 18, 2018
    Applicant: Illumina Cambridge Limited
    Inventors: Geoffrey Paul Smith, David Mark Dunstan Bailey, Raquel Maria Sanches-Kuiper, Harold Swerdlow, David James Earnshaw
  • RECOMBINASE MUTANTS
    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
  • Polymerases
    Patent number: 10059928
    Abstract: Modified DNA polymerases have an affinity for DNA such that the polymerase has an ability to incorporate one or more nucleotides into a plurality of separate DNA templates in each reaction cycle. The polymerases are capable of forming an increased number of productive polymerase-DNA complexes in each reaction cycle. The modified polymerases may be used in a number of DNA sequencing applications, especially in the context of clustered arrays.
    Type: Grant
    Filed: June 9, 2017
    Date of Patent: August 28, 2018
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Geoffrey Paul Smith, Roberto Rigatti, Tobias William Barr Ost, Shankar Balasubramanian, Raquel Maria Sanches-Kuiper
  • Sample preparation on a solid support
    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
  • SYSTEMS AND METHODS OF IMPROVING DROPLET OPERATIONS IN FLUIDIC SYSTEMS
    Publication number: 20180193840
    Abstract: Embodiments of present application are directed to micro fluidic devices and particularly digital micro fluidic devices with improved droplet operations, and methods of improving droplet operations in micro fluidic devices.
    Type: Application
    Filed: August 31, 2016
    Publication date: July 12, 2018
    Applicant: Illumina Cambridge Limited
    Inventor: Xavier VON HATTEN
  • Modified polymerases for improved incorporation of nucleotide analogues
    Patent number: 10017750
    Abstract: The invention relates to modified polymerase enzymes which exhibit improved incorporation of nucleotide analogs bearing substituents at the 3? position of the sugar moiety that are larger in size than the naturally occurring 3? hydroxyl group. Also described are methods of using the polymerases to incorporate nucleotides into polynucleotides, particularly in the context of DNA sequencing.
    Type: Grant
    Filed: August 25, 2016
    Date of Patent: July 10, 2018
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Geoffrey Paul Smith, David Mark Dunstan Bailey, Raquel Maria Sanches-Kuiper, Harold Swerdlow, David James Earnshaw
  • End modification to prevent over-representation of fragments
    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
  • Preparation of templates for nucleic acid sequencing
    Patent number: 9999866
    Abstract: The invention relates to methods of generating templates for a nucleic acid sequencing reaction which comprise: providing at least one double-stranded nucleic acid molecule, wherein both strands of the double-stranded nucleic acid molecule are attached to a solid support at the 5? end, cleaving one or both strands of the double-stranded nucleic acid molecule, and subjecting the cleaved strand(s) to denaturing conditions to remove the portion of the cleaved strand(s) not attached to the solid support, thereby generating a partially or substantially single-stranded template for a nucleic acid sequencing reaction.
    Type: Grant
    Filed: October 6, 2016
    Date of Patent: June 19, 2018
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Xiaohai Liu, John Milton, Geoffrey Paul Smith, Colin Lloyd Barnes, Isabelle Rasolonjatovo, Roberto Rigatti, Xiaolin Wu, Tobias William Barr Ost, Graham John Worsley, David James Earnshaw, Gerardo Turcatti, Anthony Romieu
  • Method for sequencing a polynucelotide template
    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
  • Reversible surface functionalization
    Patent number: 9982250
    Abstract: Some embodiments described herein relate to a substrate comprising a silane functionalized surface for reversibly immobilizing a biological molecule of interest, such as oligonucleotides, polynucleotides, or protein. Methods for immobilizing the biological molecule and the use in DNA sequencing and other diagnostic applications are also disclosed.
    Type: Grant
    Filed: August 20, 2015
    Date of Patent: May 29, 2018
    Assignee: Illumina Cambridge Limited
    Inventors: Xavier von Hatten, Wayne N. George, Alexandre Richez, Anne-Cecile Dingwall, Andrew A. Brown
  • Recombinase mutants
    Patent number: 9982244
    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: September 29, 2015
    Date of Patent: May 29, 2018
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Erin Bomati, Matthew William Kellinger, Jonathan Mark Boutell
  • Methods and systems for determining haplotypes and phasing of haplotypes
    Patent number: 9977861
    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: March 11, 2013
    Date of Patent: May 22, 2018
    Assignee: Illumina Cambridge Limited
    Inventors: Roberto Rigatti, Jonathan Mark Boutell
  • Methods, carrier assemblies, and systems for imaging samples for biological or chemical analysis
    Patent number: 9976174
    Abstract: Method includes positioning a first carrier assembly on a system stage. The carrier assembly includes a support frame having an inner frame edge that defines a window of the support frame. The first carrier assembly includes a first substrate that is positioned within the window and surrounded by the inner frame edge. The first substrate has a sample thereon. The method includes detecting optical signals from the sample of the first substrate. The method also includes replacing the first carrier assembly on the system stage with a second carrier assembly on the system stage. The second carrier assembly includes the support frame and an adapter plate held by the support frame. The second carrier assembly has a second substrate held by the adapter plate that has a sample thereon. The method also includes detecting optical signals from the sample of the second substrate.
    Type: Grant
    Filed: March 22, 2016
    Date of Patent: May 22, 2018
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Stephen Rawlings, Venkatesh Mysore Nagaraja Rao, Beng Keong Ang, Nitin Udpa
  • Method of nucleotide detection
    Patent number: 9970055
    Abstract: The invention relates to an additive which can be added to buffers used in nucleotide detection processes and improved methods of nucleic acid sequencing using this additive. In particular the invention relates to use of the additive to improve the efficiency of fluorescence-based multiple cycle nucleic acid sequencing reactions.
    Type: Grant
    Filed: February 22, 2016
    Date of Patent: May 15, 2018
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Milan Fedurco, Anthony Romieu, Gerardo Turcatti
  • Polynucleotide modification on solid support
    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
  • Methods and systems for data analysis and compression
    Patent number: 9929746
    Abstract: The present disclosure provides computer implemented methods and systems for analyzing datasets, such as large data sets output from nucleic acid sequencing technologies. In particular, the present disclosure provides for data analysis comprising computing the BWT of a collection of strings in an incremental, character by character, manner. The present disclosure also provides compression boosting strategies resulting in a BWT of a reordered collection of data that is more compressible by second stage compression methods compared to non-reordered computational analysis.
    Type: Grant
    Filed: August 5, 2015
    Date of Patent: March 27, 2018
    Assignee: Illumina Cambridge Limited
    Inventors: Anthony James Cox, Lilian Janin
  • Method for retaining even coverage of short insert libraries
    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
  • Method of nucleic acid amplification
    Patent number: 9902951
    Abstract: A nucleic acid molecule can be annealed to an appropriate immobilized primer. The primer can then be extended and the molecule and the primer can be separated from one another. The extended primer can then be annealed to another immobilized primer and the other primer can be extended. Both extended primers can then be separated from one another and can be used to provide further extended primers. The process can be repeated to provide amplified, immobilized nucleic acid molecules. These can be used for many different purposes, including sequencing, screening, diagnosis, in situ nucleic acid synthesis, monitoring gene expression, nucleic acid fingerprinting, etc.
    Type: Grant
    Filed: May 2, 2013
    Date of Patent: February 27, 2018
    Assignees: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Eric H. Kawashima, Laurent Farinelli, Pascal Mayer
  • Display screen or portion thereof with graphical user interface
    Patent number: D818481
    Type: Grant
    Filed: November 7, 2016
    Date of Patent: May 22, 2018
    Assignees: Illumina, Inc., ILLUMINA CAMBRIDGE LIMITED
    Inventors: D. Curtis Jamison, Andrew Warren, Stewart McArthur, Jun Kurihara, Eliza van Gerbig
  • Display screen or portion thereof with zygosity icons
    Patent number: D831051
    Type: Grant
    Filed: November 7, 2016
    Date of Patent: October 16, 2018
    Assignees: Illumina, Inc., Illumina Cambridge Limited
    Inventors: D. Curtis Jamison, Andrew Warren, Stewart MacArthur, Jun Kurihara, Eliza van Gerbig